src/gmxlib/mvdata.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
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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 #define  nblock_bc(cr,nr,d) { if ((nr) > 0) gmx_bcast((nr)*sizeof((d)[0]), (d),(cr)); }
  54 #define    snew_bc(cr,d,nr) { if (!MASTER(cr)) snew((d),(nr)); }
  55 /* Dirty macro with bAlloc not as an argument */
  56 #define nblock_abc(cr,nr,d) { if (bAlloc) snew((d),(nr)); nblock_bc(cr,(nr),(d)); }
  57
  58 static void bc_string(const t_commrec *cr,t_symtab *symtab,char ***s)
  59 {
  60   int handle;
  61
  62   if (MASTER(cr)) {
  63     handle = lookup_symtab(symtab,*s);
  64   }
  65   block_bc(cr,handle);
  66   if (!MASTER(cr)) {
  67     *s = get_symtab_handle(symtab,handle);
  68   }
  69 }
  70
  71 static void bc_strings(const t_commrec *cr,t_symtab *symtab,int nr,char ****nm)
  72 {
  73   int  i;
  74   int  *handle;
  75   char ***NM;
  76
  77   snew(handle,nr);
  78   if (MASTER(cr)) {
  79     NM = *nm;
  80     for(i=0; (i<nr); i++)
  81       handle[i] = lookup_symtab(symtab,NM[i]);
  82   }
  83   nblock_bc(cr,nr,handle);
  84
  85   if (!MASTER(cr)) {
  86     snew_bc(cr,*nm,nr);
  87     NM = *nm;
  88     for (i=0; (i<nr); i++)
  89       (*nm)[i] = get_symtab_handle(symtab,handle[i]);
  90   }
  91   sfree(handle);
  92 }
  93
  94 static void bc_strings_resinfo(const t_commrec *cr,t_symtab *symtab,
  95                                int nr,t_resinfo *resinfo)
  96 {
  97   int  i;
  98   int  *handle;
  99
 100   snew(handle,nr);
 101   if (MASTER(cr)) {
 102     for(i=0; (i<nr); i++)
 103       handle[i] = lookup_symtab(symtab,resinfo[i].name);
 104   }
 105   nblock_bc(cr,nr,handle);
 106
 107   if (!MASTER(cr)) {
 108     for (i=0; (i<nr); i++)
 109       resinfo[i].name = get_symtab_handle(symtab,handle[i]);
 110   }
 111   sfree(handle);
 112 }
 113
 114 static void bc_symtab(const t_commrec *cr,t_symtab *symtab)
 115 {
 116   int i,nr,len;
 117   t_symbuf *symbuf;
 118
 119   block_bc(cr,symtab->nr);
 120   nr = symtab->nr;
 121   snew_bc(cr,symtab->symbuf,1);
 122   symbuf = symtab->symbuf;
 123   symbuf->bufsize = nr;
 124   snew_bc(cr,symbuf->buf,nr);
 125   for (i=0; i<nr; i++) {
 126     if (MASTER(cr))
 127       len = strlen(symbuf->buf[i]) + 1;
 128     block_bc(cr,len);
 129     snew_bc(cr,symbuf->buf[i],len);
 130     nblock_bc(cr,len,symbuf->buf[i]);
 131   }
 132 }
 133
 134 static void bc_block(const t_commrec *cr,t_block *block)
 135 {
 136   block_bc(cr,block->nr);
 137   snew_bc(cr,block->index,block->nr+1);
 138   nblock_bc(cr,block->nr+1,block->index);
 139 }
 140
 141 static void bc_blocka(const t_commrec *cr,t_blocka *block)
 142 {
 143   block_bc(cr,block->nr);
 144   snew_bc(cr,block->index,block->nr+1);
 145   nblock_bc(cr,block->nr+1,block->index);
 146   block_bc(cr,block->nra);
 147   if (block->nra) {
 148     snew_bc(cr,block->a,block->nra);
 149     nblock_bc(cr,block->nra,block->a);
 150   }
 151 }
 152
 153 static void bc_grps(const t_commrec *cr,t_grps grps[])
 154 {
 155   int i;
 156
 157   for(i=0; (i<egcNR); i++) {
 158     block_bc(cr,grps[i].nr);
 159     snew_bc(cr,grps[i].nm_ind,grps[i].nr);
 160     nblock_bc(cr,grps[i].nr,grps[i].nm_ind);
 161   }
 162 }
 163
 164 static void bc_atoms(const t_commrec *cr,t_symtab *symtab,t_atoms *atoms)
 165 {
 166   int dummy;
 167
 168   block_bc(cr,atoms->nr);
 169   snew_bc(cr,atoms->atom,atoms->nr);
 170   nblock_bc(cr,atoms->nr,atoms->atom);
 171   bc_strings(cr,symtab,atoms->nr,&atoms->atomname);
 172   block_bc(cr,atoms->nres);
 173   snew_bc(cr,atoms->resinfo,atoms->nres);
 174   nblock_bc(cr,atoms->nres,atoms->resinfo);
 175   bc_strings_resinfo(cr,symtab,atoms->nres,atoms->resinfo);
 176   /* QMMM requires atomtypes to be known on all nodes as well */
 177   bc_strings(cr,symtab,atoms->nr,&atoms->atomtype);
 178   bc_strings(cr,symtab,atoms->nr,&atoms->atomtypeB);
 179 }
 180
 181 static void bc_groups(const t_commrec *cr,t_symtab *symtab,
 182                       int natoms,gmx_groups_t *groups)
 183 {
 184   int dummy;
 185   int g,n;
 186
 187   bc_grps(cr,groups->grps);
 188   block_bc(cr,groups->ngrpname);
 189   bc_strings(cr,symtab,groups->ngrpname,&groups->grpname);
 190   for(g=0; g<egcNR; g++) {
 191     if (MASTER(cr)) {
 192       if (groups->grpnr[g]) {
 193         n = natoms;
 194       } else {
 195         n = 0;
 196       }
 197     }
 198     block_bc(cr,n);
 199     if (n == 0) {
 200       groups->grpnr[g] = NULL;
 201     } else {
 202       snew_bc(cr,groups->grpnr[g],n);
 203       nblock_bc(cr,n,groups->grpnr[g]);
 204     }
 205   }
 206   if (debug) fprintf(debug,"after bc_groups\n");
 207 }
 208
 209 void bcast_state_setup(const t_commrec *cr,t_state *state)
 210 {
 211   block_bc(cr,state->natoms);
 212   block_bc(cr,state->ngtc);
 213   block_bc(cr,state->nnhpres);
 214   block_bc(cr,state->nhchainlength);
 215   block_bc(cr,state->nrng);
 216   block_bc(cr,state->nrngi);
 217   block_bc(cr,state->flags);
 218 }
 219
 220 void bcast_state(const t_commrec *cr,t_state *state,bool bAlloc)
 221 {
 222   int i,nnht,nnhtp;
 223
 224   bcast_state_setup(cr,state);
 225
 226   nnht = (state->ngtc)*(state->nhchainlength);
 227   nnhtp = (state->nnhpres)*(state->nhchainlength);
 228
 229   if (MASTER(cr)) {
 230     bAlloc = FALSE;
 231   }
 232   if (bAlloc) {
 233     state->nalloc = state->natoms;
 234   }
 235   for(i=0; i<estNR; i++) {
 236     if (state->flags & (1<<i)) {
 237       switch (i) {
 238       case estLAMBDA:  block_bc(cr,state->lambda); break;
 239       case estBOX:     block_bc(cr,state->box); break;
 240       case estBOX_REL: block_bc(cr,state->box_rel); break;
 241       case estBOXV:    block_bc(cr,state->boxv); break;
 242       case estPRES_PREV: block_bc(cr,state->pres_prev); break;
 243       case estSVIR_PREV: block_bc(cr,state->svir_prev); break;
 244       case estFVIR_PREV: block_bc(cr,state->fvir_prev); break;
 245       case estNH_XI:   nblock_abc(cr,nnht,state->nosehoover_xi); break;
 246       case estNH_VXI:  nblock_abc(cr,nnht,state->nosehoover_vxi); break;
 247       case estNHPRES_XI:   nblock_abc(cr,nnhtp,state->nhpres_xi); break;
 248       case estNHPRES_VXI:  nblock_abc(cr,nnhtp,state->nhpres_vxi); break;
 249       case estTC_INT:  nblock_abc(cr,state->ngtc,state->therm_integral); break;
 250       case estVETA:    block_bc(cr,state->veta); break;
 251       case estVOL0:    block_bc(cr,state->vol0); break;
 252       case estX:       nblock_abc(cr,state->natoms,state->x); break;
 253       case estV:       nblock_abc(cr,state->natoms,state->v); break;
 254       case estSDX:     nblock_abc(cr,state->natoms,state->sd_X); break;
 255       case estCGP:     nblock_abc(cr,state->natoms,state->cg_p); break;
 256           case estLD_RNG:  if(state->nrngi == 1) nblock_abc(cr,state->nrng,state->ld_rng); break;
 257           case estLD_RNGI: if(state->nrngi == 1) nblock_abc(cr,state->nrngi,state->ld_rngi); break;
 258       case estDISRE_INITF: block_bc(cr,state->hist.disre_initf); break;
 259       case estDISRE_RM3TAV:
 260           block_bc(cr,state->hist.ndisrepairs);
 261           nblock_abc(cr,state->hist.ndisrepairs,state->hist.disre_rm3tav);
 262           break;
 263       case estORIRE_INITF: block_bc(cr,state->hist.orire_initf); break;
 264       case estORIRE_DTAV:
 265           block_bc(cr,state->hist.norire_Dtav);
 266           nblock_abc(cr,state->hist.norire_Dtav,state->hist.orire_Dtav);
 267           break;
 268       default:
 269           gmx_fatal(FARGS,
 270                     "Communication is not implemented for %s in bcast_state",
 271                     est_names[i]);
 272       }
 273     }
 274   }
 275 }
 276
 277 static void bc_ilists(const t_commrec *cr,t_ilist *ilist)
 278 {
 279   int ftype;
 280
 281   /* Here we only communicate the non-zero length ilists */
 282   if (MASTER(cr)) {
 283     for(ftype=0; ftype<F_NRE; ftype++) {
 284       if (ilist[ftype].nr > 0) {
 285         block_bc(cr,ftype);
 286         block_bc(cr,ilist[ftype].nr);
 287         nblock_bc(cr,ilist[ftype].nr,ilist[ftype].iatoms);
 288       }
 289     }
 290     ftype = -1;
 291     block_bc(cr,ftype);
 292   } else {
 293     for(ftype=0; ftype<F_NRE; ftype++) {
 294       ilist[ftype].nr = 0;
 295     }
 296     do {
 297       block_bc(cr,ftype);
 298       if (ftype >= 0) {
 299         block_bc(cr,ilist[ftype].nr);
 300         snew_bc(cr,ilist[ftype].iatoms,ilist[ftype].nr);
 301         nblock_bc(cr,ilist[ftype].nr,ilist[ftype].iatoms);
 302       }
 303     } while (ftype >= 0);
 304   }
 305
 306   if (debug) fprintf(debug,"after bc_ilists\n");
 307 }
 308
 309 static void bc_idef(const t_commrec *cr,t_idef *idef)
 310 {
 311   block_bc(cr,idef->ntypes);
 312   block_bc(cr,idef->atnr);
 313   snew_bc(cr,idef->functype,idef->ntypes);
 314   snew_bc(cr,idef->iparams,idef->ntypes);
 315   nblock_bc(cr,idef->ntypes,idef->functype);
 316   nblock_bc(cr,idef->ntypes,idef->iparams);
 317   block_bc(cr,idef->fudgeQQ);
 318   bc_ilists(cr,idef->il);
 319   block_bc(cr,idef->ilsort);
 320 }
 321
 322 static void bc_cmap(const t_commrec *cr, gmx_cmap_t *cmap_grid)
 323 {
 324         int i,j,nelem,ngrid;
 325
 326         block_bc(cr,cmap_grid->ngrid);
 327         block_bc(cr,cmap_grid->grid_spacing);
 328
 329         ngrid = cmap_grid->ngrid;
 330         nelem = cmap_grid->grid_spacing * cmap_grid->grid_spacing;
 331
 332         if(ngrid>0)
 333         {
 334                 snew_bc(cr,cmap_grid->cmapdata,ngrid);
 335
 336                 for(i=0;i<ngrid;i++)
 337                 {
 338                         snew_bc(cr,cmap_grid->cmapdata[i].cmap,4*nelem);
 339                         nblock_bc(cr,4*nelem,cmap_grid->cmapdata[i].cmap);
 340                 }
 341         }
 342 }
 343
 344 static void bc_ffparams(const t_commrec *cr,gmx_ffparams_t *ffp)
 345 {
 346   int i;
 347
 348   block_bc(cr,ffp->ntypes);
 349   block_bc(cr,ffp->atnr);
 350   snew_bc(cr,ffp->functype,ffp->ntypes);
 351   snew_bc(cr,ffp->iparams,ffp->ntypes);
 352   nblock_bc(cr,ffp->ntypes,ffp->functype);
 353   nblock_bc(cr,ffp->ntypes,ffp->iparams);
 354   block_bc(cr,ffp->reppow);
 355   block_bc(cr,ffp->fudgeQQ);
 356   bc_cmap(cr,&ffp->cmap_grid);
 357 }
 358
 359 static void bc_grpopts(const t_commrec *cr,t_grpopts *g)
 360 {
 361     int i,n;
 362
 363     block_bc(cr,g->ngtc);
 364     block_bc(cr,g->ngacc);
 365     block_bc(cr,g->ngfrz);
 366     block_bc(cr,g->ngener);
 367     snew_bc(cr,g->nrdf,g->ngtc);
 368     snew_bc(cr,g->tau_t,g->ngtc);
 369     snew_bc(cr,g->ref_t,g->ngtc);
 370     snew_bc(cr,g->acc,g->ngacc);
 371     snew_bc(cr,g->nFreeze,g->ngfrz);
 372     snew_bc(cr,g->egp_flags,g->ngener*g->ngener);
 373
 374     nblock_bc(cr,g->ngtc,g->nrdf);
 375     nblock_bc(cr,g->ngtc,g->tau_t);
 376     nblock_bc(cr,g->ngtc,g->ref_t);
 377     nblock_bc(cr,g->ngacc,g->acc);
 378     nblock_bc(cr,g->ngfrz,g->nFreeze);
 379     nblock_bc(cr,g->ngener*g->ngener,g->egp_flags);
 380     snew_bc(cr,g->annealing,g->ngtc);
 381     snew_bc(cr,g->anneal_npoints,g->ngtc);
 382     snew_bc(cr,g->anneal_time,g->ngtc);
 383     snew_bc(cr,g->anneal_temp,g->ngtc);
 384     nblock_bc(cr,g->ngtc,g->annealing);
 385     nblock_bc(cr,g->ngtc,g->anneal_npoints);
 386     for(i=0;(i<g->ngtc); i++) {
 387         n = g->anneal_npoints[i];
 388         if (n > 0) {
 389           snew_bc(cr,g->anneal_time[i],n);
 390           snew_bc(cr,g->anneal_temp[i],n);
 391           nblock_bc(cr,n,g->anneal_time[i]);
 392           nblock_bc(cr,n,g->anneal_temp[i]);
 393         }
 394     }
 395
 396     /* QMMM stuff, see inputrec */
 397     block_bc(cr,g->ngQM);
 398     snew_bc(cr,g->QMmethod,g->ngQM);
 399     snew_bc(cr,g->QMbasis,g->ngQM);
 400     snew_bc(cr,g->QMcharge,g->ngQM);
 401     snew_bc(cr,g->QMmult,g->ngQM);
 402     snew_bc(cr,g->bSH,g->ngQM);
 403     snew_bc(cr,g->CASorbitals,g->ngQM);
 404     snew_bc(cr,g->CASelectrons,g->ngQM);
 405     snew_bc(cr,g->SAon,g->ngQM);
 406     snew_bc(cr,g->SAoff,g->ngQM);
 407     snew_bc(cr,g->SAsteps,g->ngQM);
 408
 409     if (g->ngQM)
 410     {
 411         nblock_bc(cr,g->ngQM,g->QMmethod);
 412         nblock_bc(cr,g->ngQM,g->QMbasis);
 413         nblock_bc(cr,g->ngQM,g->QMcharge);
 414         nblock_bc(cr,g->ngQM,g->QMmult);
 415         nblock_bc(cr,g->ngQM,g->bSH);
 416         nblock_bc(cr,g->ngQM,g->CASorbitals);
 417         nblock_bc(cr,g->ngQM,g->CASelectrons);
 418         nblock_bc(cr,g->ngQM,g->SAon);
 419         nblock_bc(cr,g->ngQM,g->SAoff);
 420         nblock_bc(cr,g->ngQM,g->SAsteps);
 421         /* end of QMMM stuff */
 422     }
 423 }
 424
 425 static void bc_cosines(const t_commrec *cr,t_cosines *cs)
 426 {
 427   block_bc(cr,cs->n);
 428   snew_bc(cr,cs->a,cs->n);
 429   snew_bc(cr,cs->phi,cs->n);
 430   if (cs->n > 0) {
 431     nblock_bc(cr,cs->n,cs->a);
 432     nblock_bc(cr,cs->n,cs->phi);
 433   }
 434 }
 435
 436 static void bc_pullgrp(const t_commrec *cr,t_pullgrp *pgrp)
 437 {
 438   block_bc(cr,*pgrp);
 439   if (pgrp->nat > 0) {
 440     snew_bc(cr,pgrp->ind,pgrp->nat);
 441     nblock_bc(cr,pgrp->nat,pgrp->ind);
 442   }
 443   if (pgrp->nweight > 0) {
 444     snew_bc(cr,pgrp->weight,pgrp->nweight);
 445     nblock_bc(cr,pgrp->nweight,pgrp->weight);
 446   }
 447 }
 448
 449 static void bc_pull(const t_commrec *cr,t_pull *pull)
 450 {
 451   int g;
 452
 453   block_bc(cr,*pull);
 454   snew_bc(cr,pull->grp,pull->ngrp+1);
 455   for(g=0; g<pull->ngrp+1; g++)
 456   {
 457       bc_pullgrp(cr,&pull->grp[g]);
 458   }
 459 }
 460
 461 static void bc_inputrec(const t_commrec *cr,t_inputrec *inputrec)
 462 {
 463   bool bAlloc=TRUE;
 464   int i;
 465
 466   block_bc(cr,*inputrec);
 467   snew_bc(cr,inputrec->flambda,inputrec->n_flambda);
 468   nblock_bc(cr,inputrec->n_flambda,inputrec->flambda);
 469   bc_grpopts(cr,&(inputrec->opts));
 470   if (inputrec->ePull != epullNO) {
 471     snew_bc(cr,inputrec->pull,1);
 472     bc_pull(cr,inputrec->pull);
 473   }
 474   for(i=0; (i<DIM); i++) {
 475     bc_cosines(cr,&(inputrec->ex[i]));
 476     bc_cosines(cr,&(inputrec->et[i]));
 477   }
 478 }
 479
 480 static void bc_moltype(const t_commrec *cr,t_symtab *symtab,
 481                        gmx_moltype_t *moltype)
 482 {
 483   bc_string(cr,symtab,&moltype->name);
 484   bc_atoms(cr,symtab,&moltype->atoms);
 485   if (debug) fprintf(debug,"after bc_atoms\n");
 486
 487   bc_ilists(cr,moltype->ilist);
 488   bc_block(cr,&moltype->cgs);
 489   bc_blocka(cr,&moltype->excls);
 490 }
 491
 492 static void bc_molblock(const t_commrec *cr,gmx_molblock_t *molb)
 493 {
 494   bool bAlloc=TRUE;
 495
 496   block_bc(cr,molb->type);
 497   block_bc(cr,molb->nmol);
 498   block_bc(cr,molb->natoms_mol);
 499   block_bc(cr,molb->nposres_xA);
 500   if (molb->nposres_xA > 0) {
 501     snew_bc(cr,molb->posres_xA,molb->nposres_xA);
 502     nblock_bc(cr,molb->nposres_xA*DIM,molb->posres_xA[0]);
 503   }
 504   block_bc(cr,molb->nposres_xB);
 505   if (molb->nposres_xB > 0) {
 506     snew_bc(cr,molb->posres_xB,molb->nposres_xB);
 507     nblock_bc(cr,molb->nposres_xB*DIM,molb->posres_xB[0]);
 508   }
 509   if (debug) fprintf(debug,"after bc_molblock\n");
 510 }
 511
 512 static void bc_atomtypes(const t_commrec *cr, t_atomtypes *atomtypes)
 513 {
 514   int nr;
 515
 516   block_bc(cr,atomtypes->nr);
 517
 518   nr = atomtypes->nr;
 519
 520   snew_bc(cr,atomtypes->radius,nr);
 521   snew_bc(cr,atomtypes->vol,nr);
 522   snew_bc(cr,atomtypes->surftens,nr);
 523   snew_bc(cr,atomtypes->gb_radius,nr);
 524   snew_bc(cr,atomtypes->S_hct,nr);
 525
 526   nblock_bc(cr,nr,atomtypes->radius);
 527   nblock_bc(cr,nr,atomtypes->vol);
 528   nblock_bc(cr,nr,atomtypes->surftens);
 529   nblock_bc(cr,nr,atomtypes->gb_radius);
 530   nblock_bc(cr,nr,atomtypes->S_hct);
 531 }
 532
 533
 534 void bcast_ir_mtop(const t_commrec *cr,t_inputrec *inputrec,gmx_mtop_t *mtop)
 535 {
 536   int i;
 537   if (debug) fprintf(debug,"in bc_data\n");
 538   bc_inputrec(cr,inputrec);
 539   if (debug) fprintf(debug,"after bc_inputrec\n");
 540   bc_symtab(cr,&mtop->symtab);
 541   if (debug) fprintf(debug,"after bc_symtab\n");
 542   bc_string(cr,&mtop->symtab,&mtop->name);
 543   if (debug) fprintf(debug,"after bc_name\n");
 544
 545   bc_ffparams(cr,&mtop->ffparams);
 546
 547   block_bc(cr,mtop->nmoltype);
 548   snew_bc(cr,mtop->moltype,mtop->nmoltype);
 549   for(i=0; i<mtop->nmoltype; i++) {
 550     bc_moltype(cr,&mtop->symtab,&mtop->moltype[i]);
 551   }
 552
 553   block_bc(cr,mtop->nmolblock);
 554   snew_bc(cr,mtop->molblock,mtop->nmolblock);
 555   for(i=0; i<mtop->nmolblock; i++) {
 556     bc_molblock(cr,&mtop->molblock[i]);
 557   }
 558
 559   block_bc(cr,mtop->natoms);
 560
 561   bc_atomtypes(cr,&mtop->atomtypes);
 562
 563   bc_block(cr,&mtop->mols);
 564   bc_groups(cr,&mtop->symtab,mtop->natoms,&mtop->groups);
 565 }