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 #ifdef HAVE_CONFIG_H
  20 #include <config.h>
  21 #endif
  22
  23 #ifndef _domdec_h
  24 #define _domdec_h
  25
  26 #include "typedefs.h"
  27 #include "vsite.h"
  28 #include "genborn.h"
  29
  30 #ifdef GMX_LIB_MPI
  31 #include <mpi.h>
  32 #endif
  33 #ifdef GMX_THREADS
  34 #include "tmpi.h"
  35 #endif
  36
  37 #ifdef __cplusplus
  38 extern "C" {
  39 #endif
  40
  41 extern int ddglatnr(gmx_domdec_t *dd,int i);
  42 /* Returns the global topology atom number belonging to local atom index i.
  43  * This function is intended for writing ascii output
  44  * and returns atom numbers starting at 1.
  45  * When dd=NULL returns i+1.
  46  */
  47
  48 extern t_block *dd_charge_groups_global(gmx_domdec_t *dd);
  49 /* Return a block struct for the charge groups of the whole system */
  50
  51 extern bool dd_filled_nsgrid_home(gmx_domdec_t *dd);
  52 /* Is the ns grid already filled with the home particles? */
  53
  54 extern void dd_store_state(gmx_domdec_t *dd,t_state *state);
  55 /* Store the global cg indices of the home cgs in state,
  56  * so it can be reset, even after a new DD partitioning.
  57  */
  58
  59 extern gmx_domdec_zones_t *domdec_zones(gmx_domdec_t *dd);
  60
  61 extern void dd_get_ns_ranges(gmx_domdec_t *dd,int icg,
  62                              int *jcg0,int *jcg1,ivec shift0,ivec shift1);
  63
  64 extern int dd_natoms_vsite(gmx_domdec_t *dd);
  65
  66 extern void dd_get_constraint_range(gmx_domdec_t *dd,
  67                                     int *at_start,int *at_end);
  68
  69 extern real dd_cutoff_mbody(gmx_domdec_t *dd);
  70
  71 extern real dd_cutoff_twobody(gmx_domdec_t *dd);
  72
  73 extern bool gmx_pmeonlynode(t_commrec *cr,int nodeid);
  74 /* Return if nodeid in cr->mpi_comm_mysim is a PME-only node */
  75
  76 extern void get_pme_ddnodes(t_commrec *cr,int pmenodeid,
  77                             int *nmy_ddnodes,int **my_ddnodes,int *node_peer);
  78 /* Returns the set of DD nodes that communicate with pme node cr->nodeid */
  79
  80 extern int dd_pme_maxshift0(gmx_domdec_t *dd);
  81 /* Returns the maximum shift for coordinate communication in PME, dim 0 */
  82
  83 extern int dd_pme_maxshift1(gmx_domdec_t *dd);
  84 /* Returns the maximum shift for coordinate communication in PME, dim 1 */
  85
  86 extern void make_dd_communicators(FILE *fplog,t_commrec *cr,int dd_node_order);
  87
  88 extern gmx_domdec_t *
  89 init_domain_decomposition(FILE *fplog,
  90                           t_commrec *cr,
  91                           unsigned long Flags,
  92                           ivec nc,
  93                           real comm_distance_min,real rconstr,
  94                           const char *dlb_opt,real dlb_scale,
  95                           const char *sizex,const char *sizey,const char *sizez,
  96                           gmx_mtop_t *mtop,t_inputrec *ir,
  97                           matrix box,rvec *x,
  98                           gmx_ddbox_t *ddbox,
  99                           int *npme_major, int *npme_minor);
 100
 101 extern void dd_init_bondeds(FILE *fplog,
 102                             gmx_domdec_t *dd,gmx_mtop_t *mtop,
 103                             gmx_vsite_t *vsite,gmx_constr_t constr,
 104                             t_inputrec *ir,bool bBCheck,cginfo_mb_t *cginfo_mb);
 105 /* Initialize data structures for bonded interactions */
 106
 107 extern void set_dd_parameters(FILE *fplog,gmx_domdec_t *dd,real dlb_scale,
 108                               t_inputrec *ir,t_forcerec *fr,
 109                               gmx_ddbox_t *ddbox);
 110 /* Set DD grid dimensions and limits,
 111  * should be called after calling dd_init_bondeds.
 112  */
 113
 114 extern void setup_dd_grid(FILE *fplog,gmx_domdec_t *dd);
 115
 116 extern void dd_collect_vec(gmx_domdec_t *dd,
 117                            t_state *state_local,rvec *lv,rvec *v);
 118
 119 extern 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 extern void dd_cycles_add(gmx_domdec_t *dd,float cycles,int ddCycl);
 125 /* Add the wallcycle count to the DD counter */
 126
 127 extern void dd_force_flop_start(gmx_domdec_t *dd,t_nrnb *nrnb);
 128 /* Start the force flop count */
 129
 130 extern void dd_force_flop_stop(gmx_domdec_t *dd,t_nrnb *nrnb);
 131 /* Stop the force flop count */
 132
 133 extern void dd_move_x(gmx_domdec_t *dd,matrix box,rvec x[]);
 134 /* Communicate the coordinates to the neighboring cells and do pbc. */
 135
 136 extern void dd_move_f(gmx_domdec_t *dd,rvec f[],rvec *fshift);
 137 /* Sum the forces over the neighboring cells.
 138  * When fshift!=NULL the shift forces are updated to obtain
 139  * the correct virial from the single sum including f.
 140  */
 141
 142 extern void dd_atom_spread_real(gmx_domdec_t *dd,real v[]);
 143 /* Communicate a real for each atom to the neighboring cells. */
 144
 145 extern void dd_atom_sum_real(gmx_domdec_t *dd,real v[]);
 146 /* Sum the contributions to a real for each atom over the neighboring cells. */
 147
 148 extern void dd_partition_system(FILE            *fplog,
 149                                 gmx_large_int_t      step,
 150                                 t_commrec       *cr,
 151                                 bool            bMasterState,
 152                                 int             nstglobalcomm,
 153                                 t_state         *state_global,
 154                                 gmx_mtop_t      *top_global,
 155                                 t_inputrec      *ir,
 156                                 t_state         *state_local,
 157                                 rvec            **f,
 158                                 t_mdatoms       *mdatoms,
 159                                 gmx_localtop_t  *top_local,
 160                                 t_forcerec      *fr,
 161                                 gmx_vsite_t     *vsite,
 162                                 gmx_shellfc_t   shellfc,
 163                                 gmx_constr_t    constr,
 164                                 t_nrnb          *nrnb,
 165                                 gmx_wallcycle_t wcycle,
 166                                 bool            bVerbose);
 167 /* Partition the system over the nodes.
 168  * step is only used for printing error messages.
 169  * If bMasterState==TRUE then state_global from the master node is used,
 170  * else state_local is redistributed between the nodes.
 171  * When f!=NULL, *f will be reallocated to the size of state_local.
 172  */
 173
 174 extern void reset_dd_statistics_counters(gmx_domdec_t *dd);
 175 /* Reset all the statistics and counters for total run counting */
 176
 177 extern void print_dd_statistics(t_commrec *cr,t_inputrec *ir,FILE *fplog);
 178
 179 /* In domdec_con.c */
 180
 181 extern void dd_move_f_vsites(gmx_domdec_t *dd,rvec *f,rvec *fshift);
 182
 183 extern void dd_clear_f_vsites(gmx_domdec_t *dd,rvec *f);
 184
 185 extern void dd_move_x_constraints(gmx_domdec_t *dd,matrix box,
 186                                   rvec *x0,rvec *x1);
 187 /* Move x0 and also x1 if x1!=NULL */
 188
 189 extern void dd_move_x_vsites(gmx_domdec_t *dd,matrix box,rvec *x);
 190
 191 extern int *dd_constraints_nlocalatoms(gmx_domdec_t *dd);
 192
 193 extern void dd_clear_local_constraint_indices(gmx_domdec_t *dd);
 194
 195 extern void dd_clear_local_vsite_indices(gmx_domdec_t *dd);
 196
 197 extern int dd_make_local_vsites(gmx_domdec_t *dd,int at_start,t_ilist *lil);
 198
 199 extern int dd_make_local_constraints(gmx_domdec_t *dd,int at_start,
 200                                      gmx_mtop_t *mtop,
 201                                      gmx_constr_t constr,int nrec,
 202                                      t_ilist *il_local);
 203
 204 extern void init_domdec_constraints(gmx_domdec_t *dd,
 205                                     int natoms,gmx_mtop_t *mtop,
 206                                     gmx_constr_t constr);
 207
 208 extern void init_domdec_vsites(gmx_domdec_t *dd,int natoms);
 209
 210
 211 /* In domdec_top.c */
 212
 213 extern void dd_print_missing_interactions(FILE *fplog,t_commrec *cr,
 214                                           int local_count,  gmx_mtop_t *top_global, t_state *state_local);
 215
 216 extern void dd_make_reverse_top(FILE *fplog,
 217                                 gmx_domdec_t *dd,gmx_mtop_t *mtop,
 218                                 gmx_vsite_t *vsite,gmx_constr_t constr,
 219                                 t_inputrec *ir,bool bBCheck);
 220
 221 extern void dd_make_local_cgs(gmx_domdec_t *dd,t_block *lcgs);
 222
 223 extern void dd_make_local_top(FILE *fplog,
 224                               gmx_domdec_t *dd,gmx_domdec_zones_t *zones,
 225                               int npbcdim,matrix box,
 226                               rvec cellsize_min,ivec npulse,
 227                               t_forcerec *fr,gmx_vsite_t *vsite,
 228                               gmx_mtop_t *top,gmx_localtop_t *ltop);
 229
 230 extern void dd_sort_local_top(gmx_domdec_t *dd,t_mdatoms *mdatoms,
 231                               gmx_localtop_t *ltop);
 232 /* Sort ltop->ilist when we are doing free energy. */
 233
 234 extern gmx_localtop_t *dd_init_local_top(gmx_mtop_t *top_global);
 235
 236 extern void dd_init_local_state(gmx_domdec_t *dd,
 237                                 t_state *state_global,t_state *local_state);
 238
 239 extern t_blocka *make_charge_group_links(gmx_mtop_t *mtop,gmx_domdec_t *dd,
 240                                          cginfo_mb_t *cginfo_mb);
 241
 242 extern void dd_bonded_cg_distance(FILE *fplog,
 243                                   gmx_domdec_t *dd,gmx_mtop_t *mtop,
 244                                   t_inputrec *ir,rvec *x,matrix box,
 245                                   bool bBCheck,
 246                                   real *r_2b,real *r_mb);
 247
 248 extern void write_dd_pdb(const char *fn,gmx_large_int_t step,const char *title,
 249                          gmx_mtop_t *mtop,
 250                          t_commrec *cr,
 251                          int natoms,rvec x[],matrix box);
 252 /* Dump a pdb file with the current DD home + communicated atoms.
 253  * When natoms=-1, dump all known atoms.
 254  */
 255
 256
 257 /* In domdec_setup.c */
 258
 259 extern real comm_box_frac(ivec dd_nc,real cutoff,gmx_ddbox_t *ddbox);
 260 /* Returns the volume fraction of the system communicated by each node */
 261
 262 extern real dd_choose_grid(FILE *fplog,
 263                            t_commrec *cr,gmx_domdec_t *dd,t_inputrec *ir,
 264                            gmx_mtop_t *mtop,matrix box,gmx_ddbox_t *ddbox,
 265                            bool bDynLoadBal,real dlb_scale,
 266                            real cellsize_limit,real cutoff_dd,
 267                            bool bInterCGBondeds,bool bInterCGMultiBody);
 268 /* Determines the optimal DD cell setup dd->nc and possibly npmenodes
 269  * for the system.
 270  * On the master node returns the actual cellsize limit used.
 271  */
 272
 273
 274 /* In domdec_box.c */
 275
 276 extern void set_ddbox(gmx_domdec_t *dd,bool bMasterState,t_commrec *cr_sum,
 277                       t_inputrec *ir,matrix box,
 278                       bool bCalcUnboundedSize,t_block *cgs,rvec *x,
 279                       gmx_ddbox_t *ddbox);
 280
 281 extern void set_ddbox_cr(t_commrec *cr,ivec *dd_nc,
 282                          t_inputrec *ir,matrix box,t_block *cgs,rvec *x,
 283                          gmx_ddbox_t *ddbox);
 284
 285 #ifdef __cplusplus
 286 }
 287 #endif
 288
 289 #endif  /* _domdec_h */