src/kernel/md_openmm.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
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  35
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <signal.h>
  41 #include <stdlib.h>
  42
  43 #include "typedefs.h"
  44 #include "smalloc.h"
  45 #include "sysstuff.h"
  46 #include "vec.h"
  47 #include "statutil.h"
  48 #include "vcm.h"
  49 #include "mdebin.h"
  50 #include "nrnb.h"
  51 #include "calcmu.h"
  52 #include "index.h"
  53 #include "vsite.h"
  54 #include "update.h"
  55 #include "ns.h"
  56 #include "trnio.h"
  57 #include "xtcio.h"
  58 #include "mdrun.h"
  59 #include "md_support.h"
  60 #include "confio.h"
  61 #include "network.h"
  62 #include "pull.h"
  63 #include "xvgr.h"
  64 #include "physics.h"
  65 #include "names.h"
  66 #include "xmdrun.h"
  67 #include "ionize.h"
  68 #include "disre.h"
  69 #include "orires.h"
  70 #include "pme.h"
  71 #include "mdatoms.h"
  72 #include "qmmm.h"
  73 #include "mpelogging.h"
  74 #include "domdec.h"
  75 #include "partdec.h"
  76 #include "topsort.h"
  77 #include "coulomb.h"
  78 #include "constr.h"
  79 #include "compute_io.h"
  80 #include "mvdata.h"
  81 #include "checkpoint.h"
  82 #include "mtop_util.h"
  83 #include "sighandler.h"
  84 #include "genborn.h"
  85 #include "string2.h"
  86 #include "copyrite.h"
  87 #include "membed.h"
  88
  89 #ifdef GMX_THREAD_MPI
  90 #include "tmpi.h"
  91 #endif
  92
  93 /* include even when OpenMM not used to force compilation of do_md_openmm */
  94 #include "openmm_wrapper.h"
  95
  96 double do_md_openmm(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
  97                     const output_env_t oenv, gmx_bool bVerbose,gmx_bool bCompact,
  98                     int nstglobalcomm,
  99                     gmx_vsite_t *vsite,gmx_constr_t constr,
 100                     int stepout,t_inputrec *ir,
 101                     gmx_mtop_t *top_global,
 102                     t_fcdata *fcd,
 103                     t_state *state_global,
 104                     t_mdatoms *mdatoms,
 105                     t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 106                     gmx_edsam_t ed,t_forcerec *fr,
 107                     int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
 108                     gmx_membed_t membed,
 109                     real cpt_period,real max_hours,
 110                     const char *deviceOptions,
 111                     unsigned long Flags,
 112                     gmx_runtime_t *runtime)
 113 {
 114     gmx_mdoutf_t *outf;
 115     gmx_large_int_t step,step_rel;
 116     double     run_time;
 117     double     t,t0,lam0;
 118     gmx_bool       bSimAnn,
 119     bFirstStep,bStateFromTPX,bLastStep,bStartingFromCpt;
 120     gmx_bool       bInitStep=TRUE;
 121     gmx_bool       do_ene,do_log, do_verbose,
 122     bX,bV,bF,bCPT;
 123     tensor     force_vir,shake_vir,total_vir,pres;
 124     int        i,m;
 125     int        mdof_flags;
 126     rvec       mu_tot;
 127     t_vcm      *vcm;
 128     int        nchkpt=1;
 129     gmx_localtop_t *top;
 130     t_mdebin *mdebin;
 131     t_state    *state=NULL;
 132     rvec       *f_global=NULL;
 133     int        n_xtc=-1;
 134     rvec       *x_xtc=NULL;
 135     gmx_enerdata_t *enerd;
 136     rvec       *f=NULL;
 137     gmx_global_stat_t gstat;
 138     gmx_update_t upd=NULL;
 139     t_graph    *graph=NULL;
 140     globsig_t   gs;
 141
 142     gmx_groups_t *groups;
 143     gmx_ekindata_t *ekind, *ekind_save;
 144     gmx_bool        bAppend;
 145     int         a0,a1;
 146     matrix      lastbox;
 147     real        reset_counters=0,reset_counters_now=0;
 148     char        sbuf[STEPSTRSIZE],sbuf2[STEPSTRSIZE];
 149     int         handled_stop_condition=gmx_stop_cond_none;
 150
 151     const char *ommOptions = NULL;
 152     void   *openmmData;
 153
 154 #ifdef GMX_DOUBLE
 155     /* Checks in cmake should prevent the compilation in double precision
 156      * with OpenMM, but just to be sure we check here.
 157      */
 158     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.");
 159 #endif
 160
 161     bAppend  = (Flags & MD_APPENDFILES);
 162     check_ir_old_tpx_versions(cr,fplog,ir,top_global);
 163
 164     groups = &top_global->groups;
 165
 166     /* Initial values */
 167     init_md(fplog,cr,ir,oenv,&t,&t0,state_global->lambda,
 168             &(state_global->fep_state),&lam0,
 169             nrnb,top_global,&upd,
 170             nfile,fnm,&outf,&mdebin,
 171             force_vir,shake_vir,mu_tot,&bSimAnn,&vcm,state_global,Flags);
 172
 173     clear_mat(total_vir);
 174     clear_mat(pres);
 175     /* Energy terms and groups */
 176     snew(enerd,1);
 177     init_enerdata(top_global->groups.grps[egcENER].nr,ir->fepvals->n_lambda,
 178                   enerd);
 179     snew(f,top_global->natoms);
 180
 181     /* Kinetic energy data */
 182     snew(ekind,1);
 183     init_ekindata(fplog,top_global,&(ir->opts),ekind);
 184     /* needed for iteration of constraints */
 185     snew(ekind_save,1);
 186     init_ekindata(fplog,top_global,&(ir->opts),ekind_save);
 187     /* Copy the cos acceleration to the groups struct */
 188     ekind->cosacc.cos_accel = ir->cos_accel;
 189
 190     gstat = global_stat_init(ir);
 191     debug_gmx();
 192
 193     {
 194         double io = compute_io(ir,top_global->natoms,groups,mdebin->ebin->nener,1);
 195         if ((io > 2000) && MASTER(cr))
 196             fprintf(stderr,
 197                     "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
 198                     io);
 199     }
 200
 201     top = gmx_mtop_generate_local_top(top_global,ir);
 202
 203     a0 = 0;
 204     a1 = top_global->natoms;
 205
 206     state = partdec_init_local_state(cr,state_global);
 207     f_global = f;
 208
 209     atoms2md(top_global,ir,0,NULL,a0,a1-a0,mdatoms);
 210
 211     if (vsite)
 212     {
 213         set_vsite_top(vsite,top,mdatoms,cr);
 214     }
 215
 216     if (ir->ePBC != epbcNONE && !ir->bPeriodicMols)
 217     {
 218         graph = mk_graph(fplog,&(top->idef),0,top_global->natoms,FALSE,FALSE);
 219     }
 220
 221     update_mdatoms(mdatoms,state->lambda[efptMASS]);
 222
 223     if (deviceOptions[0]=='\0')
 224     {
 225         /* empty options, which should default to OpenMM in this build */
 226         ommOptions=deviceOptions;
 227     }
 228     else
 229     {
 230         if (gmx_strncasecmp(deviceOptions,"OpenMM",6)!=0)
 231         {
 232             gmx_fatal(FARGS, "This Gromacs version currently only works with OpenMM. Use -device \"OpenMM:<options>\"");
 233         }
 234         else
 235         {
 236             ommOptions=strchr(deviceOptions,':');
 237             if (NULL!=ommOptions)
 238             {
 239                 /* Increase the pointer to skip the colon */
 240                 ommOptions++;
 241             }
 242         }
 243     }
 244
 245     openmmData = openmm_init(fplog, ommOptions, ir, top_global, top, mdatoms, fr, state);
 246     please_cite(fplog,"Friedrichs2009");
 247
 248     if (MASTER(cr))
 249     {
 250         /* Update mdebin with energy history if appending to output files */
 251         if ( Flags & MD_APPENDFILES )
 252         {
 253             restore_energyhistory_from_state(mdebin,&state_global->enerhist);
 254         }
 255         /* Set the initial energy history in state to zero by updating once */
 256         update_energyhistory(&state_global->enerhist,mdebin);
 257     }
 258
 259     if (constr)
 260     {
 261         set_constraints(constr,top,ir,mdatoms,cr);
 262     }
 263
 264     if (!ir->bContinuation)
 265     {
 266         if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
 267         {
 268             /* Set the velocities of frozen particles to zero */
 269             for (i=mdatoms->start; i<mdatoms->start+mdatoms->homenr; i++)
 270             {
 271                 for (m=0; m<DIM; m++)
 272                 {
 273                     if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
 274                     {
 275                         state->v[i][m] = 0;
 276                     }
 277                 }
 278             }
 279         }
 280
 281         if (constr)
 282         {
 283             /* Constrain the initial coordinates and velocities */
 284             do_constrain_first(fplog,constr,ir,mdatoms,state,f,
 285                                graph,cr,nrnb,fr,top,shake_vir);
 286         }
 287         if (vsite)
 288         {
 289             /* Construct the virtual sites for the initial configuration */
 290             construct_vsites(fplog,vsite,state->x,nrnb,ir->delta_t,NULL,
 291                              top->idef.iparams,top->idef.il,
 292                              fr->ePBC,fr->bMolPBC,graph,cr,state->box);
 293         }
 294     }
 295
 296     debug_gmx();
 297
 298     if (MASTER(cr))
 299     {
 300         char tbuf[20];
 301         fprintf(stderr,"starting mdrun '%s'\n",
 302                 *(top_global->name));
 303         if (ir->nsteps >= 0)
 304         {
 305             sprintf(tbuf,"%8.1f",(ir->init_step+ir->nsteps)*ir->delta_t);
 306         }
 307         else
 308         {
 309             sprintf(tbuf,"%s","infinite");
 310         }
 311         if (ir->init_step > 0)
 312         {
 313             fprintf(stderr,"%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
 314                     gmx_step_str(ir->init_step+ir->nsteps,sbuf),tbuf,
 315                     gmx_step_str(ir->init_step,sbuf2),
 316                     ir->init_step*ir->delta_t);
 317         }
 318         else
 319         {
 320             fprintf(stderr,"%s steps, %s ps.\n",
 321                     gmx_step_str(ir->nsteps,sbuf),tbuf);
 322         }
 323     }
 324
 325     fprintf(fplog,"\n");
 326
 327     /* Set and write start time */
 328     runtime_start(runtime);
 329     print_date_and_time(fplog,cr->nodeid,"Started mdrun",runtime);
 330     wallcycle_start(wcycle,ewcRUN);
 331     if (fplog)
 332         fprintf(fplog,"\n");
 333
 334     /* safest point to do file checkpointing is here.  More general point would be immediately before integrator call */
 335
 336     debug_gmx();
 337     /***********************************************************
 338      *
 339      *             Loop over MD steps
 340      *
 341      ************************************************************/
 342
 343     /* loop over MD steps or if rerunMD to end of input trajectory */
 344     bFirstStep = TRUE;
 345     /* Skip the first Nose-Hoover integration when we get the state from tpx */
 346     bStateFromTPX = !opt2bSet("-cpi",nfile,fnm);
 347     bInitStep = bFirstStep && bStateFromTPX;
 348     bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
 349     bLastStep = FALSE;
 350
 351     init_global_signals(&gs,cr,ir,repl_ex_nst);
 352
 353     step = ir->init_step;
 354     step_rel = 0;
 355
 356     while (!bLastStep)
 357     {
 358         wallcycle_start(wcycle,ewcSTEP);
 359
 360         GMX_MPE_LOG(ev_timestep1);
 361
 362         bLastStep = (step_rel == ir->nsteps);
 363         t = t0 + step*ir->delta_t;
 364
 365         if (gs.set[eglsSTOPCOND] != 0)
 366         {
 367             bLastStep = TRUE;
 368         }
 369
 370         do_log = do_per_step(step,ir->nstlog) || bFirstStep || bLastStep;
 371         do_verbose = bVerbose &&
 372                      (step % stepout == 0 || bFirstStep || bLastStep);
 373
 374         if (MASTER(cr) && do_log)
 375         {
 376             print_ebin_header(fplog,step,t,state->lambda[efptFEP]);
 377         }
 378
 379         clear_mat(force_vir);
 380         GMX_MPE_LOG(ev_timestep2);
 381
 382         /* We write a checkpoint at this MD step when:
 383          * either when we signalled through gs (in OpenMM NS works different),
 384          * or at the last step (but not when we do not want confout),
 385          * but never at the first step.
 386          */
 387         bCPT = ((gs.set[eglsCHKPT] ||
 388                  (bLastStep && (Flags & MD_CONFOUT))) &&
 389                 step > ir->init_step );
 390         if (bCPT)
 391         {
 392             gs.set[eglsCHKPT] = 0;
 393         }
 394
 395         /* Now we have the energies and forces corresponding to the
 396          * coordinates at time t. We must output all of this before
 397          * the update.
 398          * for RerunMD t is read from input trajectory
 399          */
 400         GMX_MPE_LOG(ev_output_start);
 401
 402         mdof_flags = 0;
 403         if (do_per_step(step,ir->nstxout))
 404         {
 405             mdof_flags |= MDOF_X;
 406         }
 407         if (do_per_step(step,ir->nstvout))
 408         {
 409             mdof_flags |= MDOF_V;
 410         }
 411         if (do_per_step(step,ir->nstfout))
 412         {
 413             mdof_flags |= MDOF_F;
 414         }
 415         if (do_per_step(step,ir->nstxtcout))
 416         {
 417             mdof_flags |= MDOF_XTC;
 418         }
 419         if (bCPT)
 420         {
 421             mdof_flags |= MDOF_CPT;
 422         };
 423         do_ene = (do_per_step(step,ir->nstenergy) || bLastStep);
 424
 425         if (mdof_flags != 0 || do_ene || do_log)
 426         {
 427             wallcycle_start(wcycle,ewcTRAJ);
 428             bF = (mdof_flags & MDOF_F);
 429             bX = (mdof_flags & (MDOF_X | MDOF_XTC | MDOF_CPT));
 430             bV = (mdof_flags & (MDOF_V | MDOF_CPT));
 431
 432             openmm_copy_state(openmmData, state, &t, f, enerd, bX, bV, bF, do_ene);
 433
 434             upd_mdebin(mdebin,FALSE,TRUE,
 435                        t,mdatoms->tmass,enerd,state,ir->fepvals,ir->expandedvals,lastbox,
 436                        shake_vir,force_vir,total_vir,pres,
 437                        ekind,mu_tot,constr);
 438             print_ebin(outf->fp_ene,do_ene,FALSE,FALSE,do_log?fplog:NULL,
 439                        step,t,
 440                        eprNORMAL,bCompact,mdebin,fcd,groups,&(ir->opts));
 441             write_traj(fplog,cr,outf,mdof_flags,top_global,
 442                        step,t,state,state_global,f,f_global,&n_xtc,&x_xtc);
 443             if (bCPT)
 444             {
 445                 nchkpt++;
 446                 bCPT = FALSE;
 447             }
 448             debug_gmx();
 449             if (bLastStep && step_rel == ir->nsteps &&
 450                     (Flags & MD_CONFOUT) && MASTER(cr))
 451             {
 452                 /* x and v have been collected in write_traj,
 453                  * because a checkpoint file will always be written
 454                  * at the last step.
 455                  */
 456                 fprintf(stderr,"\nWriting final coordinates.\n");
 457                 if (ir->ePBC != epbcNONE && !ir->bPeriodicMols)
 458                 {
 459                     /* Make molecules whole only for confout writing */
 460                     do_pbc_mtop(fplog,ir->ePBC,state->box,top_global,state_global->x);
 461                 }
 462                 write_sto_conf_mtop(ftp2fn(efSTO,nfile,fnm),
 463                                     *top_global->name,top_global,
 464                                     state_global->x,state_global->v,
 465                                     ir->ePBC,state->box);
 466                 debug_gmx();
 467             }
 468             wallcycle_stop(wcycle,ewcTRAJ);
 469         }
 470         GMX_MPE_LOG(ev_output_finish);
 471
 472
 473         /* Determine the wallclock run time up till now */
 474         run_time = gmx_gettime() - (double)runtime->real;
 475
 476         /* Check whether everything is still allright */
 477         if (((int)gmx_get_stop_condition() > handled_stop_condition)
 478 #ifdef GMX_THREAD_MPI
 479             && MASTER(cr)
 480 #endif
 481             )
 482         {
 483            /* this is just make gs.sig compatible with the hack
 484                of sending signals around by MPI_Reduce with together with
 485                other floats */
 486             /* NOTE: this only works for serial code. For code that allows
 487                MPI nodes to propagate their condition, see kernel/md.c*/
 488             if ( gmx_get_stop_condition() == gmx_stop_cond_next_ns )
 489                 gs.set[eglsSTOPCOND]=1;
 490             if ( gmx_get_stop_condition() == gmx_stop_cond_next )
 491                 gs.set[eglsSTOPCOND]=1;
 492             /* < 0 means stop at next step, > 0 means stop at next NS step */
 493             if (fplog)
 494             {
 495                 fprintf(fplog,
 496                         "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
 497                         gmx_get_signal_name(),
 498                         gs.sig[eglsSTOPCOND]==1 ? "NS " : "");
 499                 fflush(fplog);
 500             }
 501             fprintf(stderr,
 502                     "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
 503                     gmx_get_signal_name(),
 504                     gs.sig[eglsSTOPCOND]==1 ? "NS " : "");
 505             fflush(stderr);
 506             handled_stop_condition=(int)gmx_get_stop_condition();
 507         }
 508         else if (MASTER(cr) &&
 509                  (max_hours > 0 && run_time > max_hours*60.0*60.0*0.99) &&
 510                  gs.set[eglsSTOPCOND] == 0)
 511         {
 512             /* Signal to terminate the run */
 513             gs.set[eglsSTOPCOND] = 1;
 514             if (fplog)
 515             {
 516                 fprintf(fplog,"\nStep %s: Run time exceeded %.3f hours, will terminate the run\n",gmx_step_str(step,sbuf),max_hours*0.99);
 517             }
 518             fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n",gmx_step_str(step,sbuf),max_hours*0.99);
 519         }
 520
 521         /* checkpoints */
 522         if (MASTER(cr) && (cpt_period >= 0 &&
 523                            (cpt_period == 0 ||
 524                             run_time >= nchkpt*cpt_period*60.0)) &&
 525                 gs.set[eglsCHKPT] == 0)
 526         {
 527             gs.set[eglsCHKPT] = 1;
 528         }
 529
 530         /* Time for performance */
 531         if (((step % stepout) == 0) || bLastStep)
 532         {
 533             runtime_upd_proc(runtime);
 534         }
 535
 536         if (do_per_step(step,ir->nstlog))
 537         {
 538             if (fflush(fplog) != 0)
 539             {
 540                 gmx_fatal(FARGS,"Cannot flush logfile - maybe you are out of disk space?");
 541             }
 542         }
 543
 544         /* Remaining runtime */
 545         if (MULTIMASTER(cr) && (do_verbose || gmx_got_usr_signal() ))
 546         {
 547             print_time(stderr,runtime,step,ir,cr);
 548         }
 549
 550         bFirstStep = FALSE;
 551         bInitStep = FALSE;
 552         bStartingFromCpt = FALSE;
 553         step++;
 554         step_rel++;
 555
 556         openmm_take_one_step(openmmData);
 557     }
 558     /* End of main MD loop */
 559     debug_gmx();
 560
 561     /* Stop the time */
 562     runtime_end(runtime);
 563
 564     if (MASTER(cr))
 565     {
 566         if (ir->nstcalcenergy > 0)
 567         {
 568             print_ebin(outf->fp_ene,FALSE,FALSE,FALSE,fplog,step,t,
 569                        eprAVER,FALSE,mdebin,fcd,groups,&(ir->opts));
 570         }
 571     }
 572
 573     openmm_cleanup(fplog, openmmData);
 574
 575     done_mdoutf(outf);
 576
 577     debug_gmx();
 578
 579     runtime->nsteps_done = step_rel;
 580
 581     return 0;
 582 }