src/gromacs/mdrun/mimic.cpp

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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/compat/make_unique.h"
  56 #include "gromacs/domdec/collect.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/expanded.h"
  79 #include "gromacs/mdlib/force.h"
  80 #include "gromacs/mdlib/force_flags.h"
  81 #include "gromacs/mdlib/forcerec.h"
  82 #include "gromacs/mdlib/md_support.h"
  83 #include "gromacs/mdlib/mdatoms.h"
  84 #include "gromacs/mdlib/mdebin.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/nb_verlet.h"
  90 #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
  91 #include "gromacs/mdlib/ns.h"
  92 #include "gromacs/mdlib/resethandler.h"
  93 #include "gromacs/mdlib/shellfc.h"
  94 #include "gromacs/mdlib/sighandler.h"
  95 #include "gromacs/mdlib/sim_util.h"
  96 #include "gromacs/mdlib/simulationsignal.h"
  97 #include "gromacs/mdlib/stophandler.h"
  98 #include "gromacs/mdlib/tgroup.h"
  99 #include "gromacs/mdlib/trajectory_writing.h"
 100 #include "gromacs/mdlib/update.h"
 101 #include "gromacs/mdlib/vcm.h"
 102 #include "gromacs/mdlib/vsite.h"
 103 #include "gromacs/mdtypes/awh-history.h"
 104 #include "gromacs/mdtypes/awh-params.h"
 105 #include "gromacs/mdtypes/commrec.h"
 106 #include "gromacs/mdtypes/df_history.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     gmx_mdoutf              *outf = nullptr;
 146     int64_t                  step, step_rel;
 147     double                   t, lam0[efptNR];
 148     bool                     isLastStep               = false;
 149     bool                     doFreeEnergyPerturbation = false;
 150     int                      force_flags;
 151     tensor                   force_vir, shake_vir, total_vir, pres;
 152     rvec                     mu_tot;
 153     gmx_localtop_t          *top;
 154     t_mdebin                *mdebin   = nullptr;
 155     gmx_enerdata_t          *enerd;
 156     PaddedVector<gmx::RVec>  f {};
 157     gmx_global_stat_t        gstat;
 158     t_graph                 *graph = nullptr;
 159     gmx_groups_t            *groups;
 160     gmx_ekindata_t          *ekind;
 161     gmx_shellfc_t           *shellfc;
 162
 163     double                   cycles;
 164
 165     /* Domain decomposition could incorrectly miss a bonded
 166        interaction, but checking for that requires a global
 167        communication stage, which does not otherwise happen in DD
 168        code. So we do that alongside the first global energy reduction
 169        after a new DD is made. These variables handle whether the
 170        check happens, and the result it returns. */
 171     bool              shouldCheckNumberOfBondedInteractions = false;
 172     int               totalNumberOfBondedInteractions       = -1;
 173
 174     SimulationSignals signals;
 175     // Most global communnication stages don't propagate mdrun
 176     // signals, and will use this object to achieve that.
 177     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 178
 179     if (ir->bExpanded)
 180     {
 181         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 182     }
 183     if (ir->bSimTemp)
 184     {
 185         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 186     }
 187     if (ir->bDoAwh)
 188     {
 189         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 190     }
 191     if (replExParams.exchangeInterval > 0)
 192     {
 193         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 194     }
 195     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 196     {
 197         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 198     }
 199     if (ir->bIMD)
 200     {
 201         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 202     }
 203     if (isMultiSim(ms))
 204     {
 205         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 206     }
 207     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
 208                     [](int i){return i != eannNO; }))
 209     {
 210         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 211     }
 212
 213     /* Settings for rerun */
 214     ir->nstlist       = 1;
 215     ir->nstcalcenergy = 1;
 216     int        nstglobalcomm = 1;
 217     const bool bNS           = true;
 218
 219     // Communicator to interact with MiMiC
 220     MimicCommunicator mimicCommunicator {};
 221     if (MASTER(cr))
 222     {
 223         mimicCommunicator.init();
 224         mimicCommunicator.sendInitData(top_global, state_global->x);
 225         ir->nsteps = mimicCommunicator.getStepNumber();
 226     }
 227
 228     ir->nstxout_compressed                   = 0;
 229     groups                                   = &top_global->groups;
 230     top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 231
 232     /* Initial values */
 233     init_rerun(fplog, cr, outputProvider, ir, oenv, mdrunOptions,
 234                state_global, lam0, nrnb, top_global,
 235                nfile, fnm, &outf, &mdebin, wcycle);
 236
 237     /* Energy terms and groups */
 238     snew(enerd, 1);
 239     init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
 240                   enerd);
 241
 242     /* Kinetic energy data */
 243     snew(ekind, 1);
 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, mdebin->ebin->nener, 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         top = dd_init_local_top(top_global);
 272
 273         stateInstance = compat::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         snew(top, 1);
 297         mdAlgorithmsSetupAtomData(cr, ir, top_global, top, fr,
 298                                   &graph, mdAtoms, constr, vsite, shellfc);
 299     }
 300
 301     auto mdatoms = mdAtoms->mdatoms();
 302
 303     // NOTE: The global state is no longer used at this point.
 304     // But state_global is still used as temporary storage space for writing
 305     // the global state to file and potentially for replica exchange.
 306     // (Global topology should persist.)
 307
 308     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 309
 310     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 311     {
 312         doFreeEnergyPerturbation = true;
 313     }
 314
 315     {
 316         int    cglo_flags = (CGLO_INITIALIZATION | CGLO_GSTAT |
 317                              (shouldCheckNumberOfBondedInteractions ?
 318                               CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 319         bool   bSumEkinhOld = false;
 320         t_vcm *vcm          = nullptr;
 321         compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 322                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
 323                         constr, &nullSignaller, state->box,
 324                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 325     }
 326     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 327                                     top_global, top, state,
 328                                     &shouldCheckNumberOfBondedInteractions);
 329
 330     if (MASTER(cr))
 331     {
 332         fprintf(stderr, "starting MiMiC MD run '%s'\n\n",
 333                 *(top_global->name));
 334         if (mdrunOptions.verbose)
 335         {
 336             fprintf(stderr, "Calculated time to finish depends on nsteps from "
 337                     "run input file,\nwhich may not correspond to the time "
 338                     "needed to process input trajectory.\n\n");
 339         }
 340         fprintf(fplog, "\n");
 341     }
 342
 343     walltime_accounting_start_time(walltime_accounting);
 344     wallcycle_start(wcycle, ewcRUN);
 345     print_start(fplog, cr, walltime_accounting, "mdrun");
 346
 347     /***********************************************************
 348      *
 349      *             Loop over MD steps
 350      *
 351      ************************************************************/
 352
 353     if (constr)
 354     {
 355         GMX_LOG(mdlog.info).asParagraph().
 356             appendText("Simulations has constraints. Constraints will "
 357                        "be handled by CPMD.");
 358     }
 359
 360     GMX_LOG(mdlog.info).asParagraph().
 361         appendText("MiMiC does not report kinetic energy, total energy, temperature, virial and pressure.");
 362
 363     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 364                 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
 365                 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
 366                 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 367
 368     // we don't do counter resetting in rerun - finish will always be valid
 369     walltime_accounting_set_valid_finish(walltime_accounting);
 370
 371     DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion   =
 372         (DOMAINDECOMP(cr) ?
 373          DdOpenBalanceRegionBeforeForceComputation::yes :
 374          DdOpenBalanceRegionBeforeForceComputation::no);
 375     DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion  =
 376         (DOMAINDECOMP(cr) ?
 377          DdCloseBalanceRegionAfterForceComputation::yes :
 378          DdCloseBalanceRegionAfterForceComputation::no);
 379
 380     step     = ir->init_step;
 381     step_rel = 0;
 382
 383     /* and stop now if we should */
 384     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 385     while (!isLastStep)
 386     {
 387         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 388         wallcycle_start(wcycle, ewcSTEP);
 389
 390         t = step;
 391
 392         if (MASTER(cr))
 393         {
 394             mimicCommunicator.getCoords(&state_global->x, state_global->natoms);
 395         }
 396
 397         if (ir->efep != efepNO)
 398         {
 399             setCurrentLambdasLocal(step, ir->fepvals, lam0, state);
 400         }
 401
 402         if (MASTER(cr))
 403         {
 404             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 405             if (constructVsites && DOMAINDECOMP(cr))
 406             {
 407                 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
 408                           "use a single rank");
 409             }
 410         }
 411
 412         if (DOMAINDECOMP(cr))
 413         {
 414             /* Repartition the domain decomposition */
 415             const bool bMasterState = true;
 416             dd_partition_system(fplog, mdlog, step, cr,
 417                                 bMasterState, nstglobalcomm,
 418                                 state_global, top_global, ir,
 419                                 state, &f, mdAtoms, top, fr,
 420                                 vsite, constr,
 421                                 nrnb, wcycle,
 422                                 mdrunOptions.verbose);
 423             shouldCheckNumberOfBondedInteractions = true;
 424         }
 425
 426         if (MASTER(cr))
 427         {
 428             print_ebin_header(fplog, step, t); /* can we improve the information printed here? */
 429         }
 430
 431         if (ir->efep != efepNO)
 432         {
 433             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 434         }
 435
 436         force_flags = (GMX_FORCE_STATECHANGED |
 437                        GMX_FORCE_DYNAMICBOX |
 438                        GMX_FORCE_ALLFORCES |
 439                        GMX_FORCE_VIRIAL |  // TODO: Get rid of this once #2649 is solved
 440                        GMX_FORCE_ENERGY |
 441                        (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 442
 443         if (shellfc)
 444         {
 445             /* Now is the time to relax the shells */
 446             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
 447                                 enforcedRotation, step,
 448                                 ir, bNS, force_flags, top,
 449                                 constr, enerd, fcd,
 450                                 state, f.arrayRefWithPadding(), force_vir, mdatoms,
 451                                 nrnb, wcycle, graph, groups,
 452                                 shellfc, fr, t, mu_tot,
 453                                 vsite,
 454                                 ddOpenBalanceRegion, ddCloseBalanceRegion);
 455         }
 456         else
 457         {
 458             /* The coordinates (x) are shifted (to get whole molecules)
 459              * in do_force.
 460              * This is parallellized as well, and does communication too.
 461              * Check comments in sim_util.c
 462              */
 463             Awh       *awh = nullptr;
 464             gmx_edsam *ed  = nullptr;
 465             do_force(fplog, cr, ms, ir, awh, enforcedRotation,
 466                      step, nrnb, wcycle, top, groups,
 467                      state->box, state->x.arrayRefWithPadding(), &state->hist,
 468                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
 469                      state->lambda, graph,
 470                      fr, vsite, mu_tot, t, ed,
 471                      GMX_FORCE_NS | force_flags,
 472                      ddOpenBalanceRegion, ddCloseBalanceRegion);
 473         }
 474
 475         /* Now we have the energies and forces corresponding to the
 476          * coordinates at time t.
 477          */
 478         {
 479             const bool isCheckpointingStep = false;
 480             const bool doRerun             = false;
 481             const bool bSumEkinhOld        = false;
 482             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
 483                                      ir, state, state_global, observablesHistory,
 484                                      top_global, fr,
 485                                      outf, mdebin, ekind, f,
 486                                      isCheckpointingStep, doRerun, isLastStep,
 487                                      mdrunOptions.writeConfout,
 488                                      bSumEkinhOld);
 489         }
 490
 491         stopHandler->setSignal();
 492
 493         if (graph)
 494         {
 495             /* Need to unshift here */
 496             unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 497         }
 498
 499         if (vsite != nullptr)
 500         {
 501             wallcycle_start(wcycle, ewcVSITECONSTR);
 502             if (graph != nullptr)
 503             {
 504                 shift_self(graph, state->box, as_rvec_array(state->x.data()));
 505             }
 506             construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
 507                              top->idef.iparams, top->idef.il,
 508                              fr->ePBC, fr->bMolPBC, cr, state->box);
 509
 510             if (graph != nullptr)
 511             {
 512                 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 513             }
 514             wallcycle_stop(wcycle, ewcVSITECONSTR);
 515         }
 516
 517         {
 518             const bool          doInterSimSignal = false;
 519             const bool          doIntraSimSignal = true;
 520             bool                bSumEkinhOld     = false;
 521             t_vcm              *vcm              = nullptr;
 522             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 523
 524             compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 525                             wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
 526                             constr, &signaller,
 527                             state->box,
 528                             &totalNumberOfBondedInteractions, &bSumEkinhOld,
 529                             CGLO_GSTAT | CGLO_ENERGY
 530                             | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
 531                             );
 532             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 533                                             top_global, top, state,
 534                                             &shouldCheckNumberOfBondedInteractions);
 535         }
 536
 537         {
 538             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 539             gmx::ArrayRef<gmx::RVec>       ftemp;
 540             gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
 541             if (DOMAINDECOMP(cr))
 542             {
 543                 ftemp = gmx::makeArrayRef(fglobal);
 544                 dd_collect_vec(cr->dd, state, flocal, ftemp);
 545             }
 546             else
 547             {
 548                 ftemp = gmx::makeArrayRef(f);
 549             }
 550
 551             if (MASTER(cr))
 552             {
 553                 mimicCommunicator.sendEnergies(enerd->term[F_EPOT]);
 554                 mimicCommunicator.sendForces(ftemp, state_global->natoms);
 555             }
 556         }
 557
 558
 559
 560         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 561            the virial that should probably be addressed eventually. state->veta has better properies,
 562            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 563            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 564
 565         if (ir->efep != efepNO)
 566         {
 567             /* Sum up the foreign energy and dhdl terms for md and sd.
 568                Currently done every step so that dhdl is correct in the .edr */
 569             sum_dhdl(enerd, state->lambda, ir->fepvals);
 570         }
 571
 572         /* Output stuff */
 573         if (MASTER(cr))
 574         {
 575             const bool bCalcEnerStep = true;
 576             upd_mdebin(mdebin, doFreeEnergyPerturbation, bCalcEnerStep,
 577                        t, mdatoms->tmass, enerd, state,
 578                        ir->fepvals, ir->expandedvals, state->box,
 579                        shake_vir, force_vir, total_vir, pres,
 580                        ekind, mu_tot, constr);
 581
 582             const bool do_ene = true;
 583             const bool do_log = true;
 584             Awh       *awh    = nullptr;
 585             const bool do_dr  = ir->nstdisreout != 0;
 586             const bool do_or  = ir->nstorireout != 0;
 587
 588             print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : nullptr,
 589                        step, t,
 590                        eprNORMAL, mdebin, fcd, groups, &(ir->opts), awh);
 591
 592             if (do_per_step(step, ir->nstlog))
 593             {
 594                 if (fflush(fplog) != 0)
 595                 {
 596                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 597                 }
 598             }
 599         }
 600
 601         /* Print the remaining wall clock time for the run */
 602         if (isMasterSimMasterRank(ms, cr) &&
 603             (mdrunOptions.verbose || gmx_got_usr_signal()))
 604         {
 605             if (shellfc)
 606             {
 607                 fprintf(stderr, "\n");
 608             }
 609             print_time(stderr, walltime_accounting, step, ir, cr);
 610         }
 611
 612         cycles = wallcycle_stop(wcycle, ewcSTEP);
 613         if (DOMAINDECOMP(cr) && wcycle)
 614         {
 615             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 616         }
 617
 618         /* increase the MD step number */
 619         step++;
 620         step_rel++;
 621     }
 622     /* End of main MD loop */
 623
 624     /* Closing TNG files can include compressing data. Therefore it is good to do that
 625      * before stopping the time measurements. */
 626     mdoutf_tng_close(outf);
 627
 628     /* Stop measuring walltime */
 629     walltime_accounting_end_time(walltime_accounting);
 630
 631     if (MASTER(cr))
 632     {
 633         mimicCommunicator.finalize();
 634     }
 635
 636     if (!thisRankHasDuty(cr, DUTY_PME))
 637     {
 638         /* Tell the PME only node to finish */
 639         gmx_pme_send_finish(cr);
 640     }
 641
 642     done_mdebin(mdebin);
 643     done_mdoutf(outf);
 644
 645     done_shellfc(fplog, shellfc, step_rel);
 646
 647     // Clean up swapcoords
 648     if (ir->eSwapCoords != eswapNO)
 649     {
 650         finish_swapcoords(ir->swap);
 651     }
 652
 653     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 654
 655     destroy_enerdata(enerd);
 656     sfree(enerd);
 657     sfree(top);
 658 }