src/gromacs/mdrun/mimic.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018,2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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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/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/partition.h"
  61 #include "gromacs/essentialdynamics/edsam.h"
  62 #include "gromacs/ewald/pme.h"
  63 #include "gromacs/ewald/pme_load_balancing.h"
  64 #include "gromacs/fileio/trxio.h"
  65 #include "gromacs/gmxlib/network.h"
  66 #include "gromacs/gmxlib/nrnb.h"
  67 #include "gromacs/gpu_utils/gpu_utils.h"
  68 #include "gromacs/imd/imd.h"
  69 #include "gromacs/listed_forces/manage_threading.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/energyoutput.h"
  79 #include "gromacs/mdlib/expanded.h"
  80 #include "gromacs/mdlib/force.h"
  81 #include "gromacs/mdlib/force_flags.h"
  82 #include "gromacs/mdlib/forcerec.h"
  83 #include "gromacs/mdlib/md_support.h"
  84 #include "gromacs/mdlib/mdatoms.h"
  85 #include "gromacs/mdlib/mdoutf.h"
  86 #include "gromacs/mdlib/mdrun.h"
  87 #include "gromacs/mdlib/mdsetup.h"
  88 #include "gromacs/mdlib/membed.h"
  89 #include "gromacs/mdlib/ns.h"
  90 #include "gromacs/mdlib/resethandler.h"
  91 #include "gromacs/mdlib/shellfc.h"
  92 #include "gromacs/mdlib/sighandler.h"
  93 #include "gromacs/mdlib/sim_util.h"
  94 #include "gromacs/mdlib/simulationsignal.h"
  95 #include "gromacs/mdlib/stophandler.h"
  96 #include "gromacs/mdlib/tgroup.h"
  97 #include "gromacs/mdlib/trajectory_writing.h"
  98 #include "gromacs/mdlib/update.h"
  99 #include "gromacs/mdlib/vcm.h"
 100 #include "gromacs/mdlib/vsite.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/fcdata.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/observableshistory.h"
 116 #include "gromacs/mdtypes/state.h"
 117 #include "gromacs/mimic/MimicCommunicator.h"
 118 #include "gromacs/mimic/MimicUtils.h"
 119 #include "gromacs/pbcutil/mshift.h"
 120 #include "gromacs/pbcutil/pbc.h"
 121 #include "gromacs/pulling/pull.h"
 122 #include "gromacs/swap/swapcoords.h"
 123 #include "gromacs/timing/wallcycle.h"
 124 #include "gromacs/timing/walltime_accounting.h"
 125 #include "gromacs/topology/atoms.h"
 126 #include "gromacs/topology/idef.h"
 127 #include "gromacs/topology/mtop_util.h"
 128 #include "gromacs/topology/topology.h"
 129 #include "gromacs/trajectory/trajectoryframe.h"
 130 #include "gromacs/utility/basedefinitions.h"
 131 #include "gromacs/utility/cstringutil.h"
 132 #include "gromacs/utility/fatalerror.h"
 133 #include "gromacs/utility/logger.h"
 134 #include "gromacs/utility/real.h"
 135 #include "gromacs/utility/smalloc.h"
 136
 137 #include "integrator.h"
 138 #include "replicaexchange.h"
 139
 140 using gmx::SimulationSignaller;
 141
 142 void gmx::Integrator::do_mimic()
 143 {
 144     t_inputrec              *ir   = inputrec;
 145     int64_t                  step, step_rel;
 146     double                   t, lam0[efptNR];
 147     bool                     isLastStep               = false;
 148     bool                     doFreeEnergyPerturbation = false;
 149     int                      force_flags;
 150     tensor                   force_vir, shake_vir, total_vir, pres;
 151     rvec                     mu_tot;
 152     gmx_localtop_t           top;
 153     gmx_enerdata_t          *enerd;
 154     PaddedVector<gmx::RVec>  f {};
 155     gmx_global_stat_t        gstat;
 156     t_graph                 *graph = nullptr;
 157     gmx_groups_t            *groups;
 158     gmx_shellfc_t           *shellfc;
 159
 160     double                   cycles;
 161
 162     /* Domain decomposition could incorrectly miss a bonded
 163        interaction, but checking for that requires a global
 164        communication stage, which does not otherwise happen in DD
 165        code. So we do that alongside the first global energy reduction
 166        after a new DD is made. These variables handle whether the
 167        check happens, and the result it returns. */
 168     bool              shouldCheckNumberOfBondedInteractions = false;
 169     int               totalNumberOfBondedInteractions       = -1;
 170
 171     SimulationSignals signals;
 172     // Most global communnication stages don't propagate mdrun
 173     // signals, and will use this object to achieve that.
 174     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 175
 176     if (ir->bExpanded)
 177     {
 178         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 179     }
 180     if (ir->bSimTemp)
 181     {
 182         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 183     }
 184     if (ir->bDoAwh)
 185     {
 186         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 187     }
 188     if (replExParams.exchangeInterval > 0)
 189     {
 190         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 191     }
 192     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 193     {
 194         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 195     }
 196     if (ir->bIMD)
 197     {
 198         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 199     }
 200     if (isMultiSim(ms))
 201     {
 202         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 203     }
 204     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
 205                     [](int i){return i != eannNO; }))
 206     {
 207         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 208     }
 209
 210     /* Settings for rerun */
 211     ir->nstlist       = 1;
 212     ir->nstcalcenergy = 1;
 213     int        nstglobalcomm = 1;
 214     const bool bNS           = true;
 215
 216     // Communicator to interact with MiMiC
 217     MimicCommunicator mimicCommunicator {};
 218     if (MASTER(cr))
 219     {
 220         mimicCommunicator.init();
 221         mimicCommunicator.sendInitData(top_global, state_global->x);
 222         ir->nsteps = mimicCommunicator.getStepNumber();
 223     }
 224
 225     ir->nstxout_compressed                   = 0;
 226     groups                                   = &top_global->groups;
 227     top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 228
 229     initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
 230     init_nrnb(nrnb);
 231
 232     gmx_mdoutf       *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle);
 233     gmx::EnergyOutput energyOutput;
 234     energyOutput.prepare(mdoutf_get_fp_ene(outf), top_global, ir, mdoutf_get_fp_dhdl(outf), true);
 235
 236     /* Energy terms and groups */
 237     snew(enerd, 1);
 238     init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
 239                   enerd);
 240
 241     /* Kinetic energy data */
 242     std::unique_ptr<gmx_ekindata_t> eKinData = std::make_unique<gmx_ekindata_t>();
 243     gmx_ekindata_t                 *ekind    = eKinData.get();
 244     init_ekindata(fplog, top_global, &(ir->opts), ekind);
 245     /* Copy the cos acceleration to the groups struct */
 246     ekind->cosacc.cos_accel = ir->cos_accel;
 247
 248     gstat = global_stat_init(ir);
 249
 250     /* Check for polarizable models and flexible constraints */
 251     shellfc = init_shell_flexcon(fplog,
 252                                  top_global, constr ? constr->numFlexibleConstraints() : 0,
 253                                  ir->nstcalcenergy, DOMAINDECOMP(cr));
 254
 255     {
 256         double io = compute_io(ir, top_global->natoms, groups, energyOutput.numEnergyTerms(), 1);
 257         if ((io > 2000) && MASTER(cr))
 258         {
 259             fprintf(stderr,
 260                     "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
 261                     io);
 262         }
 263     }
 264
 265     // Local state only becomes valid now.
 266     std::unique_ptr<t_state> stateInstance;
 267     t_state *                state;
 268
 269     if (DOMAINDECOMP(cr))
 270     {
 271         dd_init_local_top(*top_global, &top);
 272
 273         stateInstance = std::make_unique<t_state>();
 274         state         = stateInstance.get();
 275         dd_init_local_state(cr->dd, state_global, state);
 276
 277         /* Distribute the charge groups over the nodes from the master node */
 278         dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
 279                             state_global, *top_global, ir,
 280                             state, &f, mdAtoms, &top, fr,
 281                             vsite, constr,
 282                             nrnb, nullptr, FALSE);
 283         shouldCheckNumberOfBondedInteractions = true;
 284         gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr);
 285     }
 286     else
 287     {
 288         state_change_natoms(state_global, state_global->natoms);
 289         /* We need to allocate one element extra, since we might use
 290          * (unaligned) 4-wide SIMD loads to access rvec entries.
 291          */
 292         f.resizeWithPadding(state_global->natoms);
 293         /* Copy the pointer to the global state */
 294         state = state_global;
 295
 296         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
 297                                   &graph, mdAtoms, constr, vsite, shellfc);
 298     }
 299
 300     auto mdatoms = mdAtoms->mdatoms();
 301
 302     // NOTE: The global state is no longer used at this point.
 303     // But state_global is still used as temporary storage space for writing
 304     // the global state to file and potentially for replica exchange.
 305     // (Global topology should persist.)
 306
 307     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 308
 309     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 310     {
 311         doFreeEnergyPerturbation = true;
 312     }
 313
 314     {
 315         int    cglo_flags = (CGLO_INITIALIZATION | CGLO_GSTAT |
 316                              (shouldCheckNumberOfBondedInteractions ?
 317                               CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 318         bool   bSumEkinhOld = false;
 319         t_vcm *vcm          = nullptr;
 320         compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 321                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
 322                         constr, &nullSignaller, state->box,
 323                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 324     }
 325     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 326                                     top_global, &top, state,
 327                                     &shouldCheckNumberOfBondedInteractions);
 328
 329     if (MASTER(cr))
 330     {
 331         fprintf(stderr, "starting MiMiC MD run '%s'\n\n",
 332                 *(top_global->name));
 333         if (mdrunOptions.verbose)
 334         {
 335             fprintf(stderr, "Calculated time to finish depends on nsteps from "
 336                     "run input file,\nwhich may not correspond to the time "
 337                     "needed to process input trajectory.\n\n");
 338         }
 339         fprintf(fplog, "\n");
 340     }
 341
 342     walltime_accounting_start_time(walltime_accounting);
 343     wallcycle_start(wcycle, ewcRUN);
 344     print_start(fplog, cr, walltime_accounting, "mdrun");
 345
 346     /***********************************************************
 347      *
 348      *             Loop over MD steps
 349      *
 350      ************************************************************/
 351
 352     if (constr)
 353     {
 354         GMX_LOG(mdlog.info).asParagraph().
 355             appendText("Simulations has constraints. Constraints will "
 356                        "be handled by CPMD.");
 357     }
 358
 359     GMX_LOG(mdlog.info).asParagraph().
 360         appendText("MiMiC does not report kinetic energy, total energy, temperature, virial and pressure.");
 361
 362     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 363                 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
 364                 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
 365                 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 366
 367     // we don't do counter resetting in rerun - finish will always be valid
 368     walltime_accounting_set_valid_finish(walltime_accounting);
 369
 370     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 371
 372     step     = ir->init_step;
 373     step_rel = 0;
 374
 375     /* and stop now if we should */
 376     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 377     while (!isLastStep)
 378     {
 379         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 380         wallcycle_start(wcycle, ewcSTEP);
 381
 382         t = step;
 383
 384         if (MASTER(cr))
 385         {
 386             mimicCommunicator.getCoords(&state_global->x, state_global->natoms);
 387         }
 388
 389         if (ir->efep != efepNO)
 390         {
 391             setCurrentLambdasLocal(step, ir->fepvals, lam0, state);
 392         }
 393
 394         if (MASTER(cr))
 395         {
 396             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 397             if (constructVsites && DOMAINDECOMP(cr))
 398             {
 399                 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
 400                           "use a single rank");
 401             }
 402         }
 403
 404         if (DOMAINDECOMP(cr))
 405         {
 406             /* Repartition the domain decomposition */
 407             const bool bMasterState = true;
 408             dd_partition_system(fplog, mdlog, step, cr,
 409                                 bMasterState, nstglobalcomm,
 410                                 state_global, *top_global, ir,
 411                                 state, &f, mdAtoms, &top, fr,
 412                                 vsite, constr,
 413                                 nrnb, wcycle,
 414                                 mdrunOptions.verbose);
 415             shouldCheckNumberOfBondedInteractions = true;
 416         }
 417
 418         if (MASTER(cr))
 419         {
 420             print_ebin_header(fplog, step, t); /* can we improve the information printed here? */
 421         }
 422
 423         if (ir->efep != efepNO)
 424         {
 425             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 426         }
 427
 428         force_flags = (GMX_FORCE_STATECHANGED |
 429                        GMX_FORCE_DYNAMICBOX |
 430                        GMX_FORCE_ALLFORCES |
 431                        GMX_FORCE_VIRIAL |  // TODO: Get rid of this once #2649 is solved
 432                        GMX_FORCE_ENERGY |
 433                        (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 434
 435         if (shellfc)
 436         {
 437             /* Now is the time to relax the shells */
 438             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
 439                                 enforcedRotation, step,
 440                                 ir, bNS, force_flags, &top,
 441                                 constr, enerd, fcd,
 442                                 state, f.arrayRefWithPadding(), force_vir, mdatoms,
 443                                 nrnb, wcycle, graph, groups,
 444                                 shellfc, fr, ppForceWorkload, t, mu_tot,
 445                                 vsite,
 446                                 ddBalanceRegionHandler);
 447         }
 448         else
 449         {
 450             /* The coordinates (x) are shifted (to get whole molecules)
 451              * in do_force.
 452              * This is parallellized as well, and does communication too.
 453              * Check comments in sim_util.c
 454              */
 455             Awh       *awh = nullptr;
 456             gmx_edsam *ed  = nullptr;
 457             do_force(fplog, cr, ms, ir, awh, enforcedRotation,
 458                      step, nrnb, wcycle, &top, groups,
 459                      state->box, state->x.arrayRefWithPadding(), &state->hist,
 460                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
 461                      state->lambda, graph,
 462                      fr, ppForceWorkload, vsite, mu_tot, t, ed,
 463                      GMX_FORCE_NS | force_flags,
 464                      ddBalanceRegionHandler);
 465         }
 466
 467         /* Now we have the energies and forces corresponding to the
 468          * coordinates at time t.
 469          */
 470         {
 471             const bool isCheckpointingStep = false;
 472             const bool doRerun             = false;
 473             const bool bSumEkinhOld        = false;
 474             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
 475                                      ir, state, state_global, observablesHistory,
 476                                      top_global, fr,
 477                                      outf, energyOutput, ekind, f,
 478                                      isCheckpointingStep, doRerun, isLastStep,
 479                                      mdrunOptions.writeConfout,
 480                                      bSumEkinhOld);
 481         }
 482
 483         stopHandler->setSignal();
 484
 485         if (graph)
 486         {
 487             /* Need to unshift here */
 488             unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 489         }
 490
 491         if (vsite != nullptr)
 492         {
 493             wallcycle_start(wcycle, ewcVSITECONSTR);
 494             if (graph != nullptr)
 495             {
 496                 shift_self(graph, state->box, as_rvec_array(state->x.data()));
 497             }
 498             construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
 499                              top.idef.iparams, top.idef.il,
 500                              fr->ePBC, fr->bMolPBC, cr, state->box);
 501
 502             if (graph != nullptr)
 503             {
 504                 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 505             }
 506             wallcycle_stop(wcycle, ewcVSITECONSTR);
 507         }
 508
 509         {
 510             const bool          doInterSimSignal = false;
 511             const bool          doIntraSimSignal = true;
 512             bool                bSumEkinhOld     = false;
 513             t_vcm              *vcm              = nullptr;
 514             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 515
 516             compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 517                             wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
 518                             constr, &signaller,
 519                             state->box,
 520                             &totalNumberOfBondedInteractions, &bSumEkinhOld,
 521                             CGLO_GSTAT | CGLO_ENERGY
 522                             | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
 523                             );
 524             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 525                                             top_global, &top, state,
 526                                             &shouldCheckNumberOfBondedInteractions);
 527         }
 528
 529         {
 530             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 531             gmx::ArrayRef<gmx::RVec>       ftemp;
 532             gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
 533             if (DOMAINDECOMP(cr))
 534             {
 535                 ftemp = gmx::makeArrayRef(fglobal);
 536                 dd_collect_vec(cr->dd, state, flocal, ftemp);
 537             }
 538             else
 539             {
 540                 ftemp = gmx::makeArrayRef(f);
 541             }
 542
 543             if (MASTER(cr))
 544             {
 545                 mimicCommunicator.sendEnergies(enerd->term[F_EPOT]);
 546                 mimicCommunicator.sendForces(ftemp, state_global->natoms);
 547             }
 548         }
 549
 550
 551
 552         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 553            the virial that should probably be addressed eventually. state->veta has better properies,
 554            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 555            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 556
 557         if (ir->efep != efepNO)
 558         {
 559             /* Sum up the foreign energy and dhdl terms for md and sd.
 560                Currently done every step so that dhdl is correct in the .edr */
 561             sum_dhdl(enerd, state->lambda, ir->fepvals);
 562         }
 563
 564         /* Output stuff */
 565         if (MASTER(cr))
 566         {
 567             const bool bCalcEnerStep = true;
 568             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep,
 569                                              t, mdatoms->tmass, enerd, state,
 570                                              ir->fepvals, ir->expandedvals, state->box,
 571                                              shake_vir, force_vir, total_vir, pres,
 572                                              ekind, mu_tot, constr);
 573
 574             const bool do_ene = true;
 575             const bool do_log = true;
 576             Awh       *awh    = nullptr;
 577             const bool do_dr  = ir->nstdisreout != 0;
 578             const bool do_or  = ir->nstorireout != 0;
 579
 580             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
 581                                                do_log ? fplog : nullptr,
 582                                                step, t,
 583                                                eprNORMAL, fcd, groups, &(ir->opts), awh);
 584
 585             if (do_per_step(step, ir->nstlog))
 586             {
 587                 if (fflush(fplog) != 0)
 588                 {
 589                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 590                 }
 591             }
 592         }
 593
 594         /* Print the remaining wall clock time for the run */
 595         if (isMasterSimMasterRank(ms, cr) &&
 596             (mdrunOptions.verbose || gmx_got_usr_signal()))
 597         {
 598             if (shellfc)
 599             {
 600                 fprintf(stderr, "\n");
 601             }
 602             print_time(stderr, walltime_accounting, step, ir, cr);
 603         }
 604
 605         cycles = wallcycle_stop(wcycle, ewcSTEP);
 606         if (DOMAINDECOMP(cr) && wcycle)
 607         {
 608             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 609         }
 610
 611         /* increase the MD step number */
 612         step++;
 613         step_rel++;
 614     }
 615     /* End of main MD loop */
 616
 617     /* Closing TNG files can include compressing data. Therefore it is good to do that
 618      * before stopping the time measurements. */
 619     mdoutf_tng_close(outf);
 620
 621     /* Stop measuring walltime */
 622     walltime_accounting_end_time(walltime_accounting);
 623
 624     if (MASTER(cr))
 625     {
 626         mimicCommunicator.finalize();
 627     }
 628
 629     if (!thisRankHasDuty(cr, DUTY_PME))
 630     {
 631         /* Tell the PME only node to finish */
 632         gmx_pme_send_finish(cr);
 633     }
 634
 635     done_mdoutf(outf);
 636
 637     done_shellfc(fplog, shellfc, step_rel);
 638
 639     // Clean up swapcoords
 640     if (ir->eSwapCoords != eswapNO)
 641     {
 642         finish_swapcoords(ir->swap);
 643     }
 644
 645     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 646
 647     destroy_enerdata(enerd);
 648     sfree(enerd);
 649 }