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44 #include "gmx_fatal.h"
67 #include "checkpoint.h"
69 #include "md_support.h"
73 typedef struct gmx_global_stat
80 gmx_global_stat_t global_stat_init(t_inputrec *ir)
87 snew(gs->itc0,ir->opts.ngtc);
88 snew(gs->itc1,ir->opts.ngtc);
93 void global_stat_destroy(gmx_global_stat_t gs)
101 static int filter_enerdterm(real *afrom, gmx_bool bToBuffer, real *ato,
102 gmx_bool bTemp, gmx_bool bPres, gmx_bool bEner) {
107 for (i=0;i<F_NRE;i++)
123 ato[to++] = afrom[from++];
131 ato[to++] = afrom[from++];
137 ato[to++] = afrom[from++];
146 void global_stat(FILE *fplog,gmx_global_stat_t gs,
147 t_commrec *cr,gmx_enerdata_t *enerd,
148 tensor fvir,tensor svir,rvec mu_tot,
149 t_inputrec *inputrec,
150 gmx_ekindata_t *ekind,gmx_constr_t constr,
153 gmx_mtop_t *top_global, t_state *state_local,
154 gmx_bool bSumEkinhOld, int flags)
155 /* instead of current system, gmx_booleans for summing virial, kinetic energy, and other terms */
159 int ie=0,ifv=0,isv=0,irmsd=0,imu=0;
160 int idedl=0,idvdll=0,idvdlnl=0,iepl=0,icm=0,imass=0,ica=0,inb=0;
162 int icj=-1,ici=-1,icx=-1;
164 real copyenerd[F_NRE];
166 real *rmsd_data=NULL;
168 gmx_bool bVV,bTemp,bEner,bPres,bConstrVir,bEkinAveVel,bFirstIterate,bReadEkin;
170 bVV = EI_VV(inputrec->eI);
171 bTemp = flags & CGLO_TEMPERATURE;
172 bEner = flags & CGLO_ENERGY;
173 bPres = (flags & CGLO_PRESSURE);
174 bConstrVir = (flags & CGLO_CONSTRAINT);
175 bFirstIterate = (flags & CGLO_FIRSTITERATE);
176 bEkinAveVel = (inputrec->eI==eiVV || (inputrec->eI==eiVVAK && bPres));
177 bReadEkin = (flags & CGLO_READEKIN);
185 /* This routine copies all the data to be summed to one big buffer
186 * using the t_bin struct.
189 /* First, we neeed to identify which enerd->term should be
190 communicated. Temperature and pressure terms should only be
191 communicated and summed when they need to be, to avoid repeating
192 the sums and overcounting. */
194 nener = filter_enerdterm(enerd->term,TRUE,copyenerd,bTemp,bPres,bEner);
196 /* First, the data that needs to be communicated with velocity verlet every time
197 This is just the constraint virial.*/
199 isv = add_binr(rb,DIM*DIM,svir[0]);
203 /* We need the force virial and the kinetic energy for the first time through with velocity verlet */
208 for(j=0; (j<inputrec->opts.ngtc); j++)
212 itc0[j]=add_binr(rb,DIM*DIM,ekind->tcstat[j].ekinh_old[0]);
214 if (bEkinAveVel && !bReadEkin)
216 itc1[j]=add_binr(rb,DIM*DIM,ekind->tcstat[j].ekinf[0]);
220 itc1[j]=add_binr(rb,DIM*DIM,ekind->tcstat[j].ekinh[0]);
223 /* these probably need to be put into one of these categories */
225 idedl = add_binr(rb,1,&(ekind->dekindl));
227 ica = add_binr(rb,1,&(ekind->cosacc.mvcos));
233 if ((bPres || !bVV) && bFirstIterate)
235 ifv = add_binr(rb,DIM*DIM,fvir[0]);
244 ie = add_binr(rb,nener,copyenerd);
249 rmsd_data = constr_rmsd_data(constr);
252 irmsd = add_binr(rb,inputrec->eI==eiSD2 ? 3 : 2,rmsd_data);
255 if (!NEED_MUTOT(*inputrec))
257 imu = add_binr(rb,DIM,mu_tot);
263 for(j=0; (j<egNR); j++)
265 inn[j]=add_binr(rb,enerd->grpp.nener,enerd->grpp.ener[j]);
268 if (inputrec->efep != efepNO)
270 idvdll = add_bind(rb,efptNR,enerd->dvdl_lin);
271 idvdlnl = add_bind(rb,efptNR,enerd->dvdl_nonlin);
272 if (enerd->n_lambda > 0)
274 iepl = add_bind(rb,enerd->n_lambda,enerd->enerpart_lambda);
282 icm = add_binr(rb,DIM*vcm->nr,vcm->group_p[0]);
284 imass = add_binr(rb,vcm->nr,vcm->group_mass);
286 if (vcm->mode == ecmANGULAR)
288 icj = add_binr(rb,DIM*vcm->nr,vcm->group_j[0]);
290 icx = add_binr(rb,DIM*vcm->nr,vcm->group_x[0]);
292 ici = add_binr(rb,DIM*DIM*vcm->nr,vcm->group_i[0][0]);
297 if (DOMAINDECOMP(cr))
299 nb = cr->dd->nbonded_local;
300 inb = add_bind(rb,1,&nb);
305 isig = add_binr(rb,nsig,sig);
308 /* Global sum it all */
311 fprintf(debug,"Summing %d energies\n",rb->maxreal);
316 /* Extract all the data locally */
320 extract_binr(rb,isv ,DIM*DIM,svir[0]);
323 /* We need the force virial and the kinetic energy for the first time through with velocity verlet */
328 for(j=0; (j<inputrec->opts.ngtc); j++)
332 extract_binr(rb,itc0[j],DIM*DIM,ekind->tcstat[j].ekinh_old[0]);
334 if (bEkinAveVel && !bReadEkin) {
335 extract_binr(rb,itc1[j],DIM*DIM,ekind->tcstat[j].ekinf[0]);
339 extract_binr(rb,itc1[j],DIM*DIM,ekind->tcstat[j].ekinh[0]);
342 extract_binr(rb,idedl,1,&(ekind->dekindl));
343 extract_binr(rb,ica,1,&(ekind->cosacc.mvcos));
347 if ((bPres || !bVV) && bFirstIterate)
349 extract_binr(rb,ifv ,DIM*DIM,fvir[0]);
356 extract_binr(rb,ie,nener,copyenerd);
359 extract_binr(rb,irmsd,inputrec->eI==eiSD2 ? 3 : 2,rmsd_data);
361 if (!NEED_MUTOT(*inputrec))
363 extract_binr(rb,imu,DIM,mu_tot);
366 for(j=0; (j<egNR); j++)
368 extract_binr(rb,inn[j],enerd->grpp.nener,enerd->grpp.ener[j]);
370 if (inputrec->efep != efepNO)
372 extract_bind(rb,idvdll ,efptNR,enerd->dvdl_lin);
373 extract_bind(rb,idvdlnl,efptNR,enerd->dvdl_nonlin);
374 if (enerd->n_lambda > 0)
376 extract_bind(rb,iepl,enerd->n_lambda,enerd->enerpart_lambda);
379 if (DOMAINDECOMP(cr))
381 extract_bind(rb,inb,1,&nb);
382 if ((int)(nb + 0.5) != cr->dd->nbonded_global)
384 dd_print_missing_interactions(fplog,cr,(int)(nb + 0.5),top_global,state_local);
389 filter_enerdterm(copyenerd,FALSE,enerd->term,bTemp,bPres,bEner);
395 extract_binr(rb,icm,DIM*vcm->nr,vcm->group_p[0]);
397 extract_binr(rb,imass,vcm->nr,vcm->group_mass);
399 if (vcm->mode == ecmANGULAR)
401 extract_binr(rb,icj,DIM*vcm->nr,vcm->group_j[0]);
403 extract_binr(rb,icx,DIM*vcm->nr,vcm->group_x[0]);
405 extract_binr(rb,ici,DIM*DIM*vcm->nr,vcm->group_i[0][0]);
412 extract_binr(rb,isig,nsig,sig);
417 int do_per_step(gmx_large_int_t step,gmx_large_int_t nstep)
420 return ((step % nstep)==0);
425 static void moveit(t_commrec *cr,
426 int left,int right,const char *s,rvec xx[])
431 move_rvecs(cr,FALSE,FALSE,left,right,
432 xx,NULL,(cr->nnodes-cr->npmenodes)-1,NULL);
435 gmx_mdoutf_t *init_mdoutf(int nfile,const t_filenm fnm[],int mdrun_flags,
436 const t_commrec *cr,const t_inputrec *ir,
437 const output_env_t oenv)
441 gmx_bool bAppendFiles;
451 of->eIntegrator = ir->eI;
452 of->bExpanded = ir->bExpanded;
453 of->elamstats = ir->expandedvals->elamstats;
454 of->simulation_part = ir->simulation_part;
458 bAppendFiles = (mdrun_flags & MD_APPENDFILES);
460 of->bKeepAndNumCPT = (mdrun_flags & MD_KEEPANDNUMCPT);
462 sprintf(filemode, bAppendFiles ? "a+" : "w+");
464 if ((EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
467 !(EI_DYNAMICS(ir->eI) &&
474 of->fp_trn = open_trn(ftp2fn(efTRN,nfile,fnm), filemode);
476 if (EI_DYNAMICS(ir->eI) &&
479 of->fp_xtc = open_xtc(ftp2fn(efXTC,nfile,fnm), filemode);
480 of->xtc_prec = ir->xtcprec;
482 if (EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
484 of->fp_ene = open_enx(ftp2fn(efEDR,nfile,fnm), filemode);
486 of->fn_cpt = opt2fn("-cpo",nfile,fnm);
488 if ((ir->efep != efepNO || ir->bSimTemp) && ir->fepvals->nstdhdl > 0 &&
489 (ir->fepvals->separate_dhdl_file == esepdhdlfileYES ) &&
494 of->fp_dhdl = gmx_fio_fopen(opt2fn("-dhdl",nfile,fnm),filemode);
498 of->fp_dhdl = open_dhdl(opt2fn("-dhdl",nfile,fnm),ir,oenv);
502 if (opt2bSet("-field",nfile,fnm) &&
503 (ir->ex[XX].n || ir->ex[YY].n || ir->ex[ZZ].n))
507 of->fp_dhdl = gmx_fio_fopen(opt2fn("-field",nfile,fnm),
512 of->fp_field = xvgropen(opt2fn("-field",nfile,fnm),
513 "Applied electric field","Time (ps)",
522 void done_mdoutf(gmx_mdoutf_t *of)
524 if (of->fp_ene != NULL)
526 close_enx(of->fp_ene);
530 close_xtc(of->fp_xtc);
534 close_trn(of->fp_trn);
536 if (of->fp_dhdl != NULL)
538 gmx_fio_fclose(of->fp_dhdl);
540 if (of->fp_field != NULL)
542 gmx_fio_fclose(of->fp_field);
548 void write_traj(FILE *fplog,t_commrec *cr,
551 gmx_mtop_t *top_global,
552 gmx_large_int_t step,double t,
553 t_state *state_local,t_state *state_global,
554 rvec *f_local,rvec *f_global,
555 int *n_xtc,rvec **x_xtc)
558 gmx_groups_t *groups;
563 #define MX(xvf) moveit(cr,GMX_LEFT,GMX_RIGHT,#xvf,xvf)
565 /* MRS -- defining these variables is to manage the difference
566 * between half step and full step velocities, but there must be a better way . . . */
568 local_v = state_local->v;
569 global_v = state_global->v;
571 if (DOMAINDECOMP(cr))
573 if (mdof_flags & MDOF_CPT)
575 dd_collect_state(cr->dd,state_local,state_global);
579 if (mdof_flags & (MDOF_X | MDOF_XTC))
581 dd_collect_vec(cr->dd,state_local,state_local->x,
584 if (mdof_flags & MDOF_V)
586 dd_collect_vec(cr->dd,state_local,local_v,
590 if (mdof_flags & MDOF_F)
592 dd_collect_vec(cr->dd,state_local,f_local,f_global);
597 if (mdof_flags & MDOF_CPT)
599 /* All pointers in state_local are equal to state_global,
600 * but we need to copy the non-pointer entries.
602 state_global->lambda = state_local->lambda;
603 state_global->veta = state_local->veta;
604 state_global->vol0 = state_local->vol0;
605 copy_mat(state_local->box,state_global->box);
606 copy_mat(state_local->boxv,state_global->boxv);
607 copy_mat(state_local->svir_prev,state_global->svir_prev);
608 copy_mat(state_local->fvir_prev,state_global->fvir_prev);
609 copy_mat(state_local->pres_prev,state_global->pres_prev);
613 /* Particle decomposition, collect the data on the master node */
614 if (mdof_flags & MDOF_CPT)
616 if (state_local->flags & (1<<estX)) MX(state_global->x);
617 if (state_local->flags & (1<<estV)) MX(state_global->v);
618 if (state_local->flags & (1<<estSDX)) MX(state_global->sd_X);
619 if (state_global->nrngi > 1) {
620 if (state_local->flags & (1<<estLD_RNG)) {
622 MPI_Gather(state_local->ld_rng ,
623 state_local->nrng*sizeof(state_local->ld_rng[0]),MPI_BYTE,
624 state_global->ld_rng,
625 state_local->nrng*sizeof(state_local->ld_rng[0]),MPI_BYTE,
626 MASTERRANK(cr),cr->mpi_comm_mygroup);
629 if (state_local->flags & (1<<estLD_RNGI))
632 MPI_Gather(state_local->ld_rngi,
633 sizeof(state_local->ld_rngi[0]),MPI_BYTE,
634 state_global->ld_rngi,
635 sizeof(state_local->ld_rngi[0]),MPI_BYTE,
636 MASTERRANK(cr),cr->mpi_comm_mygroup);
643 if (mdof_flags & (MDOF_X | MDOF_XTC)) MX(state_global->x);
644 if (mdof_flags & MDOF_V) MX(global_v);
646 if (mdof_flags & MDOF_F) MX(f_global);
652 if (mdof_flags & MDOF_CPT)
654 write_checkpoint(of->fn_cpt,of->bKeepAndNumCPT,
655 fplog,cr,of->eIntegrator,of->simulation_part,
656 of->bExpanded,of->elamstats,step,t,state_global);
659 if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
661 fwrite_trn(of->fp_trn,step,t,state_local->lambda[efptFEP],
662 state_local->box,top_global->natoms,
663 (mdof_flags & MDOF_X) ? state_global->x : NULL,
664 (mdof_flags & MDOF_V) ? global_v : NULL,
665 (mdof_flags & MDOF_F) ? f_global : NULL);
666 if (gmx_fio_flush(of->fp_trn) != 0)
668 gmx_file("Cannot write trajectory; maybe you are out of disk space?");
670 gmx_fio_check_file_position(of->fp_trn);
672 if (mdof_flags & MDOF_XTC) {
673 groups = &top_global->groups;
677 for(i=0; (i<top_global->natoms); i++)
679 if (ggrpnr(groups,egcXTC,i) == 0)
684 if (*n_xtc != top_global->natoms)
689 if (*n_xtc == top_global->natoms)
691 xxtc = state_global->x;
697 for(i=0; (i<top_global->natoms); i++)
699 if (ggrpnr(groups,egcXTC,i) == 0)
701 copy_rvec(state_global->x[i],xxtc[j++]);
705 if (write_xtc(of->fp_xtc,*n_xtc,step,t,
706 state_local->box,xxtc,of->xtc_prec) == 0)
708 gmx_fatal(FARGS,"XTC error - maybe you are out of disk space?");
710 gmx_fio_check_file_position(of->fp_xtc);