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
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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.h"
  64 #include "gromacs/ewald/pme_load_balancing.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/printtime.h"
  99 #include "gromacs/mdtypes/awh_history.h"
 100 #include "gromacs/mdtypes/awh_params.h"
 101 #include "gromacs/mdtypes/commrec.h"
 102 #include "gromacs/mdtypes/df_history.h"
 103 #include "gromacs/mdtypes/enerdata.h"
 104 #include "gromacs/mdtypes/energyhistory.h"
 105 #include "gromacs/mdtypes/fcdata.h"
 106 #include "gromacs/mdtypes/forcerec.h"
 107 #include "gromacs/mdtypes/group.h"
 108 #include "gromacs/mdtypes/inputrec.h"
 109 #include "gromacs/mdtypes/interaction_const.h"
 110 #include "gromacs/mdtypes/md_enums.h"
 111 #include "gromacs/mdtypes/mdatom.h"
 112 #include "gromacs/mdtypes/mdrunoptions.h"
 113 #include "gromacs/mdtypes/observableshistory.h"
 114 #include "gromacs/mdtypes/state.h"
 115 #include "gromacs/mimic/communicator.h"
 116 #include "gromacs/mimic/utilities.h"
 117 #include "gromacs/pbcutil/mshift.h"
 118 #include "gromacs/pbcutil/pbc.h"
 119 #include "gromacs/pulling/pull.h"
 120 #include "gromacs/timing/wallcycle.h"
 121 #include "gromacs/timing/walltime_accounting.h"
 122 #include "gromacs/topology/atoms.h"
 123 #include "gromacs/topology/idef.h"
 124 #include "gromacs/topology/mtop_util.h"
 125 #include "gromacs/topology/topology.h"
 126 #include "gromacs/trajectory/trajectoryframe.h"
 127 #include "gromacs/utility/basedefinitions.h"
 128 #include "gromacs/utility/cstringutil.h"
 129 #include "gromacs/utility/fatalerror.h"
 130 #include "gromacs/utility/logger.h"
 131 #include "gromacs/utility/real.h"
 132 #include "gromacs/utility/smalloc.h"
 133
 134 #include "integrator.h"
 135 #include "replicaexchange.h"
 136 #include "shellfc.h"
 137
 138 using gmx::SimulationSignaller;
 139
 140 void gmx::Integrator::do_mimic()
 141 {
 142     t_inputrec              *ir   = inputrec;
 143     int64_t                  step, step_rel;
 144     double                   t, lam0[efptNR];
 145     bool                     isLastStep               = false;
 146     bool                     doFreeEnergyPerturbation = false;
 147     int                      force_flags;
 148     tensor                   force_vir, shake_vir, total_vir, pres;
 149     rvec                     mu_tot;
 150     gmx_localtop_t           top;
 151     PaddedVector<gmx::RVec>  f {};
 152     gmx_global_stat_t        gstat;
 153     t_graph                 *graph = nullptr;
 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     // Communicator to interact with MiMiC
 213     MimicCommunicator mimicCommunicator {};
 214     if (MASTER(cr))
 215     {
 216         mimicCommunicator.init();
 217         mimicCommunicator.sendInitData(top_global, state_global->x);
 218         ir->nsteps = mimicCommunicator.getStepNumber();
 219     }
 220
 221     ir->nstxout_compressed                   = 0;
 222     SimulationGroups *groups                        = &top_global->groups;
 223     top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 224
 225     initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
 226     init_nrnb(nrnb);
 227
 228     gmx_mdoutf       *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle);
 229     gmx::EnergyOutput energyOutput;
 230     energyOutput.prepare(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, mdoutf_get_fp_dhdl(outf), true);
 231
 232     /* Kinetic energy data */
 233     std::unique_ptr<gmx_ekindata_t> eKinData = std::make_unique<gmx_ekindata_t>();
 234     gmx_ekindata_t                 *ekind    = eKinData.get();
 235     init_ekindata(fplog, top_global, &(ir->opts), ekind);
 236     /* Copy the cos acceleration to the groups struct */
 237     ekind->cosacc.cos_accel = ir->cos_accel;
 238
 239     gstat = global_stat_init(ir);
 240
 241     /* Check for polarizable models and flexible constraints */
 242     shellfc = init_shell_flexcon(fplog,
 243                                  top_global, constr ? constr->numFlexibleConstraints() : 0,
 244                                  ir->nstcalcenergy, DOMAINDECOMP(cr));
 245
 246     {
 247         double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
 248         if ((io > 2000) && MASTER(cr))
 249         {
 250             fprintf(stderr,
 251                     "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
 252                     io);
 253         }
 254     }
 255
 256     // Local state only becomes valid now.
 257     std::unique_ptr<t_state> stateInstance;
 258     t_state *                state;
 259
 260     if (DOMAINDECOMP(cr))
 261     {
 262         dd_init_local_top(*top_global, &top);
 263
 264         stateInstance = std::make_unique<t_state>();
 265         state         = stateInstance.get();
 266         dd_init_local_state(cr->dd, state_global, state);
 267
 268         /* Distribute the charge groups over the nodes from the master node */
 269         dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
 270                             state_global, *top_global, ir, imdSession,
 271                             pull_work,
 272                             state, &f, mdAtoms, &top, fr,
 273                             vsite, constr,
 274                             nrnb, nullptr, FALSE);
 275         shouldCheckNumberOfBondedInteractions = true;
 276         gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr);
 277     }
 278     else
 279     {
 280         state_change_natoms(state_global, state_global->natoms);
 281         /* We need to allocate one element extra, since we might use
 282          * (unaligned) 4-wide SIMD loads to access rvec entries.
 283          */
 284         f.resizeWithPadding(state_global->natoms);
 285         /* Copy the pointer to the global state */
 286         state = state_global;
 287
 288         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
 289                                   &graph, mdAtoms, constr, vsite, shellfc);
 290     }
 291
 292     auto mdatoms = mdAtoms->mdatoms();
 293
 294     // NOTE: The global state is no longer used at this point.
 295     // But state_global is still used as temporary storage space for writing
 296     // the global state to file and potentially for replica exchange.
 297     // (Global topology should persist.)
 298
 299     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 300
 301     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 302     {
 303         doFreeEnergyPerturbation = true;
 304     }
 305
 306     {
 307         int    cglo_flags = (CGLO_INITIALIZATION | CGLO_GSTAT |
 308                              (shouldCheckNumberOfBondedInteractions ?
 309                               CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 310         bool   bSumEkinhOld = false;
 311         t_vcm *vcm          = nullptr;
 312         compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 313                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
 314                         constr, &nullSignaller, state->box,
 315                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 316     }
 317     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 318                                     top_global, &top, state,
 319                                     &shouldCheckNumberOfBondedInteractions);
 320
 321     if (MASTER(cr))
 322     {
 323         fprintf(stderr, "starting MiMiC MD run '%s'\n\n",
 324                 *(top_global->name));
 325         if (mdrunOptions.verbose)
 326         {
 327             fprintf(stderr, "Calculated time to finish depends on nsteps from "
 328                     "run input file,\nwhich may not correspond to the time "
 329                     "needed to process input trajectory.\n\n");
 330         }
 331         fprintf(fplog, "\n");
 332     }
 333
 334     walltime_accounting_start_time(walltime_accounting);
 335     wallcycle_start(wcycle, ewcRUN);
 336     print_start(fplog, cr, walltime_accounting, "mdrun");
 337
 338     /***********************************************************
 339      *
 340      *             Loop over MD steps
 341      *
 342      ************************************************************/
 343
 344     if (constr)
 345     {
 346         GMX_LOG(mdlog.info).asParagraph().
 347             appendText("Simulations has constraints. Constraints will "
 348                        "be handled by CPMD.");
 349     }
 350
 351     GMX_LOG(mdlog.info).asParagraph().
 352         appendText("MiMiC does not report kinetic energy, total energy, temperature, virial and pressure.");
 353
 354     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 355                 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
 356                 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
 357                 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 358
 359     // we don't do counter resetting in rerun - finish will always be valid
 360     walltime_accounting_set_valid_finish(walltime_accounting);
 361
 362     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 363
 364     step     = ir->init_step;
 365     step_rel = 0;
 366
 367     /* and stop now if we should */
 368     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 369     while (!isLastStep)
 370     {
 371         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 372         wallcycle_start(wcycle, ewcSTEP);
 373
 374         t = step;
 375
 376         if (MASTER(cr))
 377         {
 378             mimicCommunicator.getCoords(&state_global->x, state_global->natoms);
 379         }
 380
 381         if (ir->efep != efepNO)
 382         {
 383             setCurrentLambdasLocal(step, ir->fepvals, lam0, state);
 384         }
 385
 386         if (MASTER(cr))
 387         {
 388             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 389             if (constructVsites && DOMAINDECOMP(cr))
 390             {
 391                 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
 392                           "use a single rank");
 393             }
 394         }
 395
 396         if (DOMAINDECOMP(cr))
 397         {
 398             /* Repartition the domain decomposition */
 399             const bool bMasterState = true;
 400             dd_partition_system(fplog, mdlog, step, cr,
 401                                 bMasterState, nstglobalcomm,
 402                                 state_global, *top_global, ir, imdSession,
 403                                 pull_work,
 404                                 state, &f, mdAtoms, &top, fr,
 405                                 vsite, constr,
 406                                 nrnb, wcycle,
 407                                 mdrunOptions.verbose);
 408             shouldCheckNumberOfBondedInteractions = true;
 409         }
 410
 411         if (MASTER(cr))
 412         {
 413             print_ebin_header(fplog, step, t); /* can we improve the information printed here? */
 414         }
 415
 416         if (ir->efep != efepNO)
 417         {
 418             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 419         }
 420
 421         force_flags = (GMX_FORCE_STATECHANGED |
 422                        GMX_FORCE_DYNAMICBOX |
 423                        GMX_FORCE_ALLFORCES |
 424                        GMX_FORCE_VIRIAL |  // TODO: Get rid of this once #2649 is solved
 425                        GMX_FORCE_ENERGY |
 426                        (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 427
 428         if (shellfc)
 429         {
 430             /* Now is the time to relax the shells */
 431             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
 432                                 enforcedRotation, step,
 433                                 ir, imdSession, pull_work, bNS, force_flags, &top,
 434                                 constr, enerd, fcd,
 435                                 state, f.arrayRefWithPadding(), force_vir, mdatoms,
 436                                 nrnb, wcycle, graph,
 437                                 shellfc, fr, ppForceWorkload, t, mu_tot,
 438                                 vsite,
 439                                 ddBalanceRegionHandler);
 440         }
 441         else
 442         {
 443             /* The coordinates (x) are shifted (to get whole molecules)
 444              * in do_force.
 445              * This is parallellized as well, and does communication too.
 446              * Check comments in sim_util.c
 447              */
 448             Awh       *awh = nullptr;
 449             gmx_edsam *ed  = nullptr;
 450             do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession,
 451                      pull_work,
 452                      step, nrnb, wcycle, &top,
 453                      state->box, state->x.arrayRefWithPadding(), &state->hist,
 454                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
 455                      state->lambda, graph,
 456                      fr, ppForceWorkload, vsite, mu_tot, t, ed,
 457                      GMX_FORCE_NS | force_flags,
 458                      ddBalanceRegionHandler);
 459         }
 460
 461         /* Now we have the energies and forces corresponding to the
 462          * coordinates at time t.
 463          */
 464         {
 465             const bool isCheckpointingStep = false;
 466             const bool doRerun             = false;
 467             const bool bSumEkinhOld        = false;
 468             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
 469                                      ir, state, state_global, observablesHistory,
 470                                      top_global, fr,
 471                                      outf, energyOutput, ekind, f,
 472                                      isCheckpointingStep, doRerun, isLastStep,
 473                                      mdrunOptions.writeConfout,
 474                                      bSumEkinhOld);
 475         }
 476
 477         stopHandler->setSignal();
 478
 479         if (graph)
 480         {
 481             /* Need to unshift here */
 482             unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 483         }
 484
 485         if (vsite != nullptr)
 486         {
 487             wallcycle_start(wcycle, ewcVSITECONSTR);
 488             if (graph != nullptr)
 489             {
 490                 shift_self(graph, state->box, as_rvec_array(state->x.data()));
 491             }
 492             construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
 493                              top.idef.iparams, top.idef.il,
 494                              fr->ePBC, fr->bMolPBC, cr, state->box);
 495
 496             if (graph != nullptr)
 497             {
 498                 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 499             }
 500             wallcycle_stop(wcycle, ewcVSITECONSTR);
 501         }
 502
 503         {
 504             const bool          doInterSimSignal = false;
 505             const bool          doIntraSimSignal = true;
 506             bool                bSumEkinhOld     = false;
 507             t_vcm              *vcm              = nullptr;
 508             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 509
 510             compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 511                             wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
 512                             constr, &signaller,
 513                             state->box,
 514                             &totalNumberOfBondedInteractions, &bSumEkinhOld,
 515                             CGLO_GSTAT | CGLO_ENERGY
 516                             | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
 517                             );
 518             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 519                                             top_global, &top, state,
 520                                             &shouldCheckNumberOfBondedInteractions);
 521         }
 522
 523         {
 524             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 525             gmx::ArrayRef<gmx::RVec>       ftemp;
 526             gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
 527             if (DOMAINDECOMP(cr))
 528             {
 529                 ftemp = gmx::makeArrayRef(fglobal);
 530                 dd_collect_vec(cr->dd, state, flocal, ftemp);
 531             }
 532             else
 533             {
 534                 ftemp = gmx::makeArrayRef(f);
 535             }
 536
 537             if (MASTER(cr))
 538             {
 539                 mimicCommunicator.sendEnergies(enerd->term[F_EPOT]);
 540                 mimicCommunicator.sendForces(ftemp, state_global->natoms);
 541             }
 542         }
 543
 544
 545
 546         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 547            the virial that should probably be addressed eventually. state->veta has better properies,
 548            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 549            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 550
 551         if (ir->efep != efepNO)
 552         {
 553             /* Sum up the foreign energy and dhdl terms for md and sd.
 554                Currently done every step so that dhdl is correct in the .edr */
 555             sum_dhdl(enerd, state->lambda, ir->fepvals);
 556         }
 557
 558         /* Output stuff */
 559         if (MASTER(cr))
 560         {
 561             const bool bCalcEnerStep = true;
 562             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep,
 563                                              t, mdatoms->tmass, enerd, state,
 564                                              ir->fepvals, ir->expandedvals, state->box,
 565                                              shake_vir, force_vir, total_vir, pres,
 566                                              ekind, mu_tot, constr);
 567
 568             const bool do_ene = true;
 569             const bool do_log = true;
 570             Awh       *awh    = nullptr;
 571             const bool do_dr  = ir->nstdisreout != 0;
 572             const bool do_or  = ir->nstorireout != 0;
 573
 574             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
 575                                                do_log ? fplog : nullptr,
 576                                                step, t,
 577                                                eprNORMAL, fcd, groups, &(ir->opts), awh);
 578
 579             if (do_per_step(step, ir->nstlog))
 580             {
 581                 if (fflush(fplog) != 0)
 582                 {
 583                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 584                 }
 585             }
 586         }
 587
 588         /* Print the remaining wall clock time for the run */
 589         if (isMasterSimMasterRank(ms, cr) &&
 590             (mdrunOptions.verbose || gmx_got_usr_signal()))
 591         {
 592             if (shellfc)
 593             {
 594                 fprintf(stderr, "\n");
 595             }
 596             print_time(stderr, walltime_accounting, step, ir, cr);
 597         }
 598
 599         cycles = wallcycle_stop(wcycle, ewcSTEP);
 600         if (DOMAINDECOMP(cr) && wcycle)
 601         {
 602             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 603         }
 604
 605         /* increase the MD step number */
 606         step++;
 607         step_rel++;
 608     }
 609     /* End of main MD loop */
 610
 611     /* Closing TNG files can include compressing data. Therefore it is good to do that
 612      * before stopping the time measurements. */
 613     mdoutf_tng_close(outf);
 614
 615     /* Stop measuring walltime */
 616     walltime_accounting_end_time(walltime_accounting);
 617
 618     if (MASTER(cr))
 619     {
 620         mimicCommunicator.finalize();
 621     }
 622
 623     if (!thisRankHasDuty(cr, DUTY_PME))
 624     {
 625         /* Tell the PME only node to finish */
 626         gmx_pme_send_finish(cr);
 627     }
 628
 629     done_mdoutf(outf);
 630
 631     done_shellfc(fplog, shellfc, step_rel);
 632
 633     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 634 }