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/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/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/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/md_support.h"
  85 #include "gromacs/mdlib/mdatoms.h"
  86 #include "gromacs/mdlib/mdoutf.h"
  87 #include "gromacs/mdlib/membed.h"
  88 #include "gromacs/mdlib/resethandler.h"
  89 #include "gromacs/mdlib/sighandler.h"
  90 #include "gromacs/mdlib/simulationsignal.h"
  91 #include "gromacs/mdlib/stat.h"
  92 #include "gromacs/mdlib/stophandler.h"
  93 #include "gromacs/mdlib/tgroup.h"
  94 #include "gromacs/mdlib/trajectory_writing.h"
  95 #include "gromacs/mdlib/update.h"
  96 #include "gromacs/mdlib/vcm.h"
  97 #include "gromacs/mdlib/vsite.h"
  98 #include "gromacs/mdrunutility/handlerestart.h"
  99 #include "gromacs/mdrunutility/multisim.h"
 100 #include "gromacs/mdrunutility/printtime.h"
 101 #include "gromacs/mdtypes/awh_history.h"
 102 #include "gromacs/mdtypes/awh_params.h"
 103 #include "gromacs/mdtypes/commrec.h"
 104 #include "gromacs/mdtypes/df_history.h"
 105 #include "gromacs/mdtypes/enerdata.h"
 106 #include "gromacs/mdtypes/energyhistory.h"
 107 #include "gromacs/mdtypes/fcdata.h"
 108 #include "gromacs/mdtypes/forcerec.h"
 109 #include "gromacs/mdtypes/group.h"
 110 #include "gromacs/mdtypes/inputrec.h"
 111 #include "gromacs/mdtypes/interaction_const.h"
 112 #include "gromacs/mdtypes/md_enums.h"
 113 #include "gromacs/mdtypes/mdatom.h"
 114 #include "gromacs/mdtypes/mdrunoptions.h"
 115 #include "gromacs/mdtypes/observableshistory.h"
 116 #include "gromacs/mdtypes/state.h"
 117 #include "gromacs/mimic/communicator.h"
 118 #include "gromacs/mimic/utilities.h"
 119 #include "gromacs/pbcutil/mshift.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, lam0[efptNR];
 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     PaddedHostVector<gmx::RVec> f{};
 153     gmx_global_stat_t           gstat;
 154     t_graph*                    graph = nullptr;
 155     gmx_shellfc_t*              shellfc;
 156
 157     double cycles;
 158
 159     /* Domain decomposition could incorrectly miss a bonded
 160        interaction, but checking for that requires a global
 161        communication stage, which does not otherwise happen in DD
 162        code. So we do that alongside the first global energy reduction
 163        after a new DD is made. These variables handle whether the
 164        check happens, and the result it returns. */
 165     bool shouldCheckNumberOfBondedInteractions = false;
 166     int  totalNumberOfBondedInteractions       = -1;
 167
 168     SimulationSignals signals;
 169     // Most global communnication stages don't propagate mdrun
 170     // signals, and will use this object to achieve that.
 171     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 172
 173     if (ir->bExpanded)
 174     {
 175         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 176     }
 177     if (ir->bSimTemp)
 178     {
 179         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 180     }
 181     if (ir->bDoAwh)
 182     {
 183         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 184     }
 185     if (replExParams.exchangeInterval > 0)
 186     {
 187         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 188     }
 189     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 190     {
 191         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 192     }
 193     if (ir->bIMD)
 194     {
 195         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 196     }
 197     if (isMultiSim(ms))
 198     {
 199         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 200     }
 201     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
 202                     [](int i) { return i != eannNO; }))
 203     {
 204         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 205     }
 206
 207     /* Settings for rerun */
 208     ir->nstlist              = 1;
 209     ir->nstcalcenergy        = 1;
 210     int        nstglobalcomm = 1;
 211     const bool bNS           = true;
 212
 213     // Communicator to interact with MiMiC
 214     MimicCommunicator mimicCommunicator{};
 215     if (MASTER(cr))
 216     {
 217         mimicCommunicator.init();
 218         mimicCommunicator.sendInitData(top_global, state_global->x);
 219         ir->nsteps = mimicCommunicator.getStepNumber();
 220     }
 221
 222     ir->nstxout_compressed                   = 0;
 223     SimulationGroups* groups                 = &top_global->groups;
 224     top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 225
 226     initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
 227
 228     const bool        simulationsShareState = false;
 229     gmx_mdoutf*       outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
 230                                    mdModulesNotifier, ir, top_global, oenv, wcycle,
 231                                    StartingBehavior::NewSimulation, simulationsShareState, ms);
 232     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
 233                                    mdoutf_get_fp_dhdl(outf), true, StartingBehavior::NewSimulation,
 234                                    mdModulesNotifier);
 235
 236     gstat = global_stat_init(ir);
 237
 238     /* Check for polarizable models and flexible constraints */
 239     shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
 240                                  ir->nstcalcenergy, DOMAINDECOMP(cr));
 241
 242     {
 243         double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
 244         if ((io > 2000) && MASTER(cr))
 245         {
 246             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 247         }
 248     }
 249
 250     // Local state only becomes valid now.
 251     std::unique_ptr<t_state> stateInstance;
 252     t_state*                 state;
 253
 254     gmx_localtop_t top(top_global->ffparams);
 255
 256     if (DOMAINDECOMP(cr))
 257     {
 258         stateInstance = std::make_unique<t_state>();
 259         state         = stateInstance.get();
 260         dd_init_local_state(cr->dd, state_global, state);
 261
 262         /* Distribute the charge groups over the nodes from the master node */
 263         dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
 264                             imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
 265                             nrnb, nullptr, FALSE);
 266         shouldCheckNumberOfBondedInteractions = true;
 267         gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr);
 268     }
 269     else
 270     {
 271         state_change_natoms(state_global, state_global->natoms);
 272         /* We need to allocate one element extra, since we might use
 273          * (unaligned) 4-wide SIMD loads to access rvec entries.
 274          */
 275         f.resizeWithPadding(state_global->natoms);
 276         /* Copy the pointer to the global state */
 277         state = state_global;
 278
 279         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &graph, mdAtoms, constr, vsite, shellfc);
 280     }
 281
 282     auto mdatoms = mdAtoms->mdatoms();
 283
 284     // NOTE: The global state is no longer used at this point.
 285     // But state_global is still used as temporary storage space for writing
 286     // the global state to file and potentially for replica exchange.
 287     // (Global topology should persist.)
 288
 289     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 290
 291     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 292     {
 293         doFreeEnergyPerturbation = true;
 294     }
 295
 296     {
 297         int cglo_flags =
 298                 (CGLO_GSTAT
 299                  | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 300         bool   bSumEkinhOld = false;
 301         t_vcm* vcm          = nullptr;
 302         compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
 303                         makeConstArrayRef(state->v), state->box, state->lambda[efptVDW], mdatoms, nrnb,
 304                         vcm, nullptr, enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
 305                         state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 306     }
 307     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
 308                                     makeConstArrayRef(state->x), state->box,
 309                                     &shouldCheckNumberOfBondedInteractions);
 310
 311     if (MASTER(cr))
 312     {
 313         fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global->name));
 314         if (mdrunOptions.verbose)
 315         {
 316             fprintf(stderr,
 317                     "Calculated time to finish depends on nsteps from "
 318                     "run input file,\nwhich may not correspond to the time "
 319                     "needed to process input trajectory.\n\n");
 320         }
 321         fprintf(fplog, "\n");
 322     }
 323
 324     walltime_accounting_start_time(walltime_accounting);
 325     wallcycle_start(wcycle, ewcRUN);
 326     print_start(fplog, cr, walltime_accounting, "mdrun");
 327
 328     /***********************************************************
 329      *
 330      *             Loop over MD steps
 331      *
 332      ************************************************************/
 333
 334     if (constr)
 335     {
 336         GMX_LOG(mdlog.info)
 337                 .asParagraph()
 338                 .appendText(
 339                         "Simulations has constraints. Constraints will "
 340                         "be handled by CPMD.");
 341     }
 342
 343     GMX_LOG(mdlog.info)
 344             .asParagraph()
 345             .appendText(
 346                     "MiMiC does not report kinetic energy, total energy, temperature, virial and "
 347                     "pressure.");
 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     step     = ir->init_step;
 360     step_rel = 0;
 361
 362     /* and stop now if we should */
 363     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 364     while (!isLastStep)
 365     {
 366         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 367         wallcycle_start(wcycle, ewcSTEP);
 368
 369         t = step;
 370
 371         if (MASTER(cr))
 372         {
 373             mimicCommunicator.getCoords(&state_global->x, state_global->natoms);
 374         }
 375
 376         if (ir->efep != efepNO)
 377         {
 378             setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
 379         }
 380
 381         if (MASTER(cr))
 382         {
 383             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 384             if (constructVsites && DOMAINDECOMP(cr))
 385             {
 386                 gmx_fatal(FARGS,
 387                           "Vsite recalculation with -rerun is not implemented with domain "
 388                           "decomposition, "
 389                           "use a single rank");
 390             }
 391         }
 392
 393         if (DOMAINDECOMP(cr))
 394         {
 395             /* Repartition the domain decomposition */
 396             const bool bMasterState = true;
 397             dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
 398                                 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
 399                                 fr, vsite, constr, nrnb, wcycle, mdrunOptions.verbose);
 400             shouldCheckNumberOfBondedInteractions = true;
 401         }
 402
 403         if (MASTER(cr))
 404         {
 405             energyOutput.printHeader(fplog, step, t); /* can we improve the information printed here? */
 406         }
 407
 408         if (ir->efep != efepNO)
 409         {
 410             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 411         }
 412
 413         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 414                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
 415                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 416
 417         if (shellfc)
 418         {
 419             /* Now is the time to relax the shells */
 420             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
 421                                 imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
 422                                 state->natoms, state->x.arrayRefWithPadding(),
 423                                 state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
 424                                 f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
 425                                 shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
 426         }
 427         else
 428         {
 429             /* The coordinates (x) are shifted (to get whole molecules)
 430              * in do_force.
 431              * This is parallellized as well, and does communication too.
 432              * Check comments in sim_util.c
 433              */
 434             Awh*       awh = nullptr;
 435             gmx_edsam* ed  = nullptr;
 436             do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
 437                      wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
 438                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
 439                      fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
 440                      ddBalanceRegionHandler);
 441         }
 442
 443         /* Now we have the energies and forces corresponding to the
 444          * coordinates at time t.
 445          */
 446         {
 447             const bool isCheckpointingStep = false;
 448             const bool doRerun             = false;
 449             const bool bSumEkinhOld        = false;
 450             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
 451                                      state_global, observablesHistory, top_global, fr, outf,
 452                                      energyOutput, ekind, f, isCheckpointingStep, doRerun,
 453                                      isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
 454         }
 455
 456         stopHandler->setSignal();
 457
 458         if (graph)
 459         {
 460             /* Need to unshift here */
 461             unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 462         }
 463
 464         if (vsite != nullptr)
 465         {
 466             wallcycle_start(wcycle, ewcVSITECONSTR);
 467             if (graph != nullptr)
 468             {
 469                 shift_self(graph, state->box, as_rvec_array(state->x.data()));
 470             }
 471             construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t,
 472                              as_rvec_array(state->v.data()), top.idef.iparams, top.idef.il,
 473                              fr->pbcType, fr->bMolPBC, cr, state->box);
 474
 475             if (graph != nullptr)
 476             {
 477                 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 478             }
 479             wallcycle_stop(wcycle, ewcVSITECONSTR);
 480         }
 481
 482         {
 483             const bool          doInterSimSignal = false;
 484             const bool          doIntraSimSignal = true;
 485             bool                bSumEkinhOld     = false;
 486             t_vcm*              vcm              = nullptr;
 487             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 488
 489             compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
 490                             makeConstArrayRef(state->v), state->box, state->lambda[efptVDW], mdatoms,
 491                             nrnb, vcm, wcycle, enerd, nullptr, nullptr, nullptr, nullptr, constr,
 492                             &signaller, state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
 493                             CGLO_GSTAT | CGLO_ENERGY
 494                                     | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
 495                                                                              : 0));
 496             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
 497                                             &top, makeConstArrayRef(state->x), state->box,
 498                                             &shouldCheckNumberOfBondedInteractions);
 499         }
 500
 501         {
 502             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 503             gmx::ArrayRef<gmx::RVec>       ftemp;
 504             gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
 505             if (DOMAINDECOMP(cr))
 506             {
 507                 ftemp = gmx::makeArrayRef(fglobal);
 508                 dd_collect_vec(cr->dd, state, flocal, ftemp);
 509             }
 510             else
 511             {
 512                 ftemp = gmx::makeArrayRef(f);
 513             }
 514
 515             if (MASTER(cr))
 516             {
 517                 mimicCommunicator.sendEnergies(enerd->term[F_EPOT]);
 518                 mimicCommunicator.sendForces(ftemp, state_global->natoms);
 519             }
 520         }
 521
 522
 523         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 524            the virial that should probably be addressed eventually. state->veta has better properies,
 525            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 526            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 527
 528         if (ir->efep != efepNO)
 529         {
 530             /* Sum up the foreign energy and dhdl terms for md and sd.
 531                Currently done every step so that dhdl is correct in the .edr */
 532             sum_dhdl(enerd, state->lambda, *ir->fepvals);
 533         }
 534
 535         /* Output stuff */
 536         if (MASTER(cr))
 537         {
 538             const bool bCalcEnerStep = true;
 539             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep, t,
 540                                              mdatoms->tmass, enerd, state, ir->fepvals,
 541                                              ir->expandedvals, state->box, shake_vir, force_vir,
 542                                              total_vir, pres, ekind, mu_tot, constr);
 543
 544             const bool do_ene = true;
 545             const bool do_log = true;
 546             Awh*       awh    = nullptr;
 547             const bool do_dr  = ir->nstdisreout != 0;
 548             const bool do_or  = ir->nstorireout != 0;
 549
 550             energyOutput.printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 551             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
 552                                                do_log ? fplog : nullptr, step, t, fcd, awh);
 553
 554             if (do_per_step(step, ir->nstlog))
 555             {
 556                 if (fflush(fplog) != 0)
 557                 {
 558                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 559                 }
 560             }
 561         }
 562
 563         /* Print the remaining wall clock time for the run */
 564         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 565         {
 566             if (shellfc)
 567             {
 568                 fprintf(stderr, "\n");
 569             }
 570             print_time(stderr, walltime_accounting, step, ir, cr);
 571         }
 572
 573         cycles = wallcycle_stop(wcycle, ewcSTEP);
 574         if (DOMAINDECOMP(cr) && wcycle)
 575         {
 576             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 577         }
 578
 579         /* increase the MD step number */
 580         step++;
 581         step_rel++;
 582     }
 583     /* End of main MD loop */
 584
 585     /* Closing TNG files can include compressing data. Therefore it is good to do that
 586      * before stopping the time measurements. */
 587     mdoutf_tng_close(outf);
 588
 589     /* Stop measuring walltime */
 590     walltime_accounting_end_time(walltime_accounting);
 591
 592     if (MASTER(cr))
 593     {
 594         mimicCommunicator.finalize();
 595     }
 596
 597     if (!thisRankHasDuty(cr, DUTY_PME))
 598     {
 599         /* Tell the PME only node to finish */
 600         gmx_pme_send_finish(cr);
 601     }
 602
 603     done_mdoutf(outf);
 604
 605     done_shellfc(fplog, shellfc, step_rel);
 606
 607     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 608 }