include/domdec.h

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   3  *
   4  * This file is part of Gromacs        Copyright (c) 1991-2008
   5  * David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
   6  *
   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.
  11  *
  12  * To help us fund GROMACS development, we humbly ask that you cite
  13  * the research papers on the package. Check out http://www.gromacs.org
  14  *
  15  * And Hey:
  16  * Gnomes, ROck Monsters And Chili Sauce
  17  */
  18
  19 #ifndef _domdec_h
  20 #define _domdec_h
  21
  22 #include "typedefs.h"
  23 #include "types/commrec.h"
  24 #include "vsite.h"
  25 #include "genborn.h"
  26
  27 #ifdef __cplusplus
  28 extern "C" {
  29 #endif
  30
  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.
  36  */
  37
  38 t_block *dd_charge_groups_global(gmx_domdec_t *dd);
  39 /* Return a block struct for the charge groups of the whole system */
  40
  41 gmx_bool dd_filled_nsgrid_home(gmx_domdec_t *dd);
  42 /* Is the ns grid already filled with the home particles? */
  43
  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.
  47  */
  48
  49 gmx_domdec_zones_t *domdec_zones(gmx_domdec_t *dd);
  50
  51 void dd_get_ns_ranges(gmx_domdec_t *dd,int icg,
  52                              int *jcg0,int *jcg1,ivec shift0,ivec shift1);
  53
  54 int dd_natoms_vsite(gmx_domdec_t *dd);
  55
  56 void dd_get_constraint_range(gmx_domdec_t *dd,
  57                                     int *at_start,int *at_end);
  58
  59 real dd_cutoff_mbody(gmx_domdec_t *dd);
  60
  61 real dd_cutoff_twobody(gmx_domdec_t *dd);
  62
  63 gmx_bool gmx_pmeonlynode(t_commrec *cr,int nodeid);
  64 /* Return if nodeid in cr->mpi_comm_mysim is a PME-only node */
  65
  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 */
  69
  70 int dd_pme_maxshift_x(gmx_domdec_t *dd);
  71 /* Returns the maximum shift for coordinate communication in PME, dim x */
  72
  73 int dd_pme_maxshift_y(gmx_domdec_t *dd);
  74 /* Returns the maximum shift for coordinate communication in PME, dim y */
  75
  76 void make_dd_communicators(FILE *fplog,t_commrec *cr,int dd_node_order);
  77
  78 gmx_domdec_t *
  79 init_domain_decomposition(FILE *fplog,
  80                           t_commrec *cr,
  81                           unsigned long Flags,
  82                           ivec nc,
  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,
  87                           matrix box,rvec *x,
  88                           gmx_ddbox_t *ddbox,
  89                           int *npme_x, int *npme_y);
  90
  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 */
  96
  97 gmx_bool dd_bonded_molpbc(gmx_domdec_t *dd,int ePBC);
  98 /* Returns if we need to do pbc for calculating bonded interactions */
  99
 100 void set_dd_parameters(FILE *fplog,gmx_domdec_t *dd,real dlb_scale,
 101                               t_inputrec *ir,t_forcerec *fr,
 102                               gmx_ddbox_t *ddbox);
 103 /* Set DD grid dimensions and limits,
 104  * should be called after calling dd_init_bondeds.
 105  */
 106
 107 gmx_bool change_dd_cutoff(t_commrec *cr,t_state *state,t_inputrec *ir,
 108                           real cutoff_req );
 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.
 112  */
 113
 114 void setup_dd_grid(FILE *fplog,gmx_domdec_t *dd);
 115
 116 void dd_collect_vec(gmx_domdec_t *dd,
 117                            t_state *state_local,rvec *lv,rvec *v);
 118
 119 void dd_collect_state(gmx_domdec_t *dd,
 120                              t_state *state_local,t_state *state);
 121
 122 enum { ddCyclStep, ddCyclPPduringPME, ddCyclF, ddCyclPME, ddCyclNr };
 123
 124 void dd_cycles_add(gmx_domdec_t *dd,float cycles,int ddCycl);
 125 /* Add the wallcycle count to the DD counter */
 126
 127 void dd_force_flop_start(gmx_domdec_t *dd,t_nrnb *nrnb);
 128 /* Start the force flop count */
 129
 130 void dd_force_flop_stop(gmx_domdec_t *dd,t_nrnb *nrnb);
 131 /* Stop the force flop count */
 132
 133 float dd_pme_f_ratio(gmx_domdec_t *dd);
 134 /* Return the PME/PP force load ratio, or -1 if nothing was measured.
 135  * Should only be called on the DD master node.
 136  */
 137
 138 void dd_move_x(gmx_domdec_t *dd,matrix box,rvec x[]);
 139 /* Communicate the coordinates to the neighboring cells and do pbc. */
 140
 141 void dd_move_f(gmx_domdec_t *dd,rvec f[],rvec *fshift);
 142 /* Sum the forces over the neighboring cells.
 143  * When fshift!=NULL the shift forces are updated to obtain
 144  * the correct virial from the single sum including f.
 145  */
 146
 147 void dd_atom_spread_real(gmx_domdec_t *dd,real v[]);
 148 /* Communicate a real for each atom to the neighboring cells. */
 149
 150 void dd_atom_sum_real(gmx_domdec_t *dd,real v[]);
 151 /* Sum the contributions to a real for each atom over the neighboring cells. */
 152
 153 void dd_partition_system(FILE            *fplog,
 154                                 gmx_large_int_t      step,
 155                                 t_commrec       *cr,
 156                                 gmx_bool            bMasterState,
 157                                 int             nstglobalcomm,
 158                                 t_state         *state_global,
 159                                 gmx_mtop_t      *top_global,
 160                                 t_inputrec      *ir,
 161                                 t_state         *state_local,
 162                                 rvec            **f,
 163                                 t_mdatoms       *mdatoms,
 164                                 gmx_localtop_t  *top_local,
 165                                 t_forcerec      *fr,
 166                                 gmx_vsite_t     *vsite,
 167                                 gmx_shellfc_t   shellfc,
 168                                 gmx_constr_t    constr,
 169                                 t_nrnb          *nrnb,
 170                                 gmx_wallcycle_t wcycle,
 171                                 gmx_bool            bVerbose);
 172 /* Partition the system over the nodes.
 173  * step is only used for printing error messages.
 174  * If bMasterState==TRUE then state_global from the master node is used,
 175  * else state_local is redistributed between the nodes.
 176  * When f!=NULL, *f will be reallocated to the size of state_local.
 177  */
 178
 179 void reset_dd_statistics_counters(gmx_domdec_t *dd);
 180 /* Reset all the statistics and counters for total run counting */
 181
 182 void print_dd_statistics(t_commrec *cr,t_inputrec *ir,FILE *fplog);
 183
 184 /* In domdec_con.c */
 185
 186 void dd_move_f_vsites(gmx_domdec_t *dd,rvec *f,rvec *fshift);
 187
 188 void dd_clear_f_vsites(gmx_domdec_t *dd,rvec *f);
 189
 190 void dd_move_x_constraints(gmx_domdec_t *dd,matrix box,
 191                                   rvec *x0,rvec *x1);
 192 /* Move x0 and also x1 if x1!=NULL */
 193
 194 void dd_move_x_vsites(gmx_domdec_t *dd,matrix box,rvec *x);
 195
 196 int *dd_constraints_nlocalatoms(gmx_domdec_t *dd);
 197
 198 void dd_clear_local_constraint_indices(gmx_domdec_t *dd);
 199
 200 void dd_clear_local_vsite_indices(gmx_domdec_t *dd);
 201
 202 int dd_make_local_vsites(gmx_domdec_t *dd,int at_start,t_ilist *lil);
 203
 204 int dd_make_local_constraints(gmx_domdec_t *dd,int at_start,
 205                               const gmx_mtop_t *mtop,
 206                               const int *cginfo,
 207                               gmx_constr_t constr,int nrec,
 208                               t_ilist *il_local);
 209
 210 void init_domdec_constraints(gmx_domdec_t *dd,
 211                              gmx_mtop_t *mtop,
 212                              gmx_constr_t constr);
 213
 214 void init_domdec_vsites(gmx_domdec_t *dd,int n_intercg_vsite);
 215
 216
 217 /* In domdec_top.c */
 218
 219 void dd_print_missing_interactions(FILE *fplog,t_commrec *cr,
 220                                           int local_count,  gmx_mtop_t *top_global, t_state *state_local);
 221
 222 void dd_make_reverse_top(FILE *fplog,
 223                                 gmx_domdec_t *dd,gmx_mtop_t *mtop,
 224                                 gmx_vsite_t *vsite,gmx_constr_t constr,
 225                                 t_inputrec *ir,gmx_bool bBCheck);
 226
 227 void dd_make_local_cgs(gmx_domdec_t *dd,t_block *lcgs);
 228
 229 void dd_make_local_top(FILE *fplog,
 230                        gmx_domdec_t *dd,gmx_domdec_zones_t *zones,
 231                        int npbcdim,matrix box,
 232                        rvec cellsize_min,ivec npulse,
 233                        t_forcerec *fr,
 234                        rvec *cgcm_or_x,
 235                        gmx_vsite_t *vsite,
 236                        gmx_mtop_t *top,gmx_localtop_t *ltop);
 237
 238 void dd_sort_local_top(gmx_domdec_t *dd,t_mdatoms *mdatoms,
 239                               gmx_localtop_t *ltop);
 240 /* Sort ltop->ilist when we are doing free energy. */
 241
 242 gmx_localtop_t *dd_init_local_top(gmx_mtop_t *top_global);
 243
 244 void dd_init_local_state(gmx_domdec_t *dd,
 245                                 t_state *state_global,t_state *local_state);
 246
 247 t_blocka *make_charge_group_links(gmx_mtop_t *mtop,gmx_domdec_t *dd,
 248                                          cginfo_mb_t *cginfo_mb);
 249
 250 void dd_bonded_cg_distance(FILE *fplog,
 251                                   gmx_domdec_t *dd,gmx_mtop_t *mtop,
 252                                   t_inputrec *ir,rvec *x,matrix box,
 253                                   gmx_bool bBCheck,
 254                                   real *r_2b,real *r_mb);
 255
 256 void write_dd_pdb(const char *fn,gmx_large_int_t step,const char *title,
 257                          gmx_mtop_t *mtop,
 258                          t_commrec *cr,
 259                          int natoms,rvec x[],matrix box);
 260 /* Dump a pdb file with the current DD home + communicated atoms.
 261  * When natoms=-1, dump all known atoms.
 262  */
 263
 264
 265 /* In domdec_setup.c */
 266
 267 real comm_box_frac(ivec dd_nc,real cutoff,gmx_ddbox_t *ddbox);
 268 /* Returns the volume fraction of the system that is communicated */
 269
 270 real dd_choose_grid(FILE *fplog,
 271                            t_commrec *cr,gmx_domdec_t *dd,t_inputrec *ir,
 272                            gmx_mtop_t *mtop,matrix box,gmx_ddbox_t *ddbox,
 273                            gmx_bool bDynLoadBal,real dlb_scale,
 274                            real cellsize_limit,real cutoff_dd,
 275                            gmx_bool bInterCGBondeds,gmx_bool bInterCGMultiBody);
 276 /* Determines the optimal DD cell setup dd->nc and possibly npmenodes
 277  * for the system.
 278  * On the master node returns the actual cellsize limit used.
 279  */
 280
 281
 282 /* In domdec_box.c */
 283
 284 void set_ddbox(gmx_domdec_t *dd,gmx_bool bMasterState,t_commrec *cr_sum,
 285                       t_inputrec *ir,matrix box,
 286                       gmx_bool bCalcUnboundedSize,t_block *cgs,rvec *x,
 287                       gmx_ddbox_t *ddbox);
 288
 289 void set_ddbox_cr(t_commrec *cr,ivec *dd_nc,
 290                          t_inputrec *ir,matrix box,t_block *cgs,rvec *x,
 291                          gmx_ddbox_t *ddbox);
 292
 293 #ifdef __cplusplus
 294 }
 295 #endif
 296
 297 #endif  /* _domdec_h */