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 "vsite.h"
  24 #include "genborn.h"
  25
  26 #ifdef __cplusplus
  27 extern "C" {
  28 #endif
  29
  30 int ddglatnr(gmx_domdec_t *dd,int i);
  31 /* Returns the global topology atom number belonging to local atom index i.
  32  * This function is intended for writing ascii output
  33  * and returns atom numbers starting at 1.
  34  * When dd=NULL returns i+1.
  35  */
  36
  37 t_block *dd_charge_groups_global(gmx_domdec_t *dd);
  38 /* Return a block struct for the charge groups of the whole system */
  39
  40 gmx_bool dd_filled_nsgrid_home(gmx_domdec_t *dd);
  41 /* Is the ns grid already filled with the home particles? */
  42
  43 void dd_store_state(gmx_domdec_t *dd,t_state *state);
  44 /* Store the global cg indices of the home cgs in state,
  45  * so it can be reset, even after a new DD partitioning.
  46  */
  47
  48 gmx_domdec_zones_t *domdec_zones(gmx_domdec_t *dd);
  49
  50 void dd_get_ns_ranges(gmx_domdec_t *dd,int icg,
  51                              int *jcg0,int *jcg1,ivec shift0,ivec shift1);
  52
  53 int dd_natoms_vsite(gmx_domdec_t *dd);
  54
  55 void dd_get_constraint_range(gmx_domdec_t *dd,
  56                                     int *at_start,int *at_end);
  57
  58 real dd_cutoff_mbody(gmx_domdec_t *dd);
  59
  60 real dd_cutoff_twobody(gmx_domdec_t *dd);
  61
  62 gmx_bool gmx_pmeonlynode(t_commrec *cr,int nodeid);
  63 /* Return if nodeid in cr->mpi_comm_mysim is a PME-only node */
  64
  65 void get_pme_ddnodes(t_commrec *cr,int pmenodeid,
  66                             int *nmy_ddnodes,int **my_ddnodes,int *node_peer);
  67 /* Returns the set of DD nodes that communicate with pme node cr->nodeid */
  68
  69 int dd_pme_maxshift_x(gmx_domdec_t *dd);
  70 /* Returns the maximum shift for coordinate communication in PME, dim x */
  71
  72 int dd_pme_maxshift_y(gmx_domdec_t *dd);
  73 /* Returns the maximum shift for coordinate communication in PME, dim y */
  74
  75 void make_dd_communicators(FILE *fplog,t_commrec *cr,int dd_node_order);
  76
  77 gmx_domdec_t *
  78 init_domain_decomposition(FILE *fplog,
  79                           t_commrec *cr,
  80                           unsigned long Flags,
  81                           ivec nc,
  82                           real comm_distance_min,real rconstr,
  83                           const char *dlb_opt,real dlb_scale,
  84                           const char *sizex,const char *sizey,const char *sizez,
  85                           gmx_mtop_t *mtop,t_inputrec *ir,
  86                           matrix box,rvec *x,
  87                           gmx_ddbox_t *ddbox,
  88                           int *npme_x, int *npme_y);
  89
  90 void dd_init_bondeds(FILE *fplog,
  91                             gmx_domdec_t *dd,gmx_mtop_t *mtop,
  92                             gmx_vsite_t *vsite,gmx_constr_t constr,
  93                             t_inputrec *ir,gmx_bool bBCheck,cginfo_mb_t *cginfo_mb);
  94 /* Initialize data structures for bonded interactions */
  95
  96 void set_dd_parameters(FILE *fplog,gmx_domdec_t *dd,real dlb_scale,
  97                               t_inputrec *ir,t_forcerec *fr,
  98                               gmx_ddbox_t *ddbox);
  99 /* Set DD grid dimensions and limits,
 100  * should be called after calling dd_init_bondeds.
 101  */
 102
 103 void setup_dd_grid(FILE *fplog,gmx_domdec_t *dd);
 104
 105 void dd_collect_vec(gmx_domdec_t *dd,
 106                            t_state *state_local,rvec *lv,rvec *v);
 107
 108 void dd_collect_state(gmx_domdec_t *dd,
 109                              t_state *state_local,t_state *state);
 110
 111 enum { ddCyclStep, ddCyclPPduringPME, ddCyclF, ddCyclPME, ddCyclNr };
 112
 113 void dd_cycles_add(gmx_domdec_t *dd,float cycles,int ddCycl);
 114 /* Add the wallcycle count to the DD counter */
 115
 116 void dd_force_flop_start(gmx_domdec_t *dd,t_nrnb *nrnb);
 117 /* Start the force flop count */
 118
 119 void dd_force_flop_stop(gmx_domdec_t *dd,t_nrnb *nrnb);
 120 /* Stop the force flop count */
 121
 122 void dd_move_x(gmx_domdec_t *dd,matrix box,rvec x[]);
 123 /* Communicate the coordinates to the neighboring cells and do pbc. */
 124
 125 void dd_move_f(gmx_domdec_t *dd,rvec f[],rvec *fshift);
 126 /* Sum the forces over the neighboring cells.
 127  * When fshift!=NULL the shift forces are updated to obtain
 128  * the correct virial from the single sum including f.
 129  */
 130
 131 void dd_atom_spread_real(gmx_domdec_t *dd,real v[]);
 132 /* Communicate a real for each atom to the neighboring cells. */
 133
 134 void dd_atom_sum_real(gmx_domdec_t *dd,real v[]);
 135 /* Sum the contributions to a real for each atom over the neighboring cells. */
 136
 137 void dd_partition_system(FILE            *fplog,
 138                                 gmx_large_int_t      step,
 139                                 t_commrec       *cr,
 140                                 gmx_bool            bMasterState,
 141                                 int             nstglobalcomm,
 142                                 t_state         *state_global,
 143                                 gmx_mtop_t      *top_global,
 144                                 t_inputrec      *ir,
 145                                 t_state         *state_local,
 146                                 rvec            **f,
 147                                 t_mdatoms       *mdatoms,
 148                                 gmx_localtop_t  *top_local,
 149                                 t_forcerec      *fr,
 150                                 gmx_vsite_t     *vsite,
 151                                 gmx_shellfc_t   shellfc,
 152                                 gmx_constr_t    constr,
 153                                 t_nrnb          *nrnb,
 154                                 gmx_wallcycle_t wcycle,
 155                                 gmx_bool            bVerbose);
 156 /* Partition the system over the nodes.
 157  * step is only used for printing error messages.
 158  * If bMasterState==TRUE then state_global from the master node is used,
 159  * else state_local is redistributed between the nodes.
 160  * When f!=NULL, *f will be reallocated to the size of state_local.
 161  */
 162
 163 void reset_dd_statistics_counters(gmx_domdec_t *dd);
 164 /* Reset all the statistics and counters for total run counting */
 165
 166 void print_dd_statistics(t_commrec *cr,t_inputrec *ir,FILE *fplog);
 167
 168 /* In domdec_con.c */
 169
 170 void dd_move_f_vsites(gmx_domdec_t *dd,rvec *f,rvec *fshift);
 171
 172 void dd_clear_f_vsites(gmx_domdec_t *dd,rvec *f);
 173
 174 void dd_move_x_constraints(gmx_domdec_t *dd,matrix box,
 175                                   rvec *x0,rvec *x1);
 176 /* Move x0 and also x1 if x1!=NULL */
 177
 178 void dd_move_x_vsites(gmx_domdec_t *dd,matrix box,rvec *x);
 179
 180 int *dd_constraints_nlocalatoms(gmx_domdec_t *dd);
 181
 182 void dd_clear_local_constraint_indices(gmx_domdec_t *dd);
 183
 184 void dd_clear_local_vsite_indices(gmx_domdec_t *dd);
 185
 186 int dd_make_local_vsites(gmx_domdec_t *dd,int at_start,t_ilist *lil);
 187
 188 int dd_make_local_constraints(gmx_domdec_t *dd,int at_start,
 189                                      gmx_mtop_t *mtop,
 190                                      gmx_constr_t constr,int nrec,
 191                                      t_ilist *il_local);
 192
 193 void init_domdec_constraints(gmx_domdec_t *dd,
 194                                     int natoms,gmx_mtop_t *mtop,
 195                                     gmx_constr_t constr);
 196
 197 void init_domdec_vsites(gmx_domdec_t *dd,int natoms);
 198
 199
 200 /* In domdec_top.c */
 201
 202 void dd_print_missing_interactions(FILE *fplog,t_commrec *cr,
 203                                           int local_count,  gmx_mtop_t *top_global, t_state *state_local);
 204
 205 void dd_make_reverse_top(FILE *fplog,
 206                                 gmx_domdec_t *dd,gmx_mtop_t *mtop,
 207                                 gmx_vsite_t *vsite,gmx_constr_t constr,
 208                                 t_inputrec *ir,gmx_bool bBCheck);
 209
 210 void dd_make_local_cgs(gmx_domdec_t *dd,t_block *lcgs);
 211
 212 void dd_make_local_top(FILE *fplog,
 213                               gmx_domdec_t *dd,gmx_domdec_zones_t *zones,
 214                               int npbcdim,matrix box,
 215                               rvec cellsize_min,ivec npulse,
 216                               t_forcerec *fr,gmx_vsite_t *vsite,
 217                               gmx_mtop_t *top,gmx_localtop_t *ltop);
 218
 219 void dd_sort_local_top(gmx_domdec_t *dd,t_mdatoms *mdatoms,
 220                               gmx_localtop_t *ltop);
 221 /* Sort ltop->ilist when we are doing free energy. */
 222
 223 gmx_localtop_t *dd_init_local_top(gmx_mtop_t *top_global);
 224
 225 void dd_init_local_state(gmx_domdec_t *dd,
 226                                 t_state *state_global,t_state *local_state);
 227
 228 t_blocka *make_charge_group_links(gmx_mtop_t *mtop,gmx_domdec_t *dd,
 229                                          cginfo_mb_t *cginfo_mb);
 230
 231 void dd_bonded_cg_distance(FILE *fplog,
 232                                   gmx_domdec_t *dd,gmx_mtop_t *mtop,
 233                                   t_inputrec *ir,rvec *x,matrix box,
 234                                   gmx_bool bBCheck,
 235                                   real *r_2b,real *r_mb);
 236
 237 void write_dd_pdb(const char *fn,gmx_large_int_t step,const char *title,
 238                          gmx_mtop_t *mtop,
 239                          t_commrec *cr,
 240                          int natoms,rvec x[],matrix box);
 241 /* Dump a pdb file with the current DD home + communicated atoms.
 242  * When natoms=-1, dump all known atoms.
 243  */
 244
 245
 246 /* In domdec_setup.c */
 247
 248 real comm_box_frac(ivec dd_nc,real cutoff,gmx_ddbox_t *ddbox);
 249 /* Returns the volume fraction of the system that is communicated */
 250
 251 real dd_choose_grid(FILE *fplog,
 252                            t_commrec *cr,gmx_domdec_t *dd,t_inputrec *ir,
 253                            gmx_mtop_t *mtop,matrix box,gmx_ddbox_t *ddbox,
 254                            gmx_bool bDynLoadBal,real dlb_scale,
 255                            real cellsize_limit,real cutoff_dd,
 256                            gmx_bool bInterCGBondeds,gmx_bool bInterCGMultiBody);
 257 /* Determines the optimal DD cell setup dd->nc and possibly npmenodes
 258  * for the system.
 259  * On the master node returns the actual cellsize limit used.
 260  */
 261
 262
 263 /* In domdec_box.c */
 264
 265 void set_ddbox(gmx_domdec_t *dd,gmx_bool bMasterState,t_commrec *cr_sum,
 266                       t_inputrec *ir,matrix box,
 267                       gmx_bool bCalcUnboundedSize,t_block *cgs,rvec *x,
 268                       gmx_ddbox_t *ddbox);
 269
 270 void set_ddbox_cr(t_commrec *cr,ivec *dd_nc,
 271                          t_inputrec *ir,matrix box,t_block *cgs,rvec *x,
 272                          gmx_ddbox_t *ddbox);
 273
 274 #ifdef __cplusplus
 275 }
 276 #endif
 277
 278 #endif  /* _domdec_h */