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 GMX_LIB_MPI
  27 #include <mpi.h>
  28 #endif
  29 #ifdef GMX_THREADS
  30 #include "tmpi.h"
  31 #endif
  32
  33 #ifdef __cplusplus
  34 extern "C" {
  35 #endif
  36
  37 int ddglatnr(gmx_domdec_t *dd,int i);
  38 /* Returns the global topology atom number belonging to local atom index i.
  39  * This function is intended for writing ascii output
  40  * and returns atom numbers starting at 1.
  41  * When dd=NULL returns i+1.
  42  */
  43
  44 t_block *dd_charge_groups_global(gmx_domdec_t *dd);
  45 /* Return a block struct for the charge groups of the whole system */
  46
  47 gmx_bool dd_filled_nsgrid_home(gmx_domdec_t *dd);
  48 /* Is the ns grid already filled with the home particles? */
  49
  50 void dd_store_state(gmx_domdec_t *dd,t_state *state);
  51 /* Store the global cg indices of the home cgs in state,
  52  * so it can be reset, even after a new DD partitioning.
  53  */
  54
  55 gmx_domdec_zones_t *domdec_zones(gmx_domdec_t *dd);
  56
  57 void dd_get_ns_ranges(gmx_domdec_t *dd,int icg,
  58                              int *jcg0,int *jcg1,ivec shift0,ivec shift1);
  59
  60 int dd_natoms_vsite(gmx_domdec_t *dd);
  61
  62 void dd_get_constraint_range(gmx_domdec_t *dd,
  63                                     int *at_start,int *at_end);
  64
  65 real dd_cutoff_mbody(gmx_domdec_t *dd);
  66
  67 real dd_cutoff_twobody(gmx_domdec_t *dd);
  68
  69 gmx_bool gmx_pmeonlynode(t_commrec *cr,int nodeid);
  70 /* Return if nodeid in cr->mpi_comm_mysim is a PME-only node */
  71
  72 void get_pme_ddnodes(t_commrec *cr,int pmenodeid,
  73                             int *nmy_ddnodes,int **my_ddnodes,int *node_peer);
  74 /* Returns the set of DD nodes that communicate with pme node cr->nodeid */
  75
  76 int dd_pme_maxshift_x(gmx_domdec_t *dd);
  77 /* Returns the maximum shift for coordinate communication in PME, dim x */
  78
  79 int dd_pme_maxshift_y(gmx_domdec_t *dd);
  80 /* Returns the maximum shift for coordinate communication in PME, dim y */
  81
  82 void make_dd_communicators(FILE *fplog,t_commrec *cr,int dd_node_order);
  83
  84 gmx_domdec_t *
  85 init_domain_decomposition(FILE *fplog,
  86                           t_commrec *cr,
  87                           unsigned long Flags,
  88                           ivec nc,
  89                           real comm_distance_min,real rconstr,
  90                           const char *dlb_opt,real dlb_scale,
  91                           const char *sizex,const char *sizey,const char *sizez,
  92                           gmx_mtop_t *mtop,t_inputrec *ir,
  93                           matrix box,rvec *x,
  94                           gmx_ddbox_t *ddbox,
  95                           int *npme_x, int *npme_y);
  96
  97 void dd_init_bondeds(FILE *fplog,
  98                             gmx_domdec_t *dd,gmx_mtop_t *mtop,
  99                             gmx_vsite_t *vsite,gmx_constr_t constr,
 100                             t_inputrec *ir,gmx_bool bBCheck,cginfo_mb_t *cginfo_mb);
 101 /* Initialize data structures for bonded interactions */
 102
 103 void set_dd_parameters(FILE *fplog,gmx_domdec_t *dd,real dlb_scale,
 104                               t_inputrec *ir,t_forcerec *fr,
 105                               gmx_ddbox_t *ddbox);
 106 /* Set DD grid dimensions and limits,
 107  * should be called after calling dd_init_bondeds.
 108  */
 109
 110 void setup_dd_grid(FILE *fplog,gmx_domdec_t *dd);
 111
 112 void dd_collect_vec(gmx_domdec_t *dd,
 113                            t_state *state_local,rvec *lv,rvec *v);
 114
 115 void dd_collect_state(gmx_domdec_t *dd,
 116                              t_state *state_local,t_state *state);
 117
 118 enum { ddCyclStep, ddCyclPPduringPME, ddCyclF, ddCyclPME, ddCyclNr };
 119
 120 void dd_cycles_add(gmx_domdec_t *dd,float cycles,int ddCycl);
 121 /* Add the wallcycle count to the DD counter */
 122
 123 void dd_force_flop_start(gmx_domdec_t *dd,t_nrnb *nrnb);
 124 /* Start the force flop count */
 125
 126 void dd_force_flop_stop(gmx_domdec_t *dd,t_nrnb *nrnb);
 127 /* Stop the force flop count */
 128
 129 void dd_move_x(gmx_domdec_t *dd,matrix box,rvec x[]);
 130 /* Communicate the coordinates to the neighboring cells and do pbc. */
 131
 132 void dd_move_f(gmx_domdec_t *dd,rvec f[],rvec *fshift);
 133 /* Sum the forces over the neighboring cells.
 134  * When fshift!=NULL the shift forces are updated to obtain
 135  * the correct virial from the single sum including f.
 136  */
 137
 138 void dd_atom_spread_real(gmx_domdec_t *dd,real v[]);
 139 /* Communicate a real for each atom to the neighboring cells. */
 140
 141 void dd_atom_sum_real(gmx_domdec_t *dd,real v[]);
 142 /* Sum the contributions to a real for each atom over the neighboring cells. */
 143
 144 void init_local_rigid_groups(t_inputrec *ir, t_mdatoms *mdatoms, t_state *state_local);
 145 /* Initialize the rigid body groups */
 146
 147 void get_local_rigid_groups(t_inputrec *ir, t_mdatoms *mdatoms);
 148 /* Update the rigid body groups according to the current domain decomposition */
 149
 150 void dd_partition_system(FILE            *fplog,
 151                                 gmx_large_int_t      step,
 152                                 t_commrec       *cr,
 153                                 gmx_bool            bMasterState,
 154                                 int             nstglobalcomm,
 155                                 t_state         *state_global,
 156                                 gmx_mtop_t      *top_global,
 157                                 t_inputrec      *ir,
 158                                 t_state         *state_local,
 159                                 rvec            **f,
 160                                 t_mdatoms       *mdatoms,
 161                                 gmx_localtop_t  *top_local,
 162                                 t_forcerec      *fr,
 163                                 gmx_vsite_t     *vsite,
 164                                 gmx_shellfc_t   shellfc,
 165                                 gmx_constr_t    constr,
 166                                 t_nrnb          *nrnb,
 167                                 gmx_wallcycle_t wcycle,
 168                                 gmx_bool            bVerbose);
 169 /* Partition the system over the nodes.
 170  * step is only used for printing error messages.
 171  * If bMasterState==TRUE then state_global from the master node is used,
 172  * else state_local is redistributed between the nodes.
 173  * When f!=NULL, *f will be reallocated to the size of state_local.
 174  */
 175
 176 void reset_dd_statistics_counters(gmx_domdec_t *dd);
 177 /* Reset all the statistics and counters for total run counting */
 178
 179 void print_dd_statistics(t_commrec *cr,t_inputrec *ir,FILE *fplog);
 180
 181 /* In domdec_con.c */
 182
 183 void dd_move_f_vsites(gmx_domdec_t *dd,rvec *f,rvec *fshift);
 184
 185 void dd_clear_f_vsites(gmx_domdec_t *dd,rvec *f);
 186
 187 void dd_move_x_constraints(gmx_domdec_t *dd,matrix box,
 188                                   rvec *x0,rvec *x1);
 189 /* Move x0 and also x1 if x1!=NULL */
 190
 191 void dd_move_x_vsites(gmx_domdec_t *dd,matrix box,rvec *x);
 192
 193 int *dd_constraints_nlocalatoms(gmx_domdec_t *dd);
 194
 195 void dd_clear_local_constraint_indices(gmx_domdec_t *dd);
 196
 197 void dd_clear_local_vsite_indices(gmx_domdec_t *dd);
 198
 199 int dd_make_local_vsites(gmx_domdec_t *dd,int at_start,t_ilist *lil);
 200
 201 int dd_make_local_constraints(gmx_domdec_t *dd,int at_start,
 202                                      gmx_mtop_t *mtop,
 203                                      gmx_constr_t constr,int nrec,
 204                                      t_ilist *il_local);
 205
 206 void init_domdec_constraints(gmx_domdec_t *dd,
 207                                     int natoms,gmx_mtop_t *mtop,
 208                                     gmx_constr_t constr);
 209
 210 void init_domdec_vsites(gmx_domdec_t *dd,int natoms);
 211
 212
 213 /* In domdec_top.c */
 214
 215 void dd_print_missing_interactions(FILE *fplog,t_commrec *cr,
 216                                           int local_count,  gmx_mtop_t *top_global, t_state *state_local);
 217
 218 void dd_make_reverse_top(FILE *fplog,
 219                                 gmx_domdec_t *dd,gmx_mtop_t *mtop,
 220                                 gmx_vsite_t *vsite,gmx_constr_t constr,
 221                                 t_inputrec *ir,gmx_bool bBCheck);
 222
 223 void dd_make_local_cgs(gmx_domdec_t *dd,t_block *lcgs);
 224
 225 void dd_make_local_top(FILE *fplog,
 226                               gmx_domdec_t *dd,gmx_domdec_zones_t *zones,
 227                               int npbcdim,matrix box,
 228                               rvec cellsize_min,ivec npulse,
 229                               t_forcerec *fr,gmx_vsite_t *vsite,
 230                               gmx_mtop_t *top,gmx_localtop_t *ltop);
 231
 232 void dd_sort_local_top(gmx_domdec_t *dd,t_mdatoms *mdatoms,
 233                               gmx_localtop_t *ltop);
 234 /* Sort ltop->ilist when we are doing free energy. */
 235
 236 gmx_localtop_t *dd_init_local_top(gmx_mtop_t *top_global);
 237
 238 void dd_init_local_state(gmx_domdec_t *dd,
 239                                 t_state *state_global,t_state *local_state);
 240
 241 t_blocka *make_charge_group_links(gmx_mtop_t *mtop,gmx_domdec_t *dd,
 242                                          cginfo_mb_t *cginfo_mb);
 243
 244 void dd_bonded_cg_distance(FILE *fplog,
 245                                   gmx_domdec_t *dd,gmx_mtop_t *mtop,
 246                                   t_inputrec *ir,rvec *x,matrix box,
 247                                   gmx_bool bBCheck,
 248                                   real *r_2b,real *r_mb);
 249
 250 void write_dd_pdb(const char *fn,gmx_large_int_t step,const char *title,
 251                          gmx_mtop_t *mtop,
 252                          t_commrec *cr,
 253                          int natoms,rvec x[],matrix box);
 254 /* Dump a pdb file with the current DD home + communicated atoms.
 255  * When natoms=-1, dump all known atoms.
 256  */
 257
 258
 259 /* In domdec_setup.c */
 260
 261 real comm_box_frac(ivec dd_nc,real cutoff,gmx_ddbox_t *ddbox);
 262 /* Returns the volume fraction of the system that is communicated */
 263
 264 real dd_choose_grid(FILE *fplog,
 265                            t_commrec *cr,gmx_domdec_t *dd,t_inputrec *ir,
 266                            gmx_mtop_t *mtop,matrix box,gmx_ddbox_t *ddbox,
 267                            gmx_bool bDynLoadBal,real dlb_scale,
 268                            real cellsize_limit,real cutoff_dd,
 269                            gmx_bool bInterCGBondeds,gmx_bool bInterCGMultiBody);
 270 /* Determines the optimal DD cell setup dd->nc and possibly npmenodes
 271  * for the system.
 272  * On the master node returns the actual cellsize limit used.
 273  */
 274
 275
 276 /* In domdec_box.c */
 277
 278 void set_ddbox(gmx_domdec_t *dd,gmx_bool bMasterState,t_commrec *cr_sum,
 279                       t_inputrec *ir,matrix box,
 280                       gmx_bool bCalcUnboundedSize,t_block *cgs,rvec *x,
 281                       gmx_ddbox_t *ddbox);
 282
 283 void set_ddbox_cr(t_commrec *cr,ivec *dd_nc,
 284                          t_inputrec *ir,matrix box,t_block *cgs,rvec *x,
 285                          gmx_ddbox_t *ddbox);
 286
 287 #ifdef __cplusplus
 288 }
 289 #endif
 290
 291 #endif  /* _domdec_h */