src/gmxlib/mvdata.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
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  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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  35 /* This file is completely threadsafe - keep it that way! */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <sysstuff.h>
  41 #include <string.h>
  42 #include "typedefs.h"
  43 #include "main.h"
  44 #include "mvdata.h"
  45 #include "network.h"
  46 #include "smalloc.h"
  47 #include "gmx_fatal.h"
  48 #include "symtab.h"
  49 #include "vec.h"
  50 #include "tgroup.h"
  51
  52 #define   block_bc(cr,   d) gmx_bcast(     sizeof(d),     &(d),(cr))
  53 /* Probably the test for (nr) > 0 in the next macro is only needed
  54  * on BlueGene(/L), where IBM's MPI_Bcast will segfault after
  55  * dereferencing a null pointer, even when no data is to be transferred. */
  56 #define  nblock_bc(cr,nr,d) { if ((nr) > 0) gmx_bcast((nr)*sizeof((d)[0]), (d),(cr)); }
  57 #define    snew_bc(cr,d,nr) { if (!MASTER(cr)) snew((d),(nr)); }
  58 /* Dirty macro with bAlloc not as an argument */
  59 #define nblock_abc(cr,nr,d) { if (bAlloc) snew((d),(nr)); nblock_bc(cr,(nr),(d)); }
  60
  61 static void bc_string(const t_commrec *cr,t_symtab *symtab,char ***s)
  62 {
  63   int handle;
  64
  65   if (MASTER(cr)) {
  66     handle = lookup_symtab(symtab,*s);
  67   }
  68   block_bc(cr,handle);
  69   if (!MASTER(cr)) {
  70     *s = get_symtab_handle(symtab,handle);
  71   }
  72 }
  73
  74 static void bc_strings(const t_commrec *cr,t_symtab *symtab,int nr,char ****nm)
  75 {
  76   int  i;
  77   int  *handle;
  78   char ***NM;
  79
  80   snew(handle,nr);
  81   if (MASTER(cr)) {
  82     NM = *nm;
  83     for(i=0; (i<nr); i++)
  84       handle[i] = lookup_symtab(symtab,NM[i]);
  85   }
  86   nblock_bc(cr,nr,handle);
  87
  88   if (!MASTER(cr)) {
  89     snew_bc(cr,*nm,nr);
  90     NM = *nm;
  91     for (i=0; (i<nr); i++)
  92       (*nm)[i] = get_symtab_handle(symtab,handle[i]);
  93   }
  94   sfree(handle);
  95 }
  96
  97 static void bc_strings_resinfo(const t_commrec *cr,t_symtab *symtab,
  98                                int nr,t_resinfo *resinfo)
  99 {
 100   int  i;
 101   int  *handle;
 102
 103   snew(handle,nr);
 104   if (MASTER(cr)) {
 105     for(i=0; (i<nr); i++)
 106       handle[i] = lookup_symtab(symtab,resinfo[i].name);
 107   }
 108   nblock_bc(cr,nr,handle);
 109
 110   if (!MASTER(cr)) {
 111     for (i=0; (i<nr); i++)
 112       resinfo[i].name = get_symtab_handle(symtab,handle[i]);
 113   }
 114   sfree(handle);
 115 }
 116
 117 static void bc_symtab(const t_commrec *cr,t_symtab *symtab)
 118 {
 119   int i,nr,len;
 120   t_symbuf *symbuf;
 121
 122   block_bc(cr,symtab->nr);
 123   nr = symtab->nr;
 124   snew_bc(cr,symtab->symbuf,1);
 125   symbuf = symtab->symbuf;
 126   symbuf->bufsize = nr;
 127   snew_bc(cr,symbuf->buf,nr);
 128   for (i=0; i<nr; i++) {
 129     if (MASTER(cr))
 130       len = strlen(symbuf->buf[i]) + 1;
 131     block_bc(cr,len);
 132     snew_bc(cr,symbuf->buf[i],len);
 133     nblock_bc(cr,len,symbuf->buf[i]);
 134   }
 135 }
 136
 137 static void bc_block(const t_commrec *cr,t_block *block)
 138 {
 139   block_bc(cr,block->nr);
 140   snew_bc(cr,block->index,block->nr+1);
 141   nblock_bc(cr,block->nr+1,block->index);
 142 }
 143
 144 static void bc_blocka(const t_commrec *cr,t_blocka *block)
 145 {
 146   block_bc(cr,block->nr);
 147   snew_bc(cr,block->index,block->nr+1);
 148   nblock_bc(cr,block->nr+1,block->index);
 149   block_bc(cr,block->nra);
 150   if (block->nra) {
 151     snew_bc(cr,block->a,block->nra);
 152     nblock_bc(cr,block->nra,block->a);
 153   }
 154 }
 155
 156 static void bc_grps(const t_commrec *cr,t_grps grps[])
 157 {
 158   int i;
 159
 160   for(i=0; (i<egcNR); i++) {
 161     block_bc(cr,grps[i].nr);
 162     snew_bc(cr,grps[i].nm_ind,grps[i].nr);
 163     nblock_bc(cr,grps[i].nr,grps[i].nm_ind);
 164   }
 165 }
 166
 167 static void bc_atoms(const t_commrec *cr,t_symtab *symtab,t_atoms *atoms)
 168 {
 169   int dummy;
 170
 171   block_bc(cr,atoms->nr);
 172   snew_bc(cr,atoms->atom,atoms->nr);
 173   nblock_bc(cr,atoms->nr,atoms->atom);
 174   bc_strings(cr,symtab,atoms->nr,&atoms->atomname);
 175   block_bc(cr,atoms->nres);
 176   snew_bc(cr,atoms->resinfo,atoms->nres);
 177   nblock_bc(cr,atoms->nres,atoms->resinfo);
 178   bc_strings_resinfo(cr,symtab,atoms->nres,atoms->resinfo);
 179   /* QMMM requires atomtypes to be known on all nodes as well */
 180   bc_strings(cr,symtab,atoms->nr,&atoms->atomtype);
 181   bc_strings(cr,symtab,atoms->nr,&atoms->atomtypeB);
 182 }
 183
 184 static void bc_groups(const t_commrec *cr,t_symtab *symtab,
 185                       int natoms,gmx_groups_t *groups)
 186 {
 187   int dummy;
 188   int g,n;
 189
 190   bc_grps(cr,groups->grps);
 191   block_bc(cr,groups->ngrpname);
 192   bc_strings(cr,symtab,groups->ngrpname,&groups->grpname);
 193   for(g=0; g<egcNR; g++) {
 194     if (MASTER(cr)) {
 195       if (groups->grpnr[g]) {
 196         n = natoms;
 197       } else {
 198         n = 0;
 199       }
 200     }
 201     block_bc(cr,n);
 202     if (n == 0) {
 203       groups->grpnr[g] = NULL;
 204     } else {
 205       snew_bc(cr,groups->grpnr[g],n);
 206       nblock_bc(cr,n,groups->grpnr[g]);
 207     }
 208   }
 209   if (debug) fprintf(debug,"after bc_groups\n");
 210 }
 211
 212 void bcast_state_setup(const t_commrec *cr,t_state *state)
 213 {
 214   block_bc(cr,state->natoms);
 215   block_bc(cr,state->ngtc);
 216   block_bc(cr,state->nnhpres);
 217   block_bc(cr,state->nhchainlength);
 218   block_bc(cr,state->nrng);
 219   block_bc(cr,state->nrngi);
 220   block_bc(cr,state->flags);
 221 }
 222
 223 void bcast_state(const t_commrec *cr,t_state *state,gmx_bool bAlloc)
 224 {
 225   int i,nnht,nnhtp;
 226
 227   bcast_state_setup(cr,state);
 228
 229   nnht = (state->ngtc)*(state->nhchainlength);
 230   nnhtp = (state->nnhpres)*(state->nhchainlength);
 231
 232   if (MASTER(cr)) {
 233     bAlloc = FALSE;
 234   }
 235   if (bAlloc) {
 236     state->nalloc = state->natoms;
 237   }
 238   for(i=0; i<estNR; i++) {
 239     if (state->flags & (1<<i)) {
 240       switch (i) {
 241       case estLAMBDA:  block_bc(cr,state->lambda); break;
 242       case estBOX:     block_bc(cr,state->box); break;
 243       case estBOX_REL: block_bc(cr,state->box_rel); break;
 244       case estBOXV:    block_bc(cr,state->boxv); break;
 245       case estPRES_PREV: block_bc(cr,state->pres_prev); break;
 246       case estSVIR_PREV: block_bc(cr,state->svir_prev); break;
 247       case estFVIR_PREV: block_bc(cr,state->fvir_prev); break;
 248       case estNH_XI:   nblock_abc(cr,nnht,state->nosehoover_xi); break;
 249       case estNH_VXI:  nblock_abc(cr,nnht,state->nosehoover_vxi); break;
 250       case estNHPRES_XI:   nblock_abc(cr,nnhtp,state->nhpres_xi); break;
 251       case estNHPRES_VXI:  nblock_abc(cr,nnhtp,state->nhpres_vxi); break;
 252       case estTC_INT:  nblock_abc(cr,state->ngtc,state->therm_integral); break;
 253       case estVETA:    block_bc(cr,state->veta); break;
 254       case estVOL0:    block_bc(cr,state->vol0); break;
 255       case estX:       nblock_abc(cr,state->natoms,state->x); break;
 256       case estV:       nblock_abc(cr,state->natoms,state->v); break;
 257       case estSDX:     nblock_abc(cr,state->natoms,state->sd_X); break;
 258       case estCGP:     nblock_abc(cr,state->natoms,state->cg_p); break;
 259           case estLD_RNG:  if(state->nrngi == 1) nblock_abc(cr,state->nrng,state->ld_rng); break;
 260           case estLD_RNGI: if(state->nrngi == 1) nblock_abc(cr,state->nrngi,state->ld_rngi); break;
 261       case estDISRE_INITF: block_bc(cr,state->hist.disre_initf); break;
 262       case estDISRE_RM3TAV:
 263           block_bc(cr,state->hist.ndisrepairs);
 264           nblock_abc(cr,state->hist.ndisrepairs,state->hist.disre_rm3tav);
 265           break;
 266       case estORIRE_INITF: block_bc(cr,state->hist.orire_initf); break;
 267       case estORIRE_DTAV:
 268           block_bc(cr,state->hist.norire_Dtav);
 269           nblock_abc(cr,state->hist.norire_Dtav,state->hist.orire_Dtav);
 270           break;
 271       default:
 272           gmx_fatal(FARGS,
 273                     "Communication is not implemented for %s in bcast_state",
 274                     est_names[i]);
 275       }
 276     }
 277   }
 278 }
 279
 280 static void bc_ilists(const t_commrec *cr,t_ilist *ilist)
 281 {
 282   int ftype;
 283
 284   /* Here we only communicate the non-zero length ilists */
 285   if (MASTER(cr)) {
 286     for(ftype=0; ftype<F_NRE; ftype++) {
 287       if (ilist[ftype].nr > 0) {
 288         block_bc(cr,ftype);
 289         block_bc(cr,ilist[ftype].nr);
 290         nblock_bc(cr,ilist[ftype].nr,ilist[ftype].iatoms);
 291       }
 292     }
 293     ftype = -1;
 294     block_bc(cr,ftype);
 295   } else {
 296     for(ftype=0; ftype<F_NRE; ftype++) {
 297       ilist[ftype].nr = 0;
 298     }
 299     do {
 300       block_bc(cr,ftype);
 301       if (ftype >= 0) {
 302         block_bc(cr,ilist[ftype].nr);
 303         snew_bc(cr,ilist[ftype].iatoms,ilist[ftype].nr);
 304         nblock_bc(cr,ilist[ftype].nr,ilist[ftype].iatoms);
 305       }
 306     } while (ftype >= 0);
 307   }
 308
 309   if (debug) fprintf(debug,"after bc_ilists\n");
 310 }
 311
 312 static void bc_idef(const t_commrec *cr,t_idef *idef)
 313 {
 314   block_bc(cr,idef->ntypes);
 315   block_bc(cr,idef->atnr);
 316   snew_bc(cr,idef->functype,idef->ntypes);
 317   snew_bc(cr,idef->iparams,idef->ntypes);
 318   nblock_bc(cr,idef->ntypes,idef->functype);
 319   nblock_bc(cr,idef->ntypes,idef->iparams);
 320   block_bc(cr,idef->fudgeQQ);
 321   bc_ilists(cr,idef->il);
 322   block_bc(cr,idef->ilsort);
 323 }
 324
 325 static void bc_cmap(const t_commrec *cr, gmx_cmap_t *cmap_grid)
 326 {
 327         int i,j,nelem,ngrid;
 328
 329         block_bc(cr,cmap_grid->ngrid);
 330         block_bc(cr,cmap_grid->grid_spacing);
 331
 332         ngrid = cmap_grid->ngrid;
 333         nelem = cmap_grid->grid_spacing * cmap_grid->grid_spacing;
 334
 335         if(ngrid>0)
 336         {
 337                 snew_bc(cr,cmap_grid->cmapdata,ngrid);
 338
 339                 for(i=0;i<ngrid;i++)
 340                 {
 341                         snew_bc(cr,cmap_grid->cmapdata[i].cmap,4*nelem);
 342                         nblock_bc(cr,4*nelem,cmap_grid->cmapdata[i].cmap);
 343                 }
 344         }
 345 }
 346
 347 static void bc_ffparams(const t_commrec *cr,gmx_ffparams_t *ffp)
 348 {
 349   int i;
 350
 351   block_bc(cr,ffp->ntypes);
 352   block_bc(cr,ffp->atnr);
 353   snew_bc(cr,ffp->functype,ffp->ntypes);
 354   snew_bc(cr,ffp->iparams,ffp->ntypes);
 355   nblock_bc(cr,ffp->ntypes,ffp->functype);
 356   nblock_bc(cr,ffp->ntypes,ffp->iparams);
 357   block_bc(cr,ffp->reppow);
 358   block_bc(cr,ffp->fudgeQQ);
 359   bc_cmap(cr,&ffp->cmap_grid);
 360 }
 361
 362 static void bc_grpopts(const t_commrec *cr,t_grpopts *g)
 363 {
 364     int i,n;
 365
 366     block_bc(cr,g->ngtc);
 367     block_bc(cr,g->ngacc);
 368     block_bc(cr,g->ngfrz);
 369     block_bc(cr,g->ngener);
 370     snew_bc(cr,g->nrdf,g->ngtc);
 371     snew_bc(cr,g->tau_t,g->ngtc);
 372     snew_bc(cr,g->ref_t,g->ngtc);
 373     snew_bc(cr,g->acc,g->ngacc);
 374     snew_bc(cr,g->nFreeze,g->ngfrz);
 375     snew_bc(cr,g->egp_flags,g->ngener*g->ngener);
 376
 377     nblock_bc(cr,g->ngtc,g->nrdf);
 378     nblock_bc(cr,g->ngtc,g->tau_t);
 379     nblock_bc(cr,g->ngtc,g->ref_t);
 380     nblock_bc(cr,g->ngacc,g->acc);
 381     nblock_bc(cr,g->ngfrz,g->nFreeze);
 382     nblock_bc(cr,g->ngener*g->ngener,g->egp_flags);
 383     snew_bc(cr,g->annealing,g->ngtc);
 384     snew_bc(cr,g->anneal_npoints,g->ngtc);
 385     snew_bc(cr,g->anneal_time,g->ngtc);
 386     snew_bc(cr,g->anneal_temp,g->ngtc);
 387     nblock_bc(cr,g->ngtc,g->annealing);
 388     nblock_bc(cr,g->ngtc,g->anneal_npoints);
 389     for(i=0;(i<g->ngtc); i++) {
 390         n = g->anneal_npoints[i];
 391         if (n > 0) {
 392           snew_bc(cr,g->anneal_time[i],n);
 393           snew_bc(cr,g->anneal_temp[i],n);
 394           nblock_bc(cr,n,g->anneal_time[i]);
 395           nblock_bc(cr,n,g->anneal_temp[i]);
 396         }
 397     }
 398
 399     /* QMMM stuff, see inputrec */
 400     block_bc(cr,g->ngQM);
 401     snew_bc(cr,g->QMmethod,g->ngQM);
 402     snew_bc(cr,g->QMbasis,g->ngQM);
 403     snew_bc(cr,g->QMcharge,g->ngQM);
 404     snew_bc(cr,g->QMmult,g->ngQM);
 405     snew_bc(cr,g->bSH,g->ngQM);
 406     snew_bc(cr,g->CASorbitals,g->ngQM);
 407     snew_bc(cr,g->CASelectrons,g->ngQM);
 408     snew_bc(cr,g->SAon,g->ngQM);
 409     snew_bc(cr,g->SAoff,g->ngQM);
 410     snew_bc(cr,g->SAsteps,g->ngQM);
 411
 412     if (g->ngQM)
 413     {
 414         nblock_bc(cr,g->ngQM,g->QMmethod);
 415         nblock_bc(cr,g->ngQM,g->QMbasis);
 416         nblock_bc(cr,g->ngQM,g->QMcharge);
 417         nblock_bc(cr,g->ngQM,g->QMmult);
 418         nblock_bc(cr,g->ngQM,g->bSH);
 419         nblock_bc(cr,g->ngQM,g->CASorbitals);
 420         nblock_bc(cr,g->ngQM,g->CASelectrons);
 421         nblock_bc(cr,g->ngQM,g->SAon);
 422         nblock_bc(cr,g->ngQM,g->SAoff);
 423         nblock_bc(cr,g->ngQM,g->SAsteps);
 424         /* end of QMMM stuff */
 425     }
 426 }
 427
 428 static void bc_cosines(const t_commrec *cr,t_cosines *cs)
 429 {
 430   block_bc(cr,cs->n);
 431   snew_bc(cr,cs->a,cs->n);
 432   snew_bc(cr,cs->phi,cs->n);
 433   if (cs->n > 0) {
 434     nblock_bc(cr,cs->n,cs->a);
 435     nblock_bc(cr,cs->n,cs->phi);
 436   }
 437 }
 438
 439 static void bc_pullgrp(const t_commrec *cr,t_pullgrp *pgrp)
 440 {
 441   block_bc(cr,*pgrp);
 442   if (pgrp->nat > 0) {
 443     snew_bc(cr,pgrp->ind,pgrp->nat);
 444     nblock_bc(cr,pgrp->nat,pgrp->ind);
 445   }
 446   if (pgrp->nweight > 0) {
 447     snew_bc(cr,pgrp->weight,pgrp->nweight);
 448     nblock_bc(cr,pgrp->nweight,pgrp->weight);
 449   }
 450 }
 451
 452 static void bc_pull(const t_commrec *cr,t_pull *pull)
 453 {
 454   int g;
 455
 456   block_bc(cr,*pull);
 457   snew_bc(cr,pull->grp,pull->ngrp+1);
 458   for(g=0; g<pull->ngrp+1; g++)
 459   {
 460       bc_pullgrp(cr,&pull->grp[g]);
 461   }
 462 }
 463
 464 static void bc_inputrec(const t_commrec *cr,t_inputrec *inputrec)
 465 {
 466   gmx_bool bAlloc=TRUE;
 467   int i;
 468
 469   block_bc(cr,*inputrec);
 470   snew_bc(cr,inputrec->flambda,inputrec->n_flambda);
 471   nblock_bc(cr,inputrec->n_flambda,inputrec->flambda);
 472   bc_grpopts(cr,&(inputrec->opts));
 473   if (inputrec->ePull != epullNO) {
 474     snew_bc(cr,inputrec->pull,1);
 475     bc_pull(cr,inputrec->pull);
 476   }
 477   for(i=0; (i<DIM); i++) {
 478     bc_cosines(cr,&(inputrec->ex[i]));
 479     bc_cosines(cr,&(inputrec->et[i]));
 480   }
 481 }
 482
 483 static void bc_moltype(const t_commrec *cr,t_symtab *symtab,
 484                        gmx_moltype_t *moltype)
 485 {
 486   bc_string(cr,symtab,&moltype->name);
 487   bc_atoms(cr,symtab,&moltype->atoms);
 488   if (debug) fprintf(debug,"after bc_atoms\n");
 489
 490   bc_ilists(cr,moltype->ilist);
 491   bc_block(cr,&moltype->cgs);
 492   bc_blocka(cr,&moltype->excls);
 493 }
 494
 495 static void bc_molblock(const t_commrec *cr,gmx_molblock_t *molb)
 496 {
 497   gmx_bool bAlloc=TRUE;
 498
 499   block_bc(cr,molb->type);
 500   block_bc(cr,molb->nmol);
 501   block_bc(cr,molb->natoms_mol);
 502   block_bc(cr,molb->nposres_xA);
 503   if (molb->nposres_xA > 0) {
 504     snew_bc(cr,molb->posres_xA,molb->nposres_xA);
 505     nblock_bc(cr,molb->nposres_xA*DIM,molb->posres_xA[0]);
 506   }
 507   block_bc(cr,molb->nposres_xB);
 508   if (molb->nposres_xB > 0) {
 509     snew_bc(cr,molb->posres_xB,molb->nposres_xB);
 510     nblock_bc(cr,molb->nposres_xB*DIM,molb->posres_xB[0]);
 511   }
 512   if (debug) fprintf(debug,"after bc_molblock\n");
 513 }
 514
 515 static void bc_atomtypes(const t_commrec *cr, t_atomtypes *atomtypes)
 516 {
 517   int nr;
 518
 519   block_bc(cr,atomtypes->nr);
 520
 521   nr = atomtypes->nr;
 522
 523   snew_bc(cr,atomtypes->radius,nr);
 524   snew_bc(cr,atomtypes->vol,nr);
 525   snew_bc(cr,atomtypes->surftens,nr);
 526   snew_bc(cr,atomtypes->gb_radius,nr);
 527   snew_bc(cr,atomtypes->S_hct,nr);
 528
 529   nblock_bc(cr,nr,atomtypes->radius);
 530   nblock_bc(cr,nr,atomtypes->vol);
 531   nblock_bc(cr,nr,atomtypes->surftens);
 532   nblock_bc(cr,nr,atomtypes->gb_radius);
 533   nblock_bc(cr,nr,atomtypes->S_hct);
 534 }
 535
 536
 537 void bcast_ir_mtop(const t_commrec *cr,t_inputrec *inputrec,gmx_mtop_t *mtop)
 538 {
 539   int i;
 540   if (debug) fprintf(debug,"in bc_data\n");
 541   bc_inputrec(cr,inputrec);
 542   if (debug) fprintf(debug,"after bc_inputrec\n");
 543   bc_symtab(cr,&mtop->symtab);
 544   if (debug) fprintf(debug,"after bc_symtab\n");
 545   bc_string(cr,&mtop->symtab,&mtop->name);
 546   if (debug) fprintf(debug,"after bc_name\n");
 547
 548   bc_ffparams(cr,&mtop->ffparams);
 549
 550   block_bc(cr,mtop->nmoltype);
 551   snew_bc(cr,mtop->moltype,mtop->nmoltype);
 552   for(i=0; i<mtop->nmoltype; i++) {
 553     bc_moltype(cr,&mtop->symtab,&mtop->moltype[i]);
 554   }
 555
 556   block_bc(cr,mtop->nmolblock);
 557   snew_bc(cr,mtop->molblock,mtop->nmolblock);
 558   for(i=0; i<mtop->nmolblock; i++) {
 559     bc_molblock(cr,&mtop->molblock[i]);
 560   }
 561
 562   block_bc(cr,mtop->natoms);
 563
 564   bc_atomtypes(cr,&mtop->atomtypes);
 565
 566   bc_block(cr,&mtop->mols);
 567   bc_groups(cr,&mtop->symtab,mtop->natoms,&mtop->groups);
 568 }