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33 * GROningen Mixture of Alchemy and Childrens' Stories
35 /* This file is completely threadsafe - keep it that way! */
47 #include "gmx_fatal.h"
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)); }
61 static void bc_string(const t_commrec *cr,t_symtab *symtab,char ***s)
66 handle = lookup_symtab(symtab,*s);
70 *s = get_symtab_handle(symtab,handle);
74 static void bc_strings(const t_commrec *cr,t_symtab *symtab,int nr,char ****nm)
84 handle[i] = lookup_symtab(symtab,NM[i]);
86 nblock_bc(cr,nr,handle);
91 for (i=0; (i<nr); i++)
92 (*nm)[i] = get_symtab_handle(symtab,handle[i]);
97 static void bc_strings_resinfo(const t_commrec *cr,t_symtab *symtab,
98 int nr,t_resinfo *resinfo)
105 for(i=0; (i<nr); i++)
106 handle[i] = lookup_symtab(symtab,resinfo[i].name);
108 nblock_bc(cr,nr,handle);
111 for (i=0; (i<nr); i++)
112 resinfo[i].name = get_symtab_handle(symtab,handle[i]);
117 static void bc_symtab(const t_commrec *cr,t_symtab *symtab)
122 block_bc(cr,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++) {
130 len = strlen(symbuf->buf[i]) + 1;
132 snew_bc(cr,symbuf->buf[i],len);
133 nblock_bc(cr,len,symbuf->buf[i]);
137 static void bc_block(const t_commrec *cr,t_block *block)
139 block_bc(cr,block->nr);
140 snew_bc(cr,block->index,block->nr+1);
141 nblock_bc(cr,block->nr+1,block->index);
144 static void bc_blocka(const t_commrec *cr,t_blocka *block)
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);
151 snew_bc(cr,block->a,block->nra);
152 nblock_bc(cr,block->nra,block->a);
156 static void bc_grps(const t_commrec *cr,t_grps grps[])
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);
167 static void bc_atoms(const t_commrec *cr,t_symtab *symtab,t_atoms *atoms)
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);
184 static void bc_groups(const t_commrec *cr,t_symtab *symtab,
185 int natoms,gmx_groups_t *groups)
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++) {
195 if (groups->grpnr[g]) {
203 groups->grpnr[g] = NULL;
205 snew_bc(cr,groups->grpnr[g],n);
206 nblock_bc(cr,n,groups->grpnr[g]);
209 if (debug) fprintf(debug,"after bc_groups\n");
212 void bcast_state_setup(const t_commrec *cr,t_state *state)
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 if (state->lambda==NULL)
223 snew_bc(cr,state->lambda,efptNR)
227 void bcast_state(const t_commrec *cr,t_state *state,gmx_bool bAlloc)
231 bcast_state_setup(cr,state);
233 nnht = (state->ngtc)*(state->nhchainlength);
234 nnhtp = (state->nnhpres)*(state->nhchainlength);
240 state->nalloc = state->natoms;
242 for(i=0; i<estNR; i++) {
243 if (state->flags & (1<<i)) {
245 case estLAMBDA: nblock_bc(cr,efptNR,state->lambda); break;
246 case estFEPSTATE: block_bc(cr,state->fep_state); break;
247 case estBOX: block_bc(cr,state->box); break;
248 case estBOX_REL: block_bc(cr,state->box_rel); break;
249 case estBOXV: block_bc(cr,state->boxv); break;
250 case estPRES_PREV: block_bc(cr,state->pres_prev); break;
251 case estSVIR_PREV: block_bc(cr,state->svir_prev); break;
252 case estFVIR_PREV: block_bc(cr,state->fvir_prev); break;
253 case estNH_XI: nblock_abc(cr,nnht,state->nosehoover_xi); break;
254 case estNH_VXI: nblock_abc(cr,nnht,state->nosehoover_vxi); break;
255 case estNHPRES_XI: nblock_abc(cr,nnhtp,state->nhpres_xi); break;
256 case estNHPRES_VXI: nblock_abc(cr,nnhtp,state->nhpres_vxi); break;
257 case estTC_INT: nblock_abc(cr,state->ngtc,state->therm_integral); break;
258 case estVETA: block_bc(cr,state->veta); break;
259 case estVOL0: block_bc(cr,state->vol0); break;
260 case estX: nblock_abc(cr,state->natoms,state->x); break;
261 case estV: nblock_abc(cr,state->natoms,state->v); break;
262 case estSDX: nblock_abc(cr,state->natoms,state->sd_X); break;
263 case estCGP: nblock_abc(cr,state->natoms,state->cg_p); break;
264 case estLD_RNG: if(state->nrngi == 1) nblock_abc(cr,state->nrng,state->ld_rng); break;
265 case estLD_RNGI: if(state->nrngi == 1) nblock_abc(cr,state->nrngi,state->ld_rngi); break;
266 case estDISRE_INITF: block_bc(cr,state->hist.disre_initf); break;
267 case estDISRE_RM3TAV:
268 block_bc(cr,state->hist.ndisrepairs);
269 nblock_abc(cr,state->hist.ndisrepairs,state->hist.disre_rm3tav);
271 case estORIRE_INITF: block_bc(cr,state->hist.orire_initf); break;
273 block_bc(cr,state->hist.norire_Dtav);
274 nblock_abc(cr,state->hist.norire_Dtav,state->hist.orire_Dtav);
278 "Communication is not implemented for %s in bcast_state",
285 static void bc_ilists(const t_commrec *cr,t_ilist *ilist)
289 /* Here we only communicate the non-zero length ilists */
291 for(ftype=0; ftype<F_NRE; ftype++) {
292 if (ilist[ftype].nr > 0) {
294 block_bc(cr,ilist[ftype].nr);
295 nblock_bc(cr,ilist[ftype].nr,ilist[ftype].iatoms);
301 for(ftype=0; ftype<F_NRE; ftype++) {
307 block_bc(cr,ilist[ftype].nr);
308 snew_bc(cr,ilist[ftype].iatoms,ilist[ftype].nr);
309 nblock_bc(cr,ilist[ftype].nr,ilist[ftype].iatoms);
311 } while (ftype >= 0);
314 if (debug) fprintf(debug,"after bc_ilists\n");
317 static void bc_cmap(const t_commrec *cr, gmx_cmap_t *cmap_grid)
321 block_bc(cr,cmap_grid->ngrid);
322 block_bc(cr,cmap_grid->grid_spacing);
324 ngrid = cmap_grid->ngrid;
325 nelem = cmap_grid->grid_spacing * cmap_grid->grid_spacing;
329 snew_bc(cr,cmap_grid->cmapdata,ngrid);
333 snew_bc(cr,cmap_grid->cmapdata[i].cmap,4*nelem);
334 nblock_bc(cr,4*nelem,cmap_grid->cmapdata[i].cmap);
339 static void bc_ffparams(const t_commrec *cr,gmx_ffparams_t *ffp)
343 block_bc(cr,ffp->ntypes);
344 block_bc(cr,ffp->atnr);
345 snew_bc(cr,ffp->functype,ffp->ntypes);
346 snew_bc(cr,ffp->iparams,ffp->ntypes);
347 nblock_bc(cr,ffp->ntypes,ffp->functype);
348 nblock_bc(cr,ffp->ntypes,ffp->iparams);
349 block_bc(cr,ffp->reppow);
350 block_bc(cr,ffp->fudgeQQ);
351 bc_cmap(cr,&ffp->cmap_grid);
354 static void bc_grpopts(const t_commrec *cr,t_grpopts *g)
358 block_bc(cr,g->ngtc);
359 block_bc(cr,g->ngacc);
360 block_bc(cr,g->ngfrz);
361 block_bc(cr,g->ngener);
362 snew_bc(cr,g->nrdf,g->ngtc);
363 snew_bc(cr,g->tau_t,g->ngtc);
364 snew_bc(cr,g->ref_t,g->ngtc);
365 snew_bc(cr,g->acc,g->ngacc);
366 snew_bc(cr,g->nFreeze,g->ngfrz);
367 snew_bc(cr,g->egp_flags,g->ngener*g->ngener);
369 nblock_bc(cr,g->ngtc,g->nrdf);
370 nblock_bc(cr,g->ngtc,g->tau_t);
371 nblock_bc(cr,g->ngtc,g->ref_t);
372 nblock_bc(cr,g->ngacc,g->acc);
373 nblock_bc(cr,g->ngfrz,g->nFreeze);
374 nblock_bc(cr,g->ngener*g->ngener,g->egp_flags);
375 snew_bc(cr,g->annealing,g->ngtc);
376 snew_bc(cr,g->anneal_npoints,g->ngtc);
377 snew_bc(cr,g->anneal_time,g->ngtc);
378 snew_bc(cr,g->anneal_temp,g->ngtc);
379 nblock_bc(cr,g->ngtc,g->annealing);
380 nblock_bc(cr,g->ngtc,g->anneal_npoints);
381 for(i=0;(i<g->ngtc); i++) {
382 n = g->anneal_npoints[i];
384 snew_bc(cr,g->anneal_time[i],n);
385 snew_bc(cr,g->anneal_temp[i],n);
386 nblock_bc(cr,n,g->anneal_time[i]);
387 nblock_bc(cr,n,g->anneal_temp[i]);
391 /* QMMM stuff, see inputrec */
392 block_bc(cr,g->ngQM);
393 snew_bc(cr,g->QMmethod,g->ngQM);
394 snew_bc(cr,g->QMbasis,g->ngQM);
395 snew_bc(cr,g->QMcharge,g->ngQM);
396 snew_bc(cr,g->QMmult,g->ngQM);
397 snew_bc(cr,g->bSH,g->ngQM);
398 snew_bc(cr,g->CASorbitals,g->ngQM);
399 snew_bc(cr,g->CASelectrons,g->ngQM);
400 snew_bc(cr,g->SAon,g->ngQM);
401 snew_bc(cr,g->SAoff,g->ngQM);
402 snew_bc(cr,g->SAsteps,g->ngQM);
406 nblock_bc(cr,g->ngQM,g->QMmethod);
407 nblock_bc(cr,g->ngQM,g->QMbasis);
408 nblock_bc(cr,g->ngQM,g->QMcharge);
409 nblock_bc(cr,g->ngQM,g->QMmult);
410 nblock_bc(cr,g->ngQM,g->bSH);
411 nblock_bc(cr,g->ngQM,g->CASorbitals);
412 nblock_bc(cr,g->ngQM,g->CASelectrons);
413 nblock_bc(cr,g->ngQM,g->SAon);
414 nblock_bc(cr,g->ngQM,g->SAoff);
415 nblock_bc(cr,g->ngQM,g->SAsteps);
416 /* end of QMMM stuff */
420 static void bc_cosines(const t_commrec *cr,t_cosines *cs)
423 snew_bc(cr,cs->a,cs->n);
424 snew_bc(cr,cs->phi,cs->n);
426 nblock_bc(cr,cs->n,cs->a);
427 nblock_bc(cr,cs->n,cs->phi);
431 static void bc_pullgrp(const t_commrec *cr,t_pullgrp *pgrp)
435 snew_bc(cr,pgrp->ind,pgrp->nat);
436 nblock_bc(cr,pgrp->nat,pgrp->ind);
438 if (pgrp->nweight > 0) {
439 snew_bc(cr,pgrp->weight,pgrp->nweight);
440 nblock_bc(cr,pgrp->nweight,pgrp->weight);
444 static void bc_pull(const t_commrec *cr,t_pull *pull)
449 snew_bc(cr,pull->grp,pull->ngrp+1);
450 for(g=0; g<pull->ngrp+1; g++)
452 bc_pullgrp(cr,&pull->grp[g]);
456 static void bc_rotgrp(const t_commrec *cr,t_rotgrp *rotg)
460 snew_bc(cr,rotg->ind,rotg->nat);
461 nblock_bc(cr,rotg->nat,rotg->ind);
462 snew_bc(cr,rotg->x_ref,rotg->nat);
463 nblock_bc(cr,rotg->nat,rotg->x_ref);
467 static void bc_rot(const t_commrec *cr,t_rot *rot)
472 snew_bc(cr,rot->grp,rot->ngrp);
473 for(g=0; g<rot->ngrp; g++)
474 bc_rotgrp(cr,&rot->grp[g]);
477 static void bc_adress(const t_commrec *cr,t_adress *adress)
479 block_bc(cr,*adress);
480 if (adress->n_tf_grps > 0) {
481 snew_bc(cr, adress->tf_table_index, adress->n_tf_grps);
482 nblock_bc(cr, adress->n_tf_grps, adress->tf_table_index);
484 if (adress->n_energy_grps > 0) {
485 snew_bc(cr, adress->group_explicit, adress->n_energy_grps);
486 nblock_bc(cr, adress->n_energy_grps, adress->group_explicit);
489 static void bc_fepvals(const t_commrec *cr,t_lambda *fep)
491 gmx_bool bAlloc=TRUE;
494 block_bc(cr,fep->nstdhdl);
495 block_bc(cr,fep->init_lambda);
496 block_bc(cr,fep->init_fep_state);
497 block_bc(cr,fep->delta_lambda);
498 block_bc(cr,fep->bPrintEnergy);
499 block_bc(cr,fep->n_lambda);
500 snew_bc(cr,fep->all_lambda,efptNR);
501 nblock_bc(cr,efptNR,fep->all_lambda);
502 for (i=0;i<efptNR;i++) {
503 snew_bc(cr,fep->all_lambda[i],fep->n_lambda);
504 nblock_bc(cr,fep->n_lambda,fep->all_lambda[i]);
506 block_bc(cr,fep->sc_alpha);
507 block_bc(cr,fep->sc_power);
508 block_bc(cr,fep->sc_r_power);
509 block_bc(cr,fep->sc_sigma);
510 block_bc(cr,fep->sc_sigma_min);
511 block_bc(cr,fep->bScCoul);
512 nblock_bc(cr,efptNR,&(fep->separate_dvdl[0]));
513 block_bc(cr,fep->dhdl_derivatives);
514 block_bc(cr,fep->dh_hist_size);
515 block_bc(cr,fep->dh_hist_spacing);
518 fprintf(debug,"after bc_fepvals\n");
522 static void bc_expandedvals(const t_commrec *cr,t_expanded *expand, int n_lambda)
524 gmx_bool bAlloc=TRUE;
527 block_bc(cr,expand->nstexpanded);
528 block_bc(cr,expand->elamstats);
529 block_bc(cr,expand->elmcmove);
530 block_bc(cr,expand->elmceq);
531 block_bc(cr,expand->equil_n_at_lam);
532 block_bc(cr,expand->equil_wl_delta);
533 block_bc(cr,expand->equil_ratio);
534 block_bc(cr,expand->equil_steps);
535 block_bc(cr,expand->equil_samples);
536 block_bc(cr,expand->lmc_seed);
537 block_bc(cr,expand->minvar);
538 block_bc(cr,expand->minvar_const);
539 block_bc(cr,expand->c_range);
540 block_bc(cr,expand->bSymmetrizedTMatrix);
541 block_bc(cr,expand->nstTij);
542 block_bc(cr,expand->lmc_repeats);
543 block_bc(cr,expand->lmc_forced_nstart);
544 block_bc(cr,expand->gibbsdeltalam);
545 block_bc(cr,expand->wl_scale);
546 block_bc(cr,expand->wl_ratio);
547 block_bc(cr,expand->init_wl_delta);
548 block_bc(cr,expand->bInit_weights);
549 snew_bc(cr,expand->init_lambda_weights,n_lambda);
550 nblock_bc(cr,n_lambda,expand->init_lambda_weights);
551 block_bc(cr,expand->mc_temp);
554 fprintf(debug,"after bc_expandedvals\n");
558 static void bc_simtempvals(const t_commrec *cr,t_simtemp *simtemp, int n_lambda)
560 gmx_bool bAlloc=TRUE;
563 block_bc(cr,simtemp->simtemp_low);
564 block_bc(cr,simtemp->simtemp_high);
565 block_bc(cr,simtemp->eSimTempScale);
566 snew_bc(cr,simtemp->temperatures,n_lambda);
567 nblock_bc(cr,n_lambda,simtemp->temperatures);
570 fprintf(debug,"after bc_simtempvals\n");
574 static void bc_inputrec(const t_commrec *cr,t_inputrec *inputrec)
576 gmx_bool bAlloc=TRUE;
579 block_bc(cr,*inputrec);
581 bc_grpopts(cr,&(inputrec->opts));
583 /* even if efep is efepNO, we need to initialize to make sure that
584 * n_lambda is set to zero */
586 snew_bc(cr,inputrec->fepvals,1);
587 if (inputrec->efep != efepNO || inputrec->bSimTemp)
589 bc_fepvals(cr,inputrec->fepvals);
591 /* need to initialize this as well because of data checked for in the logic */
592 snew_bc(cr,inputrec->expandedvals,1);
593 if (inputrec->bExpanded)
595 bc_expandedvals(cr,inputrec->expandedvals,inputrec->fepvals->n_lambda);
597 snew_bc(cr,inputrec->simtempvals,1);
598 if (inputrec->bSimTemp)
600 bc_simtempvals(cr,inputrec->simtempvals,inputrec->fepvals->n_lambda);
602 if (inputrec->ePull != epullNO) {
603 snew_bc(cr,inputrec->pull,1);
604 bc_pull(cr,inputrec->pull);
606 if (inputrec->bRot) {
607 snew_bc(cr,inputrec->rot,1);
608 bc_rot(cr,inputrec->rot);
610 for(i=0; (i<DIM); i++) {
611 bc_cosines(cr,&(inputrec->ex[i]));
612 bc_cosines(cr,&(inputrec->et[i]));
614 if (inputrec->bAdress) {
615 snew_bc(cr,inputrec->adress,1);
616 bc_adress(cr,inputrec->adress);
620 static void bc_moltype(const t_commrec *cr,t_symtab *symtab,
621 gmx_moltype_t *moltype)
623 bc_string(cr,symtab,&moltype->name);
624 bc_atoms(cr,symtab,&moltype->atoms);
625 if (debug) fprintf(debug,"after bc_atoms\n");
627 bc_ilists(cr,moltype->ilist);
628 bc_block(cr,&moltype->cgs);
629 bc_blocka(cr,&moltype->excls);
632 static void bc_molblock(const t_commrec *cr,gmx_molblock_t *molb)
634 gmx_bool bAlloc=TRUE;
636 block_bc(cr,molb->type);
637 block_bc(cr,molb->nmol);
638 block_bc(cr,molb->natoms_mol);
639 block_bc(cr,molb->nposres_xA);
640 if (molb->nposres_xA > 0) {
641 snew_bc(cr,molb->posres_xA,molb->nposres_xA);
642 nblock_bc(cr,molb->nposres_xA*DIM,molb->posres_xA[0]);
644 block_bc(cr,molb->nposres_xB);
645 if (molb->nposres_xB > 0) {
646 snew_bc(cr,molb->posres_xB,molb->nposres_xB);
647 nblock_bc(cr,molb->nposres_xB*DIM,molb->posres_xB[0]);
649 if (debug) fprintf(debug,"after bc_molblock\n");
652 static void bc_atomtypes(const t_commrec *cr, t_atomtypes *atomtypes)
656 block_bc(cr,atomtypes->nr);
660 snew_bc(cr,atomtypes->radius,nr);
661 snew_bc(cr,atomtypes->vol,nr);
662 snew_bc(cr,atomtypes->surftens,nr);
663 snew_bc(cr,atomtypes->gb_radius,nr);
664 snew_bc(cr,atomtypes->S_hct,nr);
666 nblock_bc(cr,nr,atomtypes->radius);
667 nblock_bc(cr,nr,atomtypes->vol);
668 nblock_bc(cr,nr,atomtypes->surftens);
669 nblock_bc(cr,nr,atomtypes->gb_radius);
670 nblock_bc(cr,nr,atomtypes->S_hct);
674 void bcast_ir_mtop(const t_commrec *cr,t_inputrec *inputrec,gmx_mtop_t *mtop)
677 if (debug) fprintf(debug,"in bc_data\n");
678 bc_inputrec(cr,inputrec);
679 if (debug) fprintf(debug,"after bc_inputrec\n");
680 bc_symtab(cr,&mtop->symtab);
681 if (debug) fprintf(debug,"after bc_symtab\n");
682 bc_string(cr,&mtop->symtab,&mtop->name);
683 if (debug) fprintf(debug,"after bc_name\n");
685 bc_ffparams(cr,&mtop->ffparams);
687 block_bc(cr,mtop->nmoltype);
688 snew_bc(cr,mtop->moltype,mtop->nmoltype);
689 for(i=0; i<mtop->nmoltype; i++) {
690 bc_moltype(cr,&mtop->symtab,&mtop->moltype[i]);
693 block_bc(cr,mtop->nmolblock);
694 snew_bc(cr,mtop->molblock,mtop->nmolblock);
695 for(i=0; i<mtop->nmolblock; i++) {
696 bc_molblock(cr,&mtop->molblock[i]);
699 block_bc(cr,mtop->natoms);
701 bc_atomtypes(cr,&mtop->atomtypes);
703 bc_block(cr,&mtop->mols);
704 bc_groups(cr,&mtop->symtab,mtop->natoms,&mtop->groups);