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44 #include "gmx_fatal.h"
67 #include "checkpoint.h"
71 typedef struct gmx_global_stat
78 gmx_global_stat_t global_stat_init(t_inputrec *ir)
85 snew(gs->itc0,ir->opts.ngtc);
86 snew(gs->itc1,ir->opts.ngtc);
91 void global_stat_destroy(gmx_global_stat_t gs)
99 static int filter_enerdterm(real *afrom, gmx_bool bToBuffer, real *ato,
100 gmx_bool bTemp, gmx_bool bPres, gmx_bool bEner) {
105 for (i=0;i<F_NRE;i++)
121 ato[to++] = afrom[from++];
129 ato[to++] = afrom[from++];
135 ato[to++] = afrom[from++];
144 void global_stat(FILE *fplog,gmx_global_stat_t gs,
145 t_commrec *cr,gmx_enerdata_t *enerd,
146 tensor fvir,tensor svir,rvec mu_tot,
147 t_inputrec *inputrec,
148 gmx_ekindata_t *ekind,gmx_constr_t constr,
151 gmx_mtop_t *top_global, t_state *state_local,
152 gmx_bool bSumEkinhOld, int flags)
153 /* instead of current system, gmx_booleans for summing virial, kinetic energy, and other terms */
157 int ie=0,ifv=0,isv=0,irmsd=0,imu=0;
158 int idedl=0,idvdll=0,idvdlnl=0,iepl=0,icm=0,imass=0,ica=0,inb=0;
160 int icj=-1,ici=-1,icx=-1;
162 real copyenerd[F_NRE];
164 real *rmsd_data=NULL;
166 gmx_bool bVV,bTemp,bEner,bPres,bConstrVir,bEkinAveVel,bFirstIterate,bReadEkin;
168 bVV = EI_VV(inputrec->eI);
169 bTemp = flags & CGLO_TEMPERATURE;
170 bEner = flags & CGLO_ENERGY;
171 bPres = (flags & CGLO_PRESSURE);
172 bConstrVir = (flags & CGLO_CONSTRAINT);
173 bFirstIterate = (flags & CGLO_FIRSTITERATE);
174 bEkinAveVel = (inputrec->eI==eiVV || (inputrec->eI==eiVVAK && bPres));
175 bReadEkin = (flags & CGLO_READEKIN);
183 /* This routine copies all the data to be summed to one big buffer
184 * using the t_bin struct.
187 /* First, we neeed to identify which enerd->term should be
188 communicated. Temperature and pressure terms should only be
189 communicated and summed when they need to be, to avoid repeating
190 the sums and overcounting. */
192 nener = filter_enerdterm(enerd->term,TRUE,copyenerd,bTemp,bPres,bEner);
194 /* First, the data that needs to be communicated with velocity verlet every time
195 This is just the constraint virial.*/
197 isv = add_binr(rb,DIM*DIM,svir[0]);
201 /* We need the force virial and the kinetic energy for the first time through with velocity verlet */
206 for(j=0; (j<inputrec->opts.ngtc); j++)
210 itc0[j]=add_binr(rb,DIM*DIM,ekind->tcstat[j].ekinh_old[0]);
212 if (bEkinAveVel && !bReadEkin)
214 itc1[j]=add_binr(rb,DIM*DIM,ekind->tcstat[j].ekinf[0]);
218 itc1[j]=add_binr(rb,DIM*DIM,ekind->tcstat[j].ekinh[0]);
221 /* these probably need to be put into one of these categories */
223 idedl = add_binr(rb,1,&(ekind->dekindl));
225 ica = add_binr(rb,1,&(ekind->cosacc.mvcos));
231 if ((bPres || !bVV) && bFirstIterate)
233 ifv = add_binr(rb,DIM*DIM,fvir[0]);
242 ie = add_binr(rb,nener,copyenerd);
247 rmsd_data = constr_rmsd_data(constr);
250 irmsd = add_binr(rb,inputrec->eI==eiSD2 ? 3 : 2,rmsd_data);
253 if (!NEED_MUTOT(*inputrec))
255 imu = add_binr(rb,DIM,mu_tot);
261 for(j=0; (j<egNR); j++)
263 inn[j]=add_binr(rb,enerd->grpp.nener,enerd->grpp.ener[j]);
266 if (inputrec->efep != efepNO)
268 idvdll = add_bind(rb,efptNR,enerd->dvdl_lin);
269 idvdlnl = add_bind(rb,efptNR,enerd->dvdl_nonlin);
270 if (enerd->n_lambda > 0)
272 iepl = add_bind(rb,enerd->n_lambda,enerd->enerpart_lambda);
280 icm = add_binr(rb,DIM*vcm->nr,vcm->group_p[0]);
282 imass = add_binr(rb,vcm->nr,vcm->group_mass);
284 if (vcm->mode == ecmANGULAR)
286 icj = add_binr(rb,DIM*vcm->nr,vcm->group_j[0]);
288 icx = add_binr(rb,DIM*vcm->nr,vcm->group_x[0]);
290 ici = add_binr(rb,DIM*DIM*vcm->nr,vcm->group_i[0][0]);
295 if (DOMAINDECOMP(cr))
297 nb = cr->dd->nbonded_local;
298 inb = add_bind(rb,1,&nb);
303 isig = add_binr(rb,nsig,sig);
306 /* Global sum it all */
309 fprintf(debug,"Summing %d energies\n",rb->maxreal);
314 /* Extract all the data locally */
318 extract_binr(rb,isv ,DIM*DIM,svir[0]);
321 /* We need the force virial and the kinetic energy for the first time through with velocity verlet */
326 for(j=0; (j<inputrec->opts.ngtc); j++)
330 extract_binr(rb,itc0[j],DIM*DIM,ekind->tcstat[j].ekinh_old[0]);
332 if (bEkinAveVel && !bReadEkin) {
333 extract_binr(rb,itc1[j],DIM*DIM,ekind->tcstat[j].ekinf[0]);
337 extract_binr(rb,itc1[j],DIM*DIM,ekind->tcstat[j].ekinh[0]);
340 extract_binr(rb,idedl,1,&(ekind->dekindl));
341 extract_binr(rb,ica,1,&(ekind->cosacc.mvcos));
345 if ((bPres || !bVV) && bFirstIterate)
347 extract_binr(rb,ifv ,DIM*DIM,fvir[0]);
354 extract_binr(rb,ie,nener,copyenerd);
357 extract_binr(rb,irmsd,inputrec->eI==eiSD2 ? 3 : 2,rmsd_data);
359 if (!NEED_MUTOT(*inputrec))
361 extract_binr(rb,imu,DIM,mu_tot);
364 for(j=0; (j<egNR); j++)
366 extract_binr(rb,inn[j],enerd->grpp.nener,enerd->grpp.ener[j]);
368 if (inputrec->efep != efepNO)
370 extract_bind(rb,idvdll ,efptNR,enerd->dvdl_lin);
371 extract_bind(rb,idvdlnl,efptNR,enerd->dvdl_nonlin);
372 if (enerd->n_lambda > 0)
374 extract_bind(rb,iepl,enerd->n_lambda,enerd->enerpart_lambda);
377 if (DOMAINDECOMP(cr))
379 extract_bind(rb,inb,1,&nb);
380 if ((int)(nb + 0.5) != cr->dd->nbonded_global)
382 dd_print_missing_interactions(fplog,cr,(int)(nb + 0.5),top_global,state_local);
387 filter_enerdterm(copyenerd,FALSE,enerd->term,bTemp,bPres,bEner);
393 extract_binr(rb,icm,DIM*vcm->nr,vcm->group_p[0]);
395 extract_binr(rb,imass,vcm->nr,vcm->group_mass);
397 if (vcm->mode == ecmANGULAR)
399 extract_binr(rb,icj,DIM*vcm->nr,vcm->group_j[0]);
401 extract_binr(rb,icx,DIM*vcm->nr,vcm->group_x[0]);
403 extract_binr(rb,ici,DIM*DIM*vcm->nr,vcm->group_i[0][0]);
410 extract_binr(rb,isig,nsig,sig);
415 int do_per_step(gmx_large_int_t step,gmx_large_int_t nstep)
418 return ((step % nstep)==0);
423 static void moveit(t_commrec *cr,
424 int left,int right,const char *s,rvec xx[])
429 move_rvecs(cr,FALSE,FALSE,left,right,
430 xx,NULL,(cr->nnodes-cr->npmenodes)-1,NULL);
433 gmx_mdoutf_t *init_mdoutf(int nfile,const t_filenm fnm[],int mdrun_flags,
434 const t_commrec *cr,const t_inputrec *ir,
435 const output_env_t oenv)
439 gmx_bool bAppendFiles;
449 of->eIntegrator = ir->eI;
450 of->bExpanded = ir->bExpanded;
451 of->elamstats = ir->expandedvals->elamstats;
452 of->simulation_part = ir->simulation_part;
456 bAppendFiles = (mdrun_flags & MD_APPENDFILES);
458 of->bKeepAndNumCPT = (mdrun_flags & MD_KEEPANDNUMCPT);
460 sprintf(filemode, bAppendFiles ? "a+" : "w+");
462 if ((EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
465 !(EI_DYNAMICS(ir->eI) &&
472 of->fp_trn = open_trn(ftp2fn(efTRN,nfile,fnm), filemode);
474 if (EI_DYNAMICS(ir->eI) &&
477 of->fp_xtc = open_xtc(ftp2fn(efXTC,nfile,fnm), filemode);
478 of->xtc_prec = ir->xtcprec;
480 if (EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
482 of->fp_ene = open_enx(ftp2fn(efEDR,nfile,fnm), filemode);
484 of->fn_cpt = opt2fn("-cpo",nfile,fnm);
486 if ((ir->efep != efepNO || ir->bSimTemp) && ir->fepvals->nstdhdl > 0 &&
487 (ir->fepvals->separate_dhdl_file == esepdhdlfileYES ) &&
492 of->fp_dhdl = gmx_fio_fopen(opt2fn("-dhdl",nfile,fnm),filemode);
496 of->fp_dhdl = open_dhdl(opt2fn("-dhdl",nfile,fnm),ir,oenv);
500 if (opt2bSet("-field",nfile,fnm) &&
501 (ir->ex[XX].n || ir->ex[YY].n || ir->ex[ZZ].n))
505 of->fp_dhdl = gmx_fio_fopen(opt2fn("-field",nfile,fnm),
510 of->fp_field = xvgropen(opt2fn("-field",nfile,fnm),
511 "Applied electric field","Time (ps)",
520 void done_mdoutf(gmx_mdoutf_t *of)
522 if (of->fp_ene != NULL)
524 close_enx(of->fp_ene);
528 close_xtc(of->fp_xtc);
532 close_trn(of->fp_trn);
534 if (of->fp_dhdl != NULL)
536 gmx_fio_fclose(of->fp_dhdl);
538 if (of->fp_field != NULL)
540 gmx_fio_fclose(of->fp_field);
546 void write_traj(FILE *fplog,t_commrec *cr,
549 gmx_mtop_t *top_global,
550 gmx_large_int_t step,double t,
551 t_state *state_local,t_state *state_global,
552 rvec *f_local,rvec *f_global,
553 int *n_xtc,rvec **x_xtc)
556 gmx_groups_t *groups;
561 #define MX(xvf) moveit(cr,GMX_LEFT,GMX_RIGHT,#xvf,xvf)
563 /* MRS -- defining these variables is to manage the difference
564 * between half step and full step velocities, but there must be a better way . . . */
566 local_v = state_local->v;
567 global_v = state_global->v;
569 if (DOMAINDECOMP(cr))
571 if (mdof_flags & MDOF_CPT)
573 dd_collect_state(cr->dd,state_local,state_global);
577 if (mdof_flags & (MDOF_X | MDOF_XTC))
579 dd_collect_vec(cr->dd,state_local,state_local->x,
582 if (mdof_flags & MDOF_V)
584 dd_collect_vec(cr->dd,state_local,local_v,
588 if (mdof_flags & MDOF_F)
590 dd_collect_vec(cr->dd,state_local,f_local,f_global);
595 if (mdof_flags & MDOF_CPT)
597 /* All pointers in state_local are equal to state_global,
598 * but we need to copy the non-pointer entries.
600 state_global->lambda = state_local->lambda;
601 state_global->veta = state_local->veta;
602 state_global->vol0 = state_local->vol0;
603 copy_mat(state_local->box,state_global->box);
604 copy_mat(state_local->boxv,state_global->boxv);
605 copy_mat(state_local->svir_prev,state_global->svir_prev);
606 copy_mat(state_local->fvir_prev,state_global->fvir_prev);
607 copy_mat(state_local->pres_prev,state_global->pres_prev);
611 /* Particle decomposition, collect the data on the master node */
612 if (mdof_flags & MDOF_CPT)
614 if (state_local->flags & (1<<estX)) MX(state_global->x);
615 if (state_local->flags & (1<<estV)) MX(state_global->v);
616 if (state_local->flags & (1<<estSDX)) MX(state_global->sd_X);
617 if (state_global->nrngi > 1) {
618 if (state_local->flags & (1<<estLD_RNG)) {
620 MPI_Gather(state_local->ld_rng ,
621 state_local->nrng*sizeof(state_local->ld_rng[0]),MPI_BYTE,
622 state_global->ld_rng,
623 state_local->nrng*sizeof(state_local->ld_rng[0]),MPI_BYTE,
624 MASTERRANK(cr),cr->mpi_comm_mygroup);
627 if (state_local->flags & (1<<estLD_RNGI))
630 MPI_Gather(state_local->ld_rngi,
631 sizeof(state_local->ld_rngi[0]),MPI_BYTE,
632 state_global->ld_rngi,
633 sizeof(state_local->ld_rngi[0]),MPI_BYTE,
634 MASTERRANK(cr),cr->mpi_comm_mygroup);
641 if (mdof_flags & (MDOF_X | MDOF_XTC)) MX(state_global->x);
642 if (mdof_flags & MDOF_V) MX(global_v);
644 if (mdof_flags & MDOF_F) MX(f_global);
650 if (mdof_flags & MDOF_CPT)
652 write_checkpoint(of->fn_cpt,of->bKeepAndNumCPT,
653 fplog,cr,of->eIntegrator,of->simulation_part,
654 of->bExpanded,of->elamstats,step,t,state_global);
657 if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
659 fwrite_trn(of->fp_trn,step,t,state_local->lambda[efptFEP],
660 state_local->box,top_global->natoms,
661 (mdof_flags & MDOF_X) ? state_global->x : NULL,
662 (mdof_flags & MDOF_V) ? global_v : NULL,
663 (mdof_flags & MDOF_F) ? f_global : NULL);
664 if (gmx_fio_flush(of->fp_trn) != 0)
666 gmx_file("Cannot write trajectory; maybe you are out of disk space?");
668 gmx_fio_check_file_position(of->fp_trn);
670 if (mdof_flags & MDOF_XTC) {
671 groups = &top_global->groups;
675 for(i=0; (i<top_global->natoms); i++)
677 if (ggrpnr(groups,egcXTC,i) == 0)
682 if (*n_xtc != top_global->natoms)
687 if (*n_xtc == top_global->natoms)
689 xxtc = state_global->x;
695 for(i=0; (i<top_global->natoms); i++)
697 if (ggrpnr(groups,egcXTC,i) == 0)
699 copy_rvec(state_global->x[i],xxtc[j++]);
703 if (write_xtc(of->fp_xtc,*n_xtc,step,t,
704 state_local->box,xxtc,of->xtc_prec) == 0)
706 gmx_fatal(FARGS,"XTC error - maybe you are out of disk space?");
708 gmx_fio_check_file_position(of->fp_xtc);