src/gromacs/mdlib/broadcaststructs.cpp

   1 /*
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   5  * Copyright (c) 2001-2004, The GROMACS development team.
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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "broadcaststructs.h"
  41
  42 #include <string.h>
  43
  44 #include "gromacs/gmxlib/network.h"
  45 #include "gromacs/math/vec.h"
  46 #include "gromacs/mdlib/mdrun.h"
  47 #include "gromacs/mdlib/tgroup.h"
  48 #include "gromacs/mdtypes/commrec.h"
  49 #include "gromacs/mdtypes/inputrec.h"
  50 #include "gromacs/mdtypes/md_enums.h"
  51 #include "gromacs/mdtypes/pull-params.h"
  52 #include "gromacs/mdtypes/state.h"
  53 #include "gromacs/topology/symtab.h"
  54 #include "gromacs/topology/topology.h"
  55 #include "gromacs/utility/fatalerror.h"
  56 #include "gromacs/utility/inmemoryserializer.h"
  57 #include "gromacs/utility/keyvaluetree.h"
  58 #include "gromacs/utility/keyvaluetreeserializer.h"
  59 #include "gromacs/utility/smalloc.h"
  60
  61 static void bc_cstring(const t_commrec *cr, char **s)
  62 {
  63     int size = 0;
  64
  65     if (MASTER(cr) && *s != nullptr)
  66     {
  67         /* Size of the char buffer is string length + 1 for '\0' */
  68         size = strlen(*s) + 1;
  69     }
  70     block_bc(cr, size);
  71     if (size > 0)
  72     {
  73         if (!MASTER(cr))
  74         {
  75             srenew(*s, size);
  76         }
  77         nblock_bc(cr, size, *s);
  78     }
  79     else if (!MASTER(cr) && *s != nullptr)
  80     {
  81         sfree(*s);
  82         *s = nullptr;
  83     }
  84 }
  85
  86 static void bc_string(const t_commrec *cr, t_symtab *symtab, char ***s)
  87 {
  88     int handle;
  89
  90     if (MASTER(cr))
  91     {
  92         handle = lookup_symtab(symtab, *s);
  93     }
  94     block_bc(cr, handle);
  95     if (!MASTER(cr))
  96     {
  97         *s = get_symtab_handle(symtab, handle);
  98     }
  99 }
 100
 101 static void bc_strings(const t_commrec *cr, t_symtab *symtab, int nr, char ****nm)
 102 {
 103     int     i;
 104     int    *handle;
 105
 106     snew(handle, nr);
 107     if (MASTER(cr))
 108     {
 109         for (i = 0; (i < nr); i++)
 110         {
 111             handle[i] = lookup_symtab(symtab, (*nm)[i]);
 112         }
 113     }
 114     nblock_bc(cr, nr, handle);
 115
 116     if (!MASTER(cr))
 117     {
 118         snew_bc(cr, *nm, nr);
 119         for (i = 0; (i < nr); i++)
 120         {
 121             (*nm)[i] = get_symtab_handle(symtab, handle[i]);
 122         }
 123     }
 124     sfree(handle);
 125 }
 126
 127 static void bc_strings_resinfo(const t_commrec *cr, t_symtab *symtab,
 128                                int nr, t_resinfo *resinfo)
 129 {
 130     int   i;
 131     int  *handle;
 132
 133     snew(handle, nr);
 134     if (MASTER(cr))
 135     {
 136         for (i = 0; (i < nr); i++)
 137         {
 138             handle[i] = lookup_symtab(symtab, resinfo[i].name);
 139         }
 140     }
 141     nblock_bc(cr, nr, handle);
 142
 143     if (!MASTER(cr))
 144     {
 145         for (i = 0; (i < nr); i++)
 146         {
 147             resinfo[i].name = get_symtab_handle(symtab, handle[i]);
 148         }
 149     }
 150     sfree(handle);
 151 }
 152
 153 static void bc_symtab(const t_commrec *cr, t_symtab *symtab)
 154 {
 155     int       i, nr, len;
 156     t_symbuf *symbuf;
 157
 158     block_bc(cr, symtab->nr);
 159     nr = symtab->nr;
 160     snew_bc(cr, symtab->symbuf, 1);
 161     symbuf          = symtab->symbuf;
 162     symbuf->bufsize = nr;
 163     snew_bc(cr, symbuf->buf, nr);
 164     for (i = 0; i < nr; i++)
 165     {
 166         if (MASTER(cr))
 167         {
 168             len = strlen(symbuf->buf[i]) + 1;
 169         }
 170         block_bc(cr, len);
 171         snew_bc(cr, symbuf->buf[i], len);
 172         nblock_bc(cr, len, symbuf->buf[i]);
 173     }
 174 }
 175
 176 static void bc_block(const t_commrec *cr, t_block *block)
 177 {
 178     block_bc(cr, block->nr);
 179     snew_bc(cr, block->index, block->nr+1);
 180     nblock_bc(cr, block->nr+1, block->index);
 181 }
 182
 183 static void bc_blocka(const t_commrec *cr, t_blocka *block)
 184 {
 185     block_bc(cr, block->nr);
 186     snew_bc(cr, block->index, block->nr+1);
 187     nblock_bc(cr, block->nr+1, block->index);
 188     block_bc(cr, block->nra);
 189     if (block->nra)
 190     {
 191         snew_bc(cr, block->a, block->nra);
 192         nblock_bc(cr, block->nra, block->a);
 193     }
 194 }
 195
 196 static void bc_grps(const t_commrec *cr, t_grps grps[])
 197 {
 198     int i;
 199
 200     for (i = 0; (i < egcNR); i++)
 201     {
 202         block_bc(cr, grps[i].nr);
 203         snew_bc(cr, grps[i].nm_ind, grps[i].nr);
 204         nblock_bc(cr, grps[i].nr, grps[i].nm_ind);
 205     }
 206 }
 207
 208 static void bc_atoms(const t_commrec *cr, t_symtab *symtab, t_atoms *atoms)
 209 {
 210     block_bc(cr, atoms->nr);
 211     snew_bc(cr, atoms->atom, atoms->nr);
 212     nblock_bc(cr, atoms->nr, atoms->atom);
 213     bc_strings(cr, symtab, atoms->nr, &atoms->atomname);
 214     block_bc(cr, atoms->nres);
 215     snew_bc(cr, atoms->resinfo, atoms->nres);
 216     nblock_bc(cr, atoms->nres, atoms->resinfo);
 217     bc_strings_resinfo(cr, symtab, atoms->nres, atoms->resinfo);
 218     /* QMMM requires atomtypes to be known on all nodes as well */
 219     bc_strings(cr, symtab, atoms->nr, &atoms->atomtype);
 220     bc_strings(cr, symtab, atoms->nr, &atoms->atomtypeB);
 221 }
 222
 223 static void bc_groups(const t_commrec *cr, t_symtab *symtab,
 224                       int natoms, gmx_groups_t *groups)
 225 {
 226     int g, n;
 227
 228     bc_grps(cr, groups->grps);
 229     block_bc(cr, groups->ngrpname);
 230     bc_strings(cr, symtab, groups->ngrpname, &groups->grpname);
 231     for (g = 0; g < egcNR; g++)
 232     {
 233         if (MASTER(cr))
 234         {
 235             if (groups->grpnr[g])
 236             {
 237                 n = natoms;
 238             }
 239             else
 240             {
 241                 n = 0;
 242             }
 243         }
 244         block_bc(cr, n);
 245         if (n == 0)
 246         {
 247             groups->grpnr[g] = nullptr;
 248         }
 249         else
 250         {
 251             snew_bc(cr, groups->grpnr[g], n);
 252             nblock_bc(cr, n, groups->grpnr[g]);
 253         }
 254     }
 255     if (debug)
 256     {
 257         fprintf(debug, "after bc_groups\n");
 258     }
 259 }
 260
 261 static void bcastPaddedRVecVector(const t_commrec *cr, PaddedRVecVector *v, int numAtoms)
 262 {
 263     v->resize(gmx::paddedRVecVectorSize(numAtoms));
 264     nblock_bc(cr, numAtoms, as_rvec_array(v->data()));
 265 }
 266
 267 void broadcastStateWithoutDynamics(const t_commrec *cr, t_state *state)
 268 {
 269     GMX_RELEASE_ASSERT(!DOMAINDECOMP(cr), "broadcastStateWithoutDynamics should only be used for special cases without domain decomposition");
 270
 271     if (!PAR(cr))
 272     {
 273         return;
 274     }
 275
 276     /* Broadcasts the state sizes and flags from the master to all ranks
 277      * in cr->mpi_comm_mygroup.
 278      */
 279     block_bc(cr, state->natoms);
 280     block_bc(cr, state->flags);
 281
 282     for (int i = 0; i < estNR; i++)
 283     {
 284         if (state->flags & (1 << i))
 285         {
 286             switch (i)
 287             {
 288                 case estLAMBDA:
 289                     nblock_bc(cr, efptNR, state->lambda.data());
 290                     break;
 291                 case estFEPSTATE:
 292                     block_bc(cr, state->fep_state);
 293                     break;
 294                 case estBOX:
 295                     block_bc(cr, state->box);
 296                     break;
 297                 case estX:
 298                     bcastPaddedRVecVector(cr, &state->x, state->natoms);
 299                     break;
 300                 default:
 301                     GMX_RELEASE_ASSERT(false, "The state has a dynamic entry, while no dynamic entries should be present");
 302                     break;
 303             }
 304         }
 305     }
 306 }
 307
 308 static void bc_ilists(const t_commrec *cr, t_ilist *ilist)
 309 {
 310     int ftype;
 311
 312     /* Here we only communicate the non-zero length ilists */
 313     if (MASTER(cr))
 314     {
 315         for (ftype = 0; ftype < F_NRE; ftype++)
 316         {
 317             if (ilist[ftype].nr > 0)
 318             {
 319                 block_bc(cr, ftype);
 320                 block_bc(cr, ilist[ftype].nr);
 321                 nblock_bc(cr, ilist[ftype].nr, ilist[ftype].iatoms);
 322             }
 323         }
 324         ftype = -1;
 325         block_bc(cr, ftype);
 326     }
 327     else
 328     {
 329         for (ftype = 0; ftype < F_NRE; ftype++)
 330         {
 331             ilist[ftype].nr = 0;
 332         }
 333         do
 334         {
 335             block_bc(cr, ftype);
 336             if (ftype >= 0)
 337             {
 338                 block_bc(cr, ilist[ftype].nr);
 339                 snew_bc(cr, ilist[ftype].iatoms, ilist[ftype].nr);
 340                 nblock_bc(cr, ilist[ftype].nr, ilist[ftype].iatoms);
 341             }
 342         }
 343         while (ftype >= 0);
 344     }
 345
 346     if (debug)
 347     {
 348         fprintf(debug, "after bc_ilists\n");
 349     }
 350 }
 351
 352 static void bc_cmap(const t_commrec *cr, gmx_cmap_t *cmap_grid)
 353 {
 354     int i, nelem, ngrid;
 355
 356     block_bc(cr, cmap_grid->ngrid);
 357     block_bc(cr, cmap_grid->grid_spacing);
 358
 359     ngrid = cmap_grid->ngrid;
 360     nelem = cmap_grid->grid_spacing * cmap_grid->grid_spacing;
 361
 362     if (ngrid > 0)
 363     {
 364         snew_bc(cr, cmap_grid->cmapdata, ngrid);
 365
 366         for (i = 0; i < ngrid; i++)
 367         {
 368             snew_bc(cr, cmap_grid->cmapdata[i].cmap, 4*nelem);
 369             nblock_bc(cr, 4*nelem, cmap_grid->cmapdata[i].cmap);
 370         }
 371     }
 372 }
 373
 374 static void bc_ffparams(const t_commrec *cr, gmx_ffparams_t *ffp)
 375 {
 376     block_bc(cr, ffp->ntypes);
 377     block_bc(cr, ffp->atnr);
 378     snew_bc(cr, ffp->functype, ffp->ntypes);
 379     snew_bc(cr, ffp->iparams, ffp->ntypes);
 380     nblock_bc(cr, ffp->ntypes, ffp->functype);
 381     nblock_bc(cr, ffp->ntypes, ffp->iparams);
 382     block_bc(cr, ffp->reppow);
 383     block_bc(cr, ffp->fudgeQQ);
 384     bc_cmap(cr, &ffp->cmap_grid);
 385 }
 386
 387 static void bc_grpopts(const t_commrec *cr, t_grpopts *g)
 388 {
 389     int i, n;
 390
 391     block_bc(cr, g->ngtc);
 392     block_bc(cr, g->ngacc);
 393     block_bc(cr, g->ngfrz);
 394     block_bc(cr, g->ngener);
 395     snew_bc(cr, g->nrdf, g->ngtc);
 396     snew_bc(cr, g->tau_t, g->ngtc);
 397     snew_bc(cr, g->ref_t, g->ngtc);
 398     snew_bc(cr, g->acc, g->ngacc);
 399     snew_bc(cr, g->nFreeze, g->ngfrz);
 400     snew_bc(cr, g->egp_flags, g->ngener*g->ngener);
 401
 402     nblock_bc(cr, g->ngtc, g->nrdf);
 403     nblock_bc(cr, g->ngtc, g->tau_t);
 404     nblock_bc(cr, g->ngtc, g->ref_t);
 405     nblock_bc(cr, g->ngacc, g->acc);
 406     nblock_bc(cr, g->ngfrz, g->nFreeze);
 407     nblock_bc(cr, g->ngener*g->ngener, g->egp_flags);
 408     snew_bc(cr, g->annealing, g->ngtc);
 409     snew_bc(cr, g->anneal_npoints, g->ngtc);
 410     snew_bc(cr, g->anneal_time, g->ngtc);
 411     snew_bc(cr, g->anneal_temp, g->ngtc);
 412     nblock_bc(cr, g->ngtc, g->annealing);
 413     nblock_bc(cr, g->ngtc, g->anneal_npoints);
 414     for (i = 0; (i < g->ngtc); i++)
 415     {
 416         n = g->anneal_npoints[i];
 417         if (n > 0)
 418         {
 419             snew_bc(cr, g->anneal_time[i], n);
 420             snew_bc(cr, g->anneal_temp[i], n);
 421             nblock_bc(cr, n, g->anneal_time[i]);
 422             nblock_bc(cr, n, g->anneal_temp[i]);
 423         }
 424     }
 425
 426     /* QMMM stuff, see inputrec */
 427     block_bc(cr, g->ngQM);
 428     snew_bc(cr, g->QMmethod, g->ngQM);
 429     snew_bc(cr, g->QMbasis, g->ngQM);
 430     snew_bc(cr, g->QMcharge, g->ngQM);
 431     snew_bc(cr, g->QMmult, g->ngQM);
 432     snew_bc(cr, g->bSH, g->ngQM);
 433     snew_bc(cr, g->CASorbitals, g->ngQM);
 434     snew_bc(cr, g->CASelectrons, g->ngQM);
 435     snew_bc(cr, g->SAon, g->ngQM);
 436     snew_bc(cr, g->SAoff, g->ngQM);
 437     snew_bc(cr, g->SAsteps, g->ngQM);
 438
 439     if (g->ngQM)
 440     {
 441         nblock_bc(cr, g->ngQM, g->QMmethod);
 442         nblock_bc(cr, g->ngQM, g->QMbasis);
 443         nblock_bc(cr, g->ngQM, g->QMcharge);
 444         nblock_bc(cr, g->ngQM, g->QMmult);
 445         nblock_bc(cr, g->ngQM, g->bSH);
 446         nblock_bc(cr, g->ngQM, g->CASorbitals);
 447         nblock_bc(cr, g->ngQM, g->CASelectrons);
 448         nblock_bc(cr, g->ngQM, g->SAon);
 449         nblock_bc(cr, g->ngQM, g->SAoff);
 450         nblock_bc(cr, g->ngQM, g->SAsteps);
 451         /* end of QMMM stuff */
 452     }
 453 }
 454
 455 static void bc_pull_group(const t_commrec *cr, t_pull_group *pgrp)
 456 {
 457     block_bc(cr, *pgrp);
 458     if (pgrp->nat > 0)
 459     {
 460         snew_bc(cr, pgrp->ind, pgrp->nat);
 461         nblock_bc(cr, pgrp->nat, pgrp->ind);
 462     }
 463     if (pgrp->nweight > 0)
 464     {
 465         snew_bc(cr, pgrp->weight, pgrp->nweight);
 466         nblock_bc(cr, pgrp->nweight, pgrp->weight);
 467     }
 468 }
 469
 470 static void bc_pull(const t_commrec *cr, pull_params_t *pull)
 471 {
 472     int g;
 473
 474     block_bc(cr, *pull);
 475     snew_bc(cr, pull->group, pull->ngroup);
 476     for (g = 0; g < pull->ngroup; g++)
 477     {
 478         bc_pull_group(cr, &pull->group[g]);
 479     }
 480     snew_bc(cr, pull->coord, pull->ncoord);
 481     nblock_bc(cr, pull->ncoord, pull->coord);
 482     for (int c = 0; c < pull->ncoord; c++)
 483     {
 484         if (!MASTER(cr))
 485         {
 486             pull->coord[c].externalPotentialProvider = nullptr;
 487         }
 488         if (pull->coord[c].eType == epullEXTERNAL)
 489         {
 490             bc_cstring(cr, &pull->coord[c].externalPotentialProvider);
 491         }
 492     }
 493 }
 494
 495 static void bc_rotgrp(const t_commrec *cr, t_rotgrp *rotg)
 496 {
 497     block_bc(cr, *rotg);
 498     if (rotg->nat > 0)
 499     {
 500         snew_bc(cr, rotg->ind, rotg->nat);
 501         nblock_bc(cr, rotg->nat, rotg->ind);
 502         snew_bc(cr, rotg->x_ref, rotg->nat);
 503         nblock_bc(cr, rotg->nat, rotg->x_ref);
 504     }
 505 }
 506
 507 static void bc_rot(const t_commrec *cr, t_rot *rot)
 508 {
 509     int g;
 510
 511     block_bc(cr, *rot);
 512     snew_bc(cr, rot->grp, rot->ngrp);
 513     for (g = 0; g < rot->ngrp; g++)
 514     {
 515         bc_rotgrp(cr, &rot->grp[g]);
 516     }
 517 }
 518
 519 static void bc_imd(const t_commrec *cr, t_IMD *imd)
 520 {
 521     block_bc(cr, *imd);
 522     snew_bc(cr, imd->ind, imd->nat);
 523     nblock_bc(cr, imd->nat, imd->ind);
 524 }
 525
 526 static void bc_fepvals(const t_commrec *cr, t_lambda *fep)
 527 {
 528     int      i;
 529
 530     block_bc(cr, fep->nstdhdl);
 531     block_bc(cr, fep->init_lambda);
 532     block_bc(cr, fep->init_fep_state);
 533     block_bc(cr, fep->delta_lambda);
 534     block_bc(cr, fep->edHdLPrintEnergy);
 535     block_bc(cr, fep->n_lambda);
 536     if (fep->n_lambda > 0)
 537     {
 538         snew_bc(cr, fep->all_lambda, efptNR);
 539         nblock_bc(cr, efptNR, fep->all_lambda);
 540         for (i = 0; i < efptNR; i++)
 541         {
 542             snew_bc(cr, fep->all_lambda[i], fep->n_lambda);
 543             nblock_bc(cr, fep->n_lambda, fep->all_lambda[i]);
 544         }
 545     }
 546     block_bc(cr, fep->sc_alpha);
 547     block_bc(cr, fep->sc_power);
 548     block_bc(cr, fep->sc_r_power);
 549     block_bc(cr, fep->sc_sigma);
 550     block_bc(cr, fep->sc_sigma_min);
 551     block_bc(cr, fep->bScCoul);
 552     nblock_bc(cr, efptNR, &(fep->separate_dvdl[0]));
 553     block_bc(cr, fep->dhdl_derivatives);
 554     block_bc(cr, fep->dh_hist_size);
 555     block_bc(cr, fep->dh_hist_spacing);
 556     if (debug)
 557     {
 558         fprintf(debug, "after bc_fepvals\n");
 559     }
 560 }
 561
 562 static void bc_expandedvals(const t_commrec *cr, t_expanded *expand, int n_lambda)
 563 {
 564     block_bc(cr, expand->nstexpanded);
 565     block_bc(cr, expand->elamstats);
 566     block_bc(cr, expand->elmcmove);
 567     block_bc(cr, expand->elmceq);
 568     block_bc(cr, expand->equil_n_at_lam);
 569     block_bc(cr, expand->equil_wl_delta);
 570     block_bc(cr, expand->equil_ratio);
 571     block_bc(cr, expand->equil_steps);
 572     block_bc(cr, expand->equil_samples);
 573     block_bc(cr, expand->lmc_seed);
 574     block_bc(cr, expand->minvar);
 575     block_bc(cr, expand->minvar_const);
 576     block_bc(cr, expand->c_range);
 577     block_bc(cr, expand->bSymmetrizedTMatrix);
 578     block_bc(cr, expand->nstTij);
 579     block_bc(cr, expand->lmc_repeats);
 580     block_bc(cr, expand->lmc_forced_nstart);
 581     block_bc(cr, expand->gibbsdeltalam);
 582     block_bc(cr, expand->wl_scale);
 583     block_bc(cr, expand->wl_ratio);
 584     block_bc(cr, expand->init_wl_delta);
 585     block_bc(cr, expand->bInit_weights);
 586     snew_bc(cr, expand->init_lambda_weights, n_lambda);
 587     nblock_bc(cr, n_lambda, expand->init_lambda_weights);
 588     block_bc(cr, expand->mc_temp);
 589     if (debug)
 590     {
 591         fprintf(debug, "after bc_expandedvals\n");
 592     }
 593 }
 594
 595 static void bc_simtempvals(const t_commrec *cr, t_simtemp *simtemp, int n_lambda)
 596 {
 597     block_bc(cr, simtemp->simtemp_low);
 598     block_bc(cr, simtemp->simtemp_high);
 599     block_bc(cr, simtemp->eSimTempScale);
 600     snew_bc(cr, simtemp->temperatures, n_lambda);
 601     nblock_bc(cr, n_lambda, simtemp->temperatures);
 602     if (debug)
 603     {
 604         fprintf(debug, "after bc_simtempvals\n");
 605     }
 606 }
 607
 608
 609 static void bc_swapions(const t_commrec *cr, t_swapcoords *swap)
 610 {
 611     block_bc(cr, *swap);
 612
 613     /* Broadcast atom indices for split groups, solvent group, and for all user-defined swap groups */
 614     snew_bc(cr, swap->grp, swap->ngrp);
 615     for (int i = 0; i < swap->ngrp; i++)
 616     {
 617         t_swapGroup *g = &swap->grp[i];
 618
 619         block_bc(cr, *g);
 620         snew_bc(cr, g->ind, g->nat);
 621         nblock_bc(cr, g->nat, g->ind);
 622
 623         int len = 0;
 624         if (MASTER(cr))
 625         {
 626             len = strlen(g->molname);
 627         }
 628         block_bc(cr, len);
 629         snew_bc(cr, g->molname, len);
 630         nblock_bc(cr, len, g->molname);
 631     }
 632 }
 633
 634
 635 static void bc_inputrec(const t_commrec *cr, t_inputrec *inputrec)
 636 {
 637     // Note that this overwrites pointers in inputrec, so all pointer fields
 638     // Must be initialized separately below.
 639     block_bc(cr, *inputrec);
 640     if (SIMMASTER(cr))
 641     {
 642         gmx::InMemorySerializer serializer;
 643         gmx::serializeKeyValueTree(*inputrec->params, &serializer);
 644         std::vector<char>       buffer = serializer.finishAndGetBuffer();
 645         size_t                  size   = buffer.size();
 646         block_bc(cr, size);
 647         nblock_bc(cr, size, buffer.data());
 648     }
 649     else
 650     {
 651         // block_bc() above overwrites the old pointer, so set it to a
 652         // reasonable value in case code below throws.
 653         // cppcheck-suppress redundantAssignment
 654         inputrec->params = nullptr;
 655         std::vector<char> buffer;
 656         size_t            size;
 657         block_bc(cr, size);
 658         nblock_abc(cr, size, &buffer);
 659         gmx::InMemoryDeserializer serializer(buffer);
 660         // cppcheck-suppress redundantAssignment
 661         inputrec->params = new gmx::KeyValueTreeObject(
 662                     gmx::deserializeKeyValueTree(&serializer));
 663     }
 664
 665     bc_grpopts(cr, &(inputrec->opts));
 666
 667     /* even if efep is efepNO, we need to initialize to make sure that
 668      * n_lambda is set to zero */
 669
 670     snew_bc(cr, inputrec->fepvals, 1);
 671     if (inputrec->efep != efepNO || inputrec->bSimTemp)
 672     {
 673         bc_fepvals(cr, inputrec->fepvals);
 674     }
 675     /* need to initialize this as well because of data checked for in the logic */
 676     snew_bc(cr, inputrec->expandedvals, 1);
 677     if (inputrec->bExpanded)
 678     {
 679         bc_expandedvals(cr, inputrec->expandedvals, inputrec->fepvals->n_lambda);
 680     }
 681     snew_bc(cr, inputrec->simtempvals, 1);
 682     if (inputrec->bSimTemp)
 683     {
 684         bc_simtempvals(cr, inputrec->simtempvals, inputrec->fepvals->n_lambda);
 685     }
 686     if (inputrec->bPull)
 687     {
 688         snew_bc(cr, inputrec->pull, 1);
 689         bc_pull(cr, inputrec->pull);
 690     }
 691     if (inputrec->bRot)
 692     {
 693         snew_bc(cr, inputrec->rot, 1);
 694         bc_rot(cr, inputrec->rot);
 695     }
 696     if (inputrec->bIMD)
 697     {
 698         snew_bc(cr, inputrec->imd, 1);
 699         bc_imd(cr, inputrec->imd);
 700     }
 701     if (inputrec->eSwapCoords != eswapNO)
 702     {
 703         snew_bc(cr, inputrec->swap, 1);
 704         bc_swapions(cr, inputrec->swap);
 705     }
 706 }
 707
 708 static void bc_moltype(const t_commrec *cr, t_symtab *symtab,
 709                        gmx_moltype_t *moltype)
 710 {
 711     bc_string(cr, symtab, &moltype->name);
 712     bc_atoms(cr, symtab, &moltype->atoms);
 713     if (debug)
 714     {
 715         fprintf(debug, "after bc_atoms\n");
 716     }
 717
 718     bc_ilists(cr, moltype->ilist);
 719     bc_block(cr, &moltype->cgs);
 720     bc_blocka(cr, &moltype->excls);
 721 }
 722
 723 static void bc_molblock(const t_commrec *cr, gmx_molblock_t *molb)
 724 {
 725     block_bc(cr, *molb);
 726     if (molb->nposres_xA > 0)
 727     {
 728         snew_bc(cr, molb->posres_xA, molb->nposres_xA);
 729         nblock_bc(cr, molb->nposres_xA*DIM, molb->posres_xA[0]);
 730     }
 731     if (molb->nposres_xB > 0)
 732     {
 733         snew_bc(cr, molb->posres_xB, molb->nposres_xB);
 734         nblock_bc(cr, molb->nposres_xB*DIM, molb->posres_xB[0]);
 735     }
 736     if (debug)
 737     {
 738         fprintf(debug, "after bc_molblock\n");
 739     }
 740 }
 741
 742 static void bc_atomtypes(const t_commrec *cr, t_atomtypes *atomtypes)
 743 {
 744     int nr;
 745
 746     block_bc(cr, atomtypes->nr);
 747
 748     nr = atomtypes->nr;
 749
 750     snew_bc(cr, atomtypes->radius, nr);
 751     snew_bc(cr, atomtypes->vol, nr);
 752     snew_bc(cr, atomtypes->surftens, nr);
 753     snew_bc(cr, atomtypes->gb_radius, nr);
 754     snew_bc(cr, atomtypes->S_hct, nr);
 755
 756     nblock_bc(cr, nr, atomtypes->radius);
 757     nblock_bc(cr, nr, atomtypes->vol);
 758     nblock_bc(cr, nr, atomtypes->surftens);
 759     nblock_bc(cr, nr, atomtypes->gb_radius);
 760     nblock_bc(cr, nr, atomtypes->S_hct);
 761 }
 762
 763 /*! \brief Broadcasts ir and mtop from the master to all nodes in
 764  * cr->mpi_comm_mygroup. */
 765 static
 766 void bcast_ir_mtop(const t_commrec *cr, t_inputrec *inputrec, gmx_mtop_t *mtop)
 767 {
 768     int i;
 769     if (debug)
 770     {
 771         fprintf(debug, "in bc_data\n");
 772     }
 773     bc_inputrec(cr, inputrec);
 774     if (debug)
 775     {
 776         fprintf(debug, "after bc_inputrec\n");
 777     }
 778     bc_symtab(cr, &mtop->symtab);
 779     if (debug)
 780     {
 781         fprintf(debug, "after bc_symtab\n");
 782     }
 783     bc_string(cr, &mtop->symtab, &mtop->name);
 784     if (debug)
 785     {
 786         fprintf(debug, "after bc_name\n");
 787     }
 788
 789     bc_ffparams(cr, &mtop->ffparams);
 790
 791     block_bc(cr, mtop->nmoltype);
 792     snew_bc(cr, mtop->moltype, mtop->nmoltype);
 793     for (i = 0; i < mtop->nmoltype; i++)
 794     {
 795         bc_moltype(cr, &mtop->symtab, &mtop->moltype[i]);
 796     }
 797
 798     block_bc(cr, mtop->bIntermolecularInteractions);
 799     if (mtop->bIntermolecularInteractions)
 800     {
 801         snew_bc(cr, mtop->intermolecular_ilist, F_NRE);
 802         bc_ilists(cr, mtop->intermolecular_ilist);
 803     }
 804
 805     block_bc(cr, mtop->nmolblock);
 806     snew_bc(cr, mtop->molblock, mtop->nmolblock);
 807     for (i = 0; i < mtop->nmolblock; i++)
 808     {
 809         bc_molblock(cr, &mtop->molblock[i]);
 810     }
 811
 812     block_bc(cr, mtop->natoms);
 813
 814     bc_atomtypes(cr, &mtop->atomtypes);
 815
 816     bc_block(cr, &mtop->mols);
 817     bc_groups(cr, &mtop->symtab, mtop->natoms, &mtop->groups);
 818 }
 819
 820 void init_parallel(t_commrec *cr, t_inputrec *inputrec,
 821                    gmx_mtop_t *mtop)
 822 {
 823     bcast_ir_mtop(cr, inputrec, mtop);
 824 }