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