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33 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
78 #include "compute_io.h"
80 #include "checkpoint.h"
81 #include "mtop_util.h"
82 #include "sighandler.h"
92 /* include even when OpenMM not used to force compilation of do_md_openmm */
93 #include "openmm_wrapper.h"
95 double do_md_openmm(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
96 const output_env_t oenv, gmx_bool bVerbose,gmx_bool bCompact,
98 gmx_vsite_t *vsite,gmx_constr_t constr,
99 int stepout,t_inputrec *ir,
100 gmx_mtop_t *top_global,
102 t_state *state_global,
104 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
105 gmx_edsam_t ed,t_forcerec *fr,
106 int repl_ex_nst,int repl_ex_seed,
108 real cpt_period,real max_hours,
109 const char *deviceOptions,
111 gmx_runtime_t *runtime)
114 gmx_large_int_t step,step_rel;
118 bFirstStep,bStateFromTPX,bLastStep,bStartingFromCpt;
119 gmx_bool bInitStep=TRUE;
120 gmx_bool do_ene,do_log, do_verbose,
122 tensor force_vir,shake_vir,total_vir,pres;
134 gmx_enerdata_t *enerd;
136 gmx_global_stat_t gstat;
137 gmx_update_t upd=NULL;
141 gmx_groups_t *groups;
142 gmx_ekindata_t *ekind, *ekind_save;
146 real reset_counters=0,reset_counters_now=0;
147 char sbuf[STEPSTRSIZE],sbuf2[STEPSTRSIZE];
148 int handled_stop_condition=gmx_stop_cond_none;
150 const char *ommOptions = NULL;
154 /* Checks in cmake should prevent the compilation in double precision
155 * with OpenMM, but just to be sure we check here.
157 gmx_fatal(FARGS,"Compilation was performed in double precision, but OpenMM only supports single precision. If you want to use to OpenMM, compile in single precision.");
160 bAppend = (Flags & MD_APPENDFILES);
161 check_ir_old_tpx_versions(cr,fplog,ir,top_global);
163 groups = &top_global->groups;
166 init_md(fplog,cr,ir,oenv,&t,&t0,&state_global->lambda,&lam0,
167 nrnb,top_global,&upd,
168 nfile,fnm,&outf,&mdebin,
169 force_vir,shake_vir,mu_tot,&bSimAnn,&vcm,state_global,Flags);
171 clear_mat(total_vir);
173 /* Energy terms and groups */
175 init_enerdata(top_global->groups.grps[egcENER].nr,ir->n_flambda,enerd);
176 snew(f,top_global->natoms);
178 /* Kinetic energy data */
180 init_ekindata(fplog,top_global,&(ir->opts),ekind);
181 /* needed for iteration of constraints */
183 init_ekindata(fplog,top_global,&(ir->opts),ekind_save);
184 /* Copy the cos acceleration to the groups struct */
185 ekind->cosacc.cos_accel = ir->cos_accel;
187 gstat = global_stat_init(ir);
191 double io = compute_io(ir,top_global->natoms,groups,mdebin->ebin->nener,1);
192 if ((io > 2000) && MASTER(cr))
194 "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
198 top = gmx_mtop_generate_local_top(top_global,ir);
201 a1 = top_global->natoms;
203 state = partdec_init_local_state(cr,state_global);
206 atoms2md(top_global,ir,0,NULL,a0,a1-a0,mdatoms);
210 set_vsite_top(vsite,top,mdatoms,cr);
213 if (ir->ePBC != epbcNONE && !ir->bPeriodicMols)
215 graph = mk_graph(fplog,&(top->idef),0,top_global->natoms,FALSE,FALSE);
218 update_mdatoms(mdatoms,state->lambda);
220 if (deviceOptions[0]=='\0')
222 /* empty options, which should default to OpenMM in this build */
223 ommOptions=deviceOptions;
227 if (gmx_strncasecmp(deviceOptions,"OpenMM",6)!=0)
229 gmx_fatal(FARGS, "This Gromacs version currently only works with OpenMM. Use -device \"OpenMM:<options>\"");
233 ommOptions=strchr(deviceOptions,':');
234 if (NULL!=ommOptions)
236 /* Increase the pointer to skip the colon */
242 openmmData = openmm_init(fplog, ommOptions, ir, top_global, top, mdatoms, fr, state);
243 please_cite(fplog,"Friedrichs2009");
247 /* Update mdebin with energy history if appending to output files */
248 if ( Flags & MD_APPENDFILES )
250 restore_energyhistory_from_state(mdebin,&state_global->enerhist);
252 /* Set the initial energy history in state to zero by updating once */
253 update_energyhistory(&state_global->enerhist,mdebin);
258 set_constraints(constr,top,ir,mdatoms,cr);
261 if (!ir->bContinuation)
263 if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
265 /* Set the velocities of frozen particles to zero */
266 for (i=mdatoms->start; i<mdatoms->start+mdatoms->homenr; i++)
268 for (m=0; m<DIM; m++)
270 if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
280 /* Constrain the initial coordinates and velocities */
281 do_constrain_first(fplog,constr,ir,mdatoms,state,f,
282 graph,cr,nrnb,fr,top,shake_vir);
286 /* Construct the virtual sites for the initial configuration */
287 construct_vsites(fplog,vsite,state->x,nrnb,ir->delta_t,NULL,
288 top->idef.iparams,top->idef.il,
289 fr->ePBC,fr->bMolPBC,graph,cr,state->box);
298 fprintf(stderr,"starting mdrun '%s'\n",
299 *(top_global->name));
302 sprintf(tbuf,"%8.1f",(ir->init_step+ir->nsteps)*ir->delta_t);
306 sprintf(tbuf,"%s","infinite");
308 if (ir->init_step > 0)
310 fprintf(stderr,"%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
311 gmx_step_str(ir->init_step+ir->nsteps,sbuf),tbuf,
312 gmx_step_str(ir->init_step,sbuf2),
313 ir->init_step*ir->delta_t);
317 fprintf(stderr,"%s steps, %s ps.\n",
318 gmx_step_str(ir->nsteps,sbuf),tbuf);
324 /* Set and write start time */
325 runtime_start(runtime);
326 print_date_and_time(fplog,cr->nodeid,"Started mdrun",runtime);
327 wallcycle_start(wcycle,ewcRUN);
331 /* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
334 /***********************************************************
338 ************************************************************/
340 /* loop over MD steps or if rerunMD to end of input trajectory */
342 /* Skip the first Nose-Hoover integration when we get the state from tpx */
343 bStateFromTPX = !opt2bSet("-cpi",nfile,fnm);
344 bInitStep = bFirstStep && bStateFromTPX;
345 bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
348 init_global_signals(&gs,cr,ir,repl_ex_nst);
350 step = ir->init_step;
355 wallcycle_start(wcycle,ewcSTEP);
357 bLastStep = (step_rel == ir->nsteps);
358 t = t0 + step*ir->delta_t;
360 if (gs.set[eglsSTOPCOND] != 0)
365 do_log = do_per_step(step,ir->nstlog) || bFirstStep || bLastStep;
366 do_verbose = bVerbose &&
367 (step % stepout == 0 || bFirstStep || bLastStep);
369 if (MASTER(cr) && do_log)
371 print_ebin_header(fplog,step,t,state->lambda);
374 clear_mat(force_vir);
376 /* We write a checkpoint at this MD step when:
377 * either when we signalled through gs (in OpenMM NS works different),
378 * or at the last step (but not when we do not want confout),
379 * but never at the first step.
381 bCPT = ((gs.set[eglsCHKPT] ||
382 (bLastStep && (Flags & MD_CONFOUT))) &&
383 step > ir->init_step );
386 gs.set[eglsCHKPT] = 0;
389 /* Now we have the energies and forces corresponding to the
390 * coordinates at time t. We must output all of this before
392 * for RerunMD t is read from input trajectory
395 if (do_per_step(step,ir->nstxout))
397 mdof_flags |= MDOF_X;
399 if (do_per_step(step,ir->nstvout))
401 mdof_flags |= MDOF_V;
403 if (do_per_step(step,ir->nstfout))
405 mdof_flags |= MDOF_F;
407 if (do_per_step(step,ir->nstxtcout))
409 mdof_flags |= MDOF_XTC;
413 mdof_flags |= MDOF_CPT;
415 do_ene = (do_per_step(step,ir->nstenergy) || bLastStep);
417 if (mdof_flags != 0 || do_ene || do_log)
419 wallcycle_start(wcycle,ewcTRAJ);
420 bF = (mdof_flags & MDOF_F);
421 bX = (mdof_flags & (MDOF_X | MDOF_XTC | MDOF_CPT));
422 bV = (mdof_flags & (MDOF_V | MDOF_CPT));
424 openmm_copy_state(openmmData, state, &t, f, enerd, bX, bV, bF, do_ene);
426 upd_mdebin(mdebin,FALSE,TRUE,
427 t,mdatoms->tmass,enerd,state,lastbox,
428 shake_vir,force_vir,total_vir,pres,
429 ekind,mu_tot,constr);
430 print_ebin(outf->fp_ene,do_ene,FALSE,FALSE,do_log?fplog:NULL,
432 eprNORMAL,bCompact,mdebin,fcd,groups,&(ir->opts));
433 write_traj(fplog,cr,outf,mdof_flags,top_global,
434 step,t,state,state_global,f,f_global,&n_xtc,&x_xtc);
441 if (bLastStep && step_rel == ir->nsteps &&
442 (Flags & MD_CONFOUT) && MASTER(cr))
444 /* x and v have been collected in write_traj,
445 * because a checkpoint file will always be written
448 fprintf(stderr,"\nWriting final coordinates.\n");
449 if (ir->ePBC != epbcNONE && !ir->bPeriodicMols)
451 /* Make molecules whole only for confout writing */
452 do_pbc_mtop(fplog,ir->ePBC,state->box,top_global,state_global->x);
454 write_sto_conf_mtop(ftp2fn(efSTO,nfile,fnm),
455 *top_global->name,top_global,
456 state_global->x,state_global->v,
457 ir->ePBC,state->box);
460 wallcycle_stop(wcycle,ewcTRAJ);
463 /* Determine the wallclock run time up till now */
464 run_time = gmx_gettime() - (double)runtime->real;
466 /* Check whether everything is still allright */
467 if (((int)gmx_get_stop_condition() > handled_stop_condition)
468 #ifdef GMX_THREAD_MPI
473 /* this is just make gs.sig compatible with the hack
474 of sending signals around by MPI_Reduce with together with
476 /* NOTE: this only works for serial code. For code that allows
477 MPI nodes to propagate their condition, see kernel/md.c*/
478 if ( gmx_get_stop_condition() == gmx_stop_cond_next_ns )
479 gs.set[eglsSTOPCOND]=1;
480 if ( gmx_get_stop_condition() == gmx_stop_cond_next )
481 gs.set[eglsSTOPCOND]=1;
482 /* < 0 means stop at next step, > 0 means stop at next NS step */
486 "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
487 gmx_get_signal_name(),
488 gs.sig[eglsSTOPCOND]==1 ? "NS " : "");
492 "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
493 gmx_get_signal_name(),
494 gs.sig[eglsSTOPCOND]==1 ? "NS " : "");
496 handled_stop_condition=(int)gmx_get_stop_condition();
498 else if (MASTER(cr) &&
499 (max_hours > 0 && run_time > max_hours*60.0*60.0*0.99) &&
500 gs.set[eglsSTOPCOND] == 0)
502 /* Signal to terminate the run */
503 gs.set[eglsSTOPCOND] = 1;
506 fprintf(fplog,"\nStep %s: Run time exceeded %.3f hours, will terminate the run\n",gmx_step_str(step,sbuf),max_hours*0.99);
508 fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n",gmx_step_str(step,sbuf),max_hours*0.99);
512 if (MASTER(cr) && (cpt_period >= 0 &&
514 run_time >= nchkpt*cpt_period*60.0)) &&
515 gs.set[eglsCHKPT] == 0)
517 gs.set[eglsCHKPT] = 1;
520 /* Time for performance */
521 if (((step % stepout) == 0) || bLastStep)
523 runtime_upd_proc(runtime);
526 if (do_per_step(step,ir->nstlog))
528 if (fflush(fplog) != 0)
530 gmx_fatal(FARGS,"Cannot flush logfile - maybe you are out of disk space?");
534 /* Remaining runtime */
535 if (MULTIMASTER(cr) && (do_verbose || gmx_got_usr_signal() ))
537 print_time(stderr,runtime,step,ir,cr);
542 bStartingFromCpt = FALSE;
546 openmm_take_one_step(openmmData);
548 /* End of main MD loop */
552 runtime_end(runtime);
556 if (ir->nstcalcenergy > 0)
558 print_ebin(outf->fp_ene,FALSE,FALSE,FALSE,fplog,step,t,
559 eprAVER,FALSE,mdebin,fcd,groups,&(ir->opts));
563 openmm_cleanup(fplog, openmmData);
569 runtime->nsteps_done = step_rel;