src/gromacs/mdrun/mimic.cpp

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   4  * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
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  35
  36 /*! \internal \file
  37  *
  38  * \brief Declares the loop for MiMiC QM/MM
  39  *
  40  * \author Viacheslav Bolnykh <v.bolnykh@hpc-leap.eu>
  41  * \ingroup module_mdrun
  42  */
  43 #include "gmxpre.h"
  44
  45 #include <cinttypes>
  46 #include <cmath>
  47 #include <cstdio>
  48 #include <cstdlib>
  49
  50 #include <algorithm>
  51 #include <memory>
  52
  53 #include "gromacs/applied_forces/awh/awh.h"
  54 #include "gromacs/commandline/filenm.h"
  55 #include "gromacs/domdec/collect.h"
  56 #include "gromacs/domdec/dlbtiming.h"
  57 #include "gromacs/domdec/domdec.h"
  58 #include "gromacs/domdec/domdec_network.h"
  59 #include "gromacs/domdec/domdec_struct.h"
  60 #include "gromacs/domdec/mdsetup.h"
  61 #include "gromacs/domdec/partition.h"
  62 #include "gromacs/essentialdynamics/edsam.h"
  63 #include "gromacs/ewald/pme_load_balancing.h"
  64 #include "gromacs/ewald/pme_pp.h"
  65 #include "gromacs/fileio/trxio.h"
  66 #include "gromacs/gmxlib/network.h"
  67 #include "gromacs/gmxlib/nrnb.h"
  68 #include "gromacs/gpu_utils/gpu_utils.h"
  69 #include "gromacs/listed_forces/listed_forces.h"
  70 #include "gromacs/math/functions.h"
  71 #include "gromacs/math/utilities.h"
  72 #include "gromacs/math/vec.h"
  73 #include "gromacs/math/vectypes.h"
  74 #include "gromacs/mdlib/checkpointhandler.h"
  75 #include "gromacs/mdlib/compute_io.h"
  76 #include "gromacs/mdlib/constr.h"
  77 #include "gromacs/mdlib/ebin.h"
  78 #include "gromacs/mdlib/enerdata_utils.h"
  79 #include "gromacs/mdlib/energyoutput.h"
  80 #include "gromacs/mdlib/expanded.h"
  81 #include "gromacs/mdlib/force.h"
  82 #include "gromacs/mdlib/force_flags.h"
  83 #include "gromacs/mdlib/forcerec.h"
  84 #include "gromacs/mdlib/freeenergyparameters.h"
  85 #include "gromacs/mdlib/md_support.h"
  86 #include "gromacs/mdlib/mdatoms.h"
  87 #include "gromacs/mdlib/mdoutf.h"
  88 #include "gromacs/mdlib/membed.h"
  89 #include "gromacs/mdlib/resethandler.h"
  90 #include "gromacs/mdlib/sighandler.h"
  91 #include "gromacs/mdlib/simulationsignal.h"
  92 #include "gromacs/mdlib/stat.h"
  93 #include "gromacs/mdlib/stophandler.h"
  94 #include "gromacs/mdlib/tgroup.h"
  95 #include "gromacs/mdlib/trajectory_writing.h"
  96 #include "gromacs/mdlib/update.h"
  97 #include "gromacs/mdlib/vcm.h"
  98 #include "gromacs/mdlib/vsite.h"
  99 #include "gromacs/mdrunutility/handlerestart.h"
 100 #include "gromacs/mdrunutility/multisim.h"
 101 #include "gromacs/mdrunutility/printtime.h"
 102 #include "gromacs/mdtypes/awh_history.h"
 103 #include "gromacs/mdtypes/awh_params.h"
 104 #include "gromacs/mdtypes/commrec.h"
 105 #include "gromacs/mdtypes/df_history.h"
 106 #include "gromacs/mdtypes/enerdata.h"
 107 #include "gromacs/mdtypes/energyhistory.h"
 108 #include "gromacs/mdtypes/forcebuffers.h"
 109 #include "gromacs/mdtypes/forcerec.h"
 110 #include "gromacs/mdtypes/group.h"
 111 #include "gromacs/mdtypes/inputrec.h"
 112 #include "gromacs/mdtypes/interaction_const.h"
 113 #include "gromacs/mdtypes/md_enums.h"
 114 #include "gromacs/mdtypes/mdatom.h"
 115 #include "gromacs/mdtypes/mdrunoptions.h"
 116 #include "gromacs/mdtypes/observableshistory.h"
 117 #include "gromacs/mdtypes/state.h"
 118 #include "gromacs/mimic/communicator.h"
 119 #include "gromacs/mimic/utilities.h"
 120 #include "gromacs/pbcutil/pbc.h"
 121 #include "gromacs/pulling/pull.h"
 122 #include "gromacs/timing/wallcycle.h"
 123 #include "gromacs/timing/walltime_accounting.h"
 124 #include "gromacs/topology/atoms.h"
 125 #include "gromacs/topology/idef.h"
 126 #include "gromacs/topology/mtop_util.h"
 127 #include "gromacs/topology/topology.h"
 128 #include "gromacs/trajectory/trajectoryframe.h"
 129 #include "gromacs/utility/basedefinitions.h"
 130 #include "gromacs/utility/cstringutil.h"
 131 #include "gromacs/utility/fatalerror.h"
 132 #include "gromacs/utility/logger.h"
 133 #include "gromacs/utility/real.h"
 134 #include "gromacs/utility/smalloc.h"
 135
 136 #include "legacysimulator.h"
 137 #include "replicaexchange.h"
 138 #include "shellfc.h"
 139
 140 using gmx::SimulationSignaller;
 141
 142 void gmx::LegacySimulator::do_mimic()
 143 {
 144     t_inputrec*       ir = inputrec;
 145     int64_t           step, step_rel;
 146     double            t;
 147     bool              isLastStep               = false;
 148     bool              doFreeEnergyPerturbation = false;
 149     unsigned int      force_flags;
 150     tensor            force_vir, shake_vir, total_vir, pres;
 151     rvec              mu_tot;
 152     ForceBuffers      f;
 153     gmx_global_stat_t gstat;
 154     gmx_shellfc_t*    shellfc;
 155
 156     double cycles;
 157
 158     /* Domain decomposition could incorrectly miss a bonded
 159        interaction, but checking for that requires a global
 160        communication stage, which does not otherwise happen in DD
 161        code. So we do that alongside the first global energy reduction
 162        after a new DD is made. These variables handle whether the
 163        check happens, and the result it returns. */
 164     bool shouldCheckNumberOfBondedInteractions = false;
 165     int  totalNumberOfBondedInteractions       = -1;
 166
 167     SimulationSignals signals;
 168     // Most global communnication stages don't propagate mdrun
 169     // signals, and will use this object to achieve that.
 170     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 171
 172     if (ir->bExpanded)
 173     {
 174         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 175     }
 176     if (ir->bSimTemp)
 177     {
 178         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 179     }
 180     if (ir->bDoAwh)
 181     {
 182         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 183     }
 184     if (replExParams.exchangeInterval > 0)
 185     {
 186         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 187     }
 188     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 189     {
 190         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 191     }
 192     if (ir->bIMD)
 193     {
 194         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 195     }
 196     if (isMultiSim(ms))
 197     {
 198         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 199     }
 200     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
 201                     [](int i) { return i != eannNO; }))
 202     {
 203         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 204     }
 205
 206     /* Settings for rerun */
 207     ir->nstlist              = 1;
 208     ir->nstcalcenergy        = 1;
 209     int        nstglobalcomm = 1;
 210     const bool bNS           = true;
 211
 212     if (MASTER(cr))
 213     {
 214         MimicCommunicator::init();
 215         auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(top_global);
 216         MimicCommunicator::sendInitData(nonConstGlobalTopology, state_global->x);
 217         ir->nsteps = MimicCommunicator::getStepNumber();
 218     }
 219
 220     ir->nstxout_compressed         = 0;
 221     const SimulationGroups* groups = &top_global->groups;
 222     {
 223         auto nonConstGlobalTopology                          = const_cast<gmx_mtop_t*>(top_global);
 224         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 225     }
 226
 227     initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda);
 228
 229     const bool        simulationsShareState = false;
 230     gmx_mdoutf*       outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
 231                                    mdModulesNotifier, ir, top_global, oenv, wcycle,
 232                                    StartingBehavior::NewSimulation, simulationsShareState, ms);
 233     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
 234                                    mdoutf_get_fp_dhdl(outf), true, StartingBehavior::NewSimulation,
 235                                    mdModulesNotifier);
 236
 237     gstat = global_stat_init(ir);
 238
 239     /* Check for polarizable models and flexible constraints */
 240     shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
 241                                  ir->nstcalcenergy, DOMAINDECOMP(cr));
 242
 243     {
 244         double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
 245         if ((io > 2000) && MASTER(cr))
 246         {
 247             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 248         }
 249     }
 250
 251     // Local state only becomes valid now.
 252     std::unique_ptr<t_state> stateInstance;
 253     t_state*                 state;
 254
 255     gmx_localtop_t top(top_global->ffparams);
 256
 257     if (DOMAINDECOMP(cr))
 258     {
 259         stateInstance = std::make_unique<t_state>();
 260         state         = stateInstance.get();
 261         dd_init_local_state(cr->dd, state_global, state);
 262
 263         /* Distribute the charge groups over the nodes from the master node */
 264         dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
 265                             imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
 266                             nrnb, nullptr, FALSE);
 267         shouldCheckNumberOfBondedInteractions = true;
 268         gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr->mpi_comm_mygroup);
 269     }
 270     else
 271     {
 272         state_change_natoms(state_global, state_global->natoms);
 273         /* Copy the pointer to the global state */
 274         state = state_global;
 275
 276         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 277     }
 278
 279     auto mdatoms = mdAtoms->mdatoms();
 280
 281     // NOTE: The global state is no longer used at this point.
 282     // But state_global is still used as temporary storage space for writing
 283     // the global state to file and potentially for replica exchange.
 284     // (Global topology should persist.)
 285
 286     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 287
 288     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 289     {
 290         doFreeEnergyPerturbation = true;
 291     }
 292
 293     {
 294         int cglo_flags =
 295                 (CGLO_GSTAT
 296                  | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 297         bool   bSumEkinhOld = false;
 298         t_vcm* vcm          = nullptr;
 299         compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
 300                         makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
 301                         force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
 302                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 303     }
 304     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
 305                                     makeConstArrayRef(state->x), state->box,
 306                                     &shouldCheckNumberOfBondedInteractions);
 307
 308     if (MASTER(cr))
 309     {
 310         fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global->name));
 311         if (mdrunOptions.verbose)
 312         {
 313             fprintf(stderr,
 314                     "Calculated time to finish depends on nsteps from "
 315                     "run input file,\nwhich may not correspond to the time "
 316                     "needed to process input trajectory.\n\n");
 317         }
 318         fprintf(fplog, "\n");
 319     }
 320
 321     walltime_accounting_start_time(walltime_accounting);
 322     wallcycle_start(wcycle, ewcRUN);
 323     print_start(fplog, cr, walltime_accounting, "mdrun");
 324
 325     /***********************************************************
 326      *
 327      *             Loop over MD steps
 328      *
 329      ************************************************************/
 330
 331     if (constr)
 332     {
 333         GMX_LOG(mdlog.info)
 334                 .asParagraph()
 335                 .appendText(
 336                         "Simulations has constraints. Constraints will "
 337                         "be handled by CPMD.");
 338     }
 339
 340     GMX_LOG(mdlog.info)
 341             .asParagraph()
 342             .appendText(
 343                     "MiMiC does not report kinetic energy, total energy, temperature, virial and "
 344                     "pressure.");
 345
 346     step     = ir->init_step;
 347     step_rel = 0;
 348
 349     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 350             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false, MASTER(cr),
 351             ir->nstlist, mdrunOptions.reproducible, nstglobalcomm, mdrunOptions.maximumHoursToRun,
 352             ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 353
 354     // we don't do counter resetting in rerun - finish will always be valid
 355     walltime_accounting_set_valid_finish(walltime_accounting);
 356
 357     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 358
 359     /* and stop now if we should */
 360     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 361     while (!isLastStep)
 362     {
 363         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 364         wallcycle_start(wcycle, ewcSTEP);
 365
 366         t = step;
 367
 368         if (MASTER(cr))
 369         {
 370             MimicCommunicator::getCoords(&state_global->x, state_global->natoms);
 371         }
 372
 373         if (ir->efep != efepNO)
 374         {
 375             state->lambda = currentLambdas(step, *(ir->fepvals), state_global->fep_state);
 376         }
 377
 378         if (MASTER(cr))
 379         {
 380             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 381             if (constructVsites && DOMAINDECOMP(cr))
 382             {
 383                 gmx_fatal(FARGS,
 384                           "Vsite recalculation with -rerun is not implemented with domain "
 385                           "decomposition, "
 386                           "use a single rank");
 387             }
 388         }
 389
 390         if (DOMAINDECOMP(cr))
 391         {
 392             /* Repartition the domain decomposition */
 393             const bool bMasterState = true;
 394             dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
 395                                 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
 396                                 fr, vsite, constr, nrnb, wcycle, mdrunOptions.verbose);
 397             shouldCheckNumberOfBondedInteractions = true;
 398         }
 399
 400         if (MASTER(cr))
 401         {
 402             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 403         }
 404
 405         if (ir->efep != efepNO)
 406         {
 407             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 408         }
 409
 410         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 411                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
 412                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 413
 414         if (shellfc)
 415         {
 416             /* Now is the time to relax the shells */
 417             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
 418                                 imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
 419                                 state->natoms, state->x.arrayRefWithPadding(),
 420                                 state->v.arrayRefWithPadding(), state->box, state->lambda,
 421                                 &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
 422                                 fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
 423         }
 424         else
 425         {
 426             /* The coordinates (x) are shifted (to get whole molecules)
 427              * in do_force.
 428              * This is parallellized as well, and does communication too.
 429              * Check comments in sim_util.c
 430              */
 431             Awh*       awh = nullptr;
 432             gmx_edsam* ed  = nullptr;
 433             do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
 434                      wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
 435                      &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
 436                      vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
 437         }
 438
 439         /* Now we have the energies and forces corresponding to the
 440          * coordinates at time t.
 441          */
 442         {
 443             const bool isCheckpointingStep = false;
 444             const bool doRerun             = false;
 445             const bool bSumEkinhOld        = false;
 446             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
 447                                      state_global, observablesHistory, top_global, fr, outf,
 448                                      energyOutput, ekind, f.view().force(), isCheckpointingStep,
 449                                      doRerun, isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
 450         }
 451
 452         stopHandler->setSignal();
 453
 454         if (vsite != nullptr)
 455         {
 456             wallcycle_start(wcycle, ewcVSITECONSTR);
 457             vsite->construct(state->x, ir->delta_t, state->v, state->box);
 458             wallcycle_stop(wcycle, ewcVSITECONSTR);
 459         }
 460
 461         {
 462             const bool          doInterSimSignal = false;
 463             const bool          doIntraSimSignal = true;
 464             bool                bSumEkinhOld     = false;
 465             t_vcm*              vcm              = nullptr;
 466             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 467
 468             compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
 469                             makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
 470                             enerd, nullptr, nullptr, nullptr, nullptr, constr, &signaller,
 471                             state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
 472                             CGLO_GSTAT | CGLO_ENERGY
 473                                     | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
 474                                                                              : 0));
 475             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
 476                                             &top, makeConstArrayRef(state->x), state->box,
 477                                             &shouldCheckNumberOfBondedInteractions);
 478         }
 479
 480         {
 481             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 482             gmx::ArrayRef<gmx::RVec>       ftemp;
 483             gmx::ArrayRef<const gmx::RVec> flocal = f.view().force();
 484             if (DOMAINDECOMP(cr))
 485             {
 486                 ftemp = gmx::makeArrayRef(fglobal);
 487                 dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl,
 488                                flocal, ftemp);
 489             }
 490             else
 491             {
 492                 ftemp = f.view().force();
 493             }
 494
 495             if (MASTER(cr))
 496             {
 497                 MimicCommunicator::sendEnergies(enerd->term[F_EPOT]);
 498                 MimicCommunicator::sendForces(ftemp, state_global->natoms);
 499             }
 500         }
 501
 502
 503         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 504            the virial that should probably be addressed eventually. state->veta has better properies,
 505            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 506            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 507
 508         if (ir->efep != efepNO)
 509         {
 510             /* Sum up the foreign energy and dhdl terms for md and sd.
 511                Currently done every step so that dhdl is correct in the .edr */
 512             accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
 513         }
 514
 515         /* Output stuff */
 516         if (MASTER(cr))
 517         {
 518             const bool bCalcEnerStep = true;
 519             energyOutput.addDataAtEnergyStep(
 520                     doFreeEnergyPerturbation, bCalcEnerStep, t, mdatoms->tmass, enerd, ir->fepvals,
 521                     ir->expandedvals, state->box,
 522                     PTCouplingArrays({ state->boxv, state->nosehoover_xi, state->nosehoover_vxi,
 523                                        state->nhpres_xi, state->nhpres_vxi }),
 524                     state->fep_state, shake_vir, force_vir, total_vir, pres, ekind, mu_tot, constr);
 525
 526             const bool do_ene = true;
 527             const bool do_log = true;
 528             Awh*       awh    = nullptr;
 529             const bool do_dr  = ir->nstdisreout != 0;
 530             const bool do_or  = ir->nstorireout != 0;
 531
 532             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 533             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
 534                                                do_log ? fplog : nullptr, step, t, fr->fcdata.get(), awh);
 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
 545         /* Print the remaining wall clock time for the run */
 546         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 547         {
 548             if (shellfc)
 549             {
 550                 fprintf(stderr, "\n");
 551             }
 552             print_time(stderr, walltime_accounting, step, ir, cr);
 553         }
 554
 555         cycles = wallcycle_stop(wcycle, ewcSTEP);
 556         if (DOMAINDECOMP(cr) && wcycle)
 557         {
 558             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 559         }
 560
 561         /* increase the MD step number */
 562         step++;
 563         step_rel++;
 564     }
 565     /* End of main MD loop */
 566
 567     /* Closing TNG files can include compressing data. Therefore it is good to do that
 568      * before stopping the time measurements. */
 569     mdoutf_tng_close(outf);
 570
 571     /* Stop measuring walltime */
 572     walltime_accounting_end_time(walltime_accounting);
 573
 574     if (MASTER(cr))
 575     {
 576         MimicCommunicator::finalize();
 577     }
 578
 579     if (!thisRankHasDuty(cr, DUTY_PME))
 580     {
 581         /* Tell the PME only node to finish */
 582         gmx_pme_send_finish(cr);
 583     }
 584
 585     done_mdoutf(outf);
 586
 587     done_shellfc(fplog, shellfc, step_rel);
 588
 589     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 590 }