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/multisim.h"
  99 #include "gromacs/mdrunutility/printtime.h"
 100 #include "gromacs/mdtypes/awh_history.h"
 101 #include "gromacs/mdtypes/awh_params.h"
 102 #include "gromacs/mdtypes/commrec.h"
 103 #include "gromacs/mdtypes/df_history.h"
 104 #include "gromacs/mdtypes/enerdata.h"
 105 #include "gromacs/mdtypes/energyhistory.h"
 106 #include "gromacs/mdtypes/fcdata.h"
 107 #include "gromacs/mdtypes/forcerec.h"
 108 #include "gromacs/mdtypes/group.h"
 109 #include "gromacs/mdtypes/inputrec.h"
 110 #include "gromacs/mdtypes/interaction_const.h"
 111 #include "gromacs/mdtypes/md_enums.h"
 112 #include "gromacs/mdtypes/mdatom.h"
 113 #include "gromacs/mdtypes/mdrunoptions.h"
 114 #include "gromacs/mdtypes/observableshistory.h"
 115 #include "gromacs/mdtypes/state.h"
 116 #include "gromacs/mimic/communicator.h"
 117 #include "gromacs/mimic/utilities.h"
 118 #include "gromacs/pbcutil/mshift.h"
 119 #include "gromacs/pbcutil/pbc.h"
 120 #include "gromacs/pulling/pull.h"
 121 #include "gromacs/timing/wallcycle.h"
 122 #include "gromacs/timing/walltime_accounting.h"
 123 #include "gromacs/topology/atoms.h"
 124 #include "gromacs/topology/idef.h"
 125 #include "gromacs/topology/mtop_util.h"
 126 #include "gromacs/topology/topology.h"
 127 #include "gromacs/trajectory/trajectoryframe.h"
 128 #include "gromacs/utility/basedefinitions.h"
 129 #include "gromacs/utility/cstringutil.h"
 130 #include "gromacs/utility/fatalerror.h"
 131 #include "gromacs/utility/logger.h"
 132 #include "gromacs/utility/real.h"
 133 #include "gromacs/utility/smalloc.h"
 134
 135 #include "integrator.h"
 136 #include "replicaexchange.h"
 137 #include "shellfc.h"
 138
 139 using gmx::SimulationSignaller;
 140
 141 void gmx::Integrator::do_mimic()
 142 {
 143     t_inputrec              *ir   = inputrec;
 144     int64_t                  step, step_rel;
 145     double                   t, lam0[efptNR];
 146     bool                     isLastStep               = false;
 147     bool                     doFreeEnergyPerturbation = false;
 148     int                      force_flags;
 149     tensor                   force_vir, shake_vir, total_vir, pres;
 150     rvec                     mu_tot;
 151     gmx_localtop_t           top;
 152     PaddedVector<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     init_nrnb(nrnb);
 228
 229     gmx_mdoutf       *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle);
 230     gmx::EnergyOutput energyOutput;
 231     energyOutput.prepare(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, mdoutf_get_fp_dhdl(outf), true);
 232
 233     /* Kinetic energy data */
 234     std::unique_ptr<gmx_ekindata_t> eKinData = std::make_unique<gmx_ekindata_t>();
 235     gmx_ekindata_t                 *ekind    = eKinData.get();
 236     init_ekindata(fplog, top_global, &(ir->opts), ekind);
 237     /* Copy the cos acceleration to the groups struct */
 238     ekind->cosacc.cos_accel = ir->cos_accel;
 239
 240     gstat = global_stat_init(ir);
 241
 242     /* Check for polarizable models and flexible constraints */
 243     shellfc = init_shell_flexcon(fplog,
 244                                  top_global, constr ? constr->numFlexibleConstraints() : 0,
 245                                  ir->nstcalcenergy, DOMAINDECOMP(cr));
 246
 247     {
 248         double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
 249         if ((io > 2000) && MASTER(cr))
 250         {
 251             fprintf(stderr,
 252                     "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
 253                     io);
 254         }
 255     }
 256
 257     // Local state only becomes valid now.
 258     std::unique_ptr<t_state> stateInstance;
 259     t_state *                state;
 260
 261     if (DOMAINDECOMP(cr))
 262     {
 263         dd_init_local_top(*top_global, &top);
 264
 265         stateInstance = std::make_unique<t_state>();
 266         state         = stateInstance.get();
 267         dd_init_local_state(cr->dd, state_global, state);
 268
 269         /* Distribute the charge groups over the nodes from the master node */
 270         dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
 271                             state_global, *top_global, ir, imdSession,
 272                             pull_work,
 273                             state, &f, mdAtoms, &top, fr,
 274                             vsite, constr,
 275                             nrnb, nullptr, FALSE);
 276         shouldCheckNumberOfBondedInteractions = true;
 277         gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr);
 278     }
 279     else
 280     {
 281         state_change_natoms(state_global, state_global->natoms);
 282         /* We need to allocate one element extra, since we might use
 283          * (unaligned) 4-wide SIMD loads to access rvec entries.
 284          */
 285         f.resizeWithPadding(state_global->natoms);
 286         /* Copy the pointer to the global state */
 287         state = state_global;
 288
 289         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
 290                                   &graph, mdAtoms, constr, vsite, shellfc);
 291     }
 292
 293     auto mdatoms = mdAtoms->mdatoms();
 294
 295     // NOTE: The global state is no longer used at this point.
 296     // But state_global is still used as temporary storage space for writing
 297     // the global state to file and potentially for replica exchange.
 298     // (Global topology should persist.)
 299
 300     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 301
 302     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 303     {
 304         doFreeEnergyPerturbation = true;
 305     }
 306
 307     {
 308         int    cglo_flags = (CGLO_INITIALIZATION | CGLO_GSTAT |
 309                              (shouldCheckNumberOfBondedInteractions ?
 310                               CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 311         bool   bSumEkinhOld = false;
 312         t_vcm *vcm          = nullptr;
 313         compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 314                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
 315                         constr, &nullSignaller, state->box,
 316                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 317     }
 318     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 319                                     top_global, &top, state,
 320                                     &shouldCheckNumberOfBondedInteractions);
 321
 322     if (MASTER(cr))
 323     {
 324         fprintf(stderr, "starting MiMiC MD run '%s'\n\n",
 325                 *(top_global->name));
 326         if (mdrunOptions.verbose)
 327         {
 328             fprintf(stderr, "Calculated time to finish depends on nsteps from "
 329                     "run input file,\nwhich may not correspond to the time "
 330                     "needed to process input trajectory.\n\n");
 331         }
 332         fprintf(fplog, "\n");
 333     }
 334
 335     walltime_accounting_start_time(walltime_accounting);
 336     wallcycle_start(wcycle, ewcRUN);
 337     print_start(fplog, cr, walltime_accounting, "mdrun");
 338
 339     /***********************************************************
 340      *
 341      *             Loop over MD steps
 342      *
 343      ************************************************************/
 344
 345     if (constr)
 346     {
 347         GMX_LOG(mdlog.info).asParagraph().
 348             appendText("Simulations has constraints. Constraints will "
 349                        "be handled by CPMD.");
 350     }
 351
 352     GMX_LOG(mdlog.info).asParagraph().
 353         appendText("MiMiC does not report kinetic energy, total energy, temperature, virial and pressure.");
 354
 355     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 356                 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
 357                 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
 358                 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 359
 360     // we don't do counter resetting in rerun - finish will always be valid
 361     walltime_accounting_set_valid_finish(walltime_accounting);
 362
 363     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 364
 365     step     = ir->init_step;
 366     step_rel = 0;
 367
 368     /* and stop now if we should */
 369     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 370     while (!isLastStep)
 371     {
 372         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 373         wallcycle_start(wcycle, ewcSTEP);
 374
 375         t = step;
 376
 377         if (MASTER(cr))
 378         {
 379             mimicCommunicator.getCoords(&state_global->x, state_global->natoms);
 380         }
 381
 382         if (ir->efep != efepNO)
 383         {
 384             setCurrentLambdasLocal(step, ir->fepvals, lam0, state);
 385         }
 386
 387         if (MASTER(cr))
 388         {
 389             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 390             if (constructVsites && DOMAINDECOMP(cr))
 391             {
 392                 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
 393                           "use a single rank");
 394             }
 395         }
 396
 397         if (DOMAINDECOMP(cr))
 398         {
 399             /* Repartition the domain decomposition */
 400             const bool bMasterState = true;
 401             dd_partition_system(fplog, mdlog, step, cr,
 402                                 bMasterState, nstglobalcomm,
 403                                 state_global, *top_global, ir, imdSession,
 404                                 pull_work,
 405                                 state, &f, mdAtoms, &top, fr,
 406                                 vsite, constr,
 407                                 nrnb, wcycle,
 408                                 mdrunOptions.verbose);
 409             shouldCheckNumberOfBondedInteractions = true;
 410         }
 411
 412         if (MASTER(cr))
 413         {
 414             print_ebin_header(fplog, step, t); /* can we improve the information printed here? */
 415         }
 416
 417         if (ir->efep != efepNO)
 418         {
 419             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 420         }
 421
 422         force_flags = (GMX_FORCE_STATECHANGED |
 423                        GMX_FORCE_DYNAMICBOX |
 424                        GMX_FORCE_ALLFORCES |
 425                        GMX_FORCE_VIRIAL |  // TODO: Get rid of this once #2649 is solved
 426                        GMX_FORCE_ENERGY |
 427                        (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 428
 429         if (shellfc)
 430         {
 431             /* Now is the time to relax the shells */
 432             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
 433                                 enforcedRotation, step,
 434                                 ir, imdSession, pull_work, bNS, force_flags, &top,
 435                                 constr, enerd, fcd,
 436                                 state, f.arrayRefWithPadding(), force_vir, mdatoms,
 437                                 nrnb, wcycle, graph,
 438                                 shellfc, fr, ppForceWorkload, t, mu_tot,
 439                                 vsite,
 440                                 ddBalanceRegionHandler);
 441         }
 442         else
 443         {
 444             /* The coordinates (x) are shifted (to get whole molecules)
 445              * in do_force.
 446              * This is parallellized as well, and does communication too.
 447              * Check comments in sim_util.c
 448              */
 449             Awh       *awh = nullptr;
 450             gmx_edsam *ed  = nullptr;
 451             do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession,
 452                      pull_work,
 453                      step, nrnb, wcycle, &top,
 454                      state->box, state->x.arrayRefWithPadding(), &state->hist,
 455                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
 456                      state->lambda, graph,
 457                      fr, ppForceWorkload, vsite, mu_tot, t, ed,
 458                      GMX_FORCE_NS | force_flags,
 459                      ddBalanceRegionHandler);
 460         }
 461
 462         /* Now we have the energies and forces corresponding to the
 463          * coordinates at time t.
 464          */
 465         {
 466             const bool isCheckpointingStep = false;
 467             const bool doRerun             = false;
 468             const bool bSumEkinhOld        = false;
 469             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
 470                                      ir, state, state_global, observablesHistory,
 471                                      top_global, fr,
 472                                      outf, energyOutput, ekind, f,
 473                                      isCheckpointingStep, doRerun, isLastStep,
 474                                      mdrunOptions.writeConfout,
 475                                      bSumEkinhOld);
 476         }
 477
 478         stopHandler->setSignal();
 479
 480         if (graph)
 481         {
 482             /* Need to unshift here */
 483             unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 484         }
 485
 486         if (vsite != nullptr)
 487         {
 488             wallcycle_start(wcycle, ewcVSITECONSTR);
 489             if (graph != nullptr)
 490             {
 491                 shift_self(graph, state->box, as_rvec_array(state->x.data()));
 492             }
 493             construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
 494                              top.idef.iparams, top.idef.il,
 495                              fr->ePBC, fr->bMolPBC, cr, state->box);
 496
 497             if (graph != nullptr)
 498             {
 499                 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 500             }
 501             wallcycle_stop(wcycle, ewcVSITECONSTR);
 502         }
 503
 504         {
 505             const bool          doInterSimSignal = false;
 506             const bool          doIntraSimSignal = true;
 507             bool                bSumEkinhOld     = false;
 508             t_vcm              *vcm              = nullptr;
 509             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 510
 511             compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 512                             wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
 513                             constr, &signaller,
 514                             state->box,
 515                             &totalNumberOfBondedInteractions, &bSumEkinhOld,
 516                             CGLO_GSTAT | CGLO_ENERGY
 517                             | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
 518                             );
 519             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 520                                             top_global, &top, state,
 521                                             &shouldCheckNumberOfBondedInteractions);
 522         }
 523
 524         {
 525             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 526             gmx::ArrayRef<gmx::RVec>       ftemp;
 527             gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
 528             if (DOMAINDECOMP(cr))
 529             {
 530                 ftemp = gmx::makeArrayRef(fglobal);
 531                 dd_collect_vec(cr->dd, state, flocal, ftemp);
 532             }
 533             else
 534             {
 535                 ftemp = gmx::makeArrayRef(f);
 536             }
 537
 538             if (MASTER(cr))
 539             {
 540                 mimicCommunicator.sendEnergies(enerd->term[F_EPOT]);
 541                 mimicCommunicator.sendForces(ftemp, state_global->natoms);
 542             }
 543         }
 544
 545
 546
 547         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 548            the virial that should probably be addressed eventually. state->veta has better properies,
 549            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 550            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 551
 552         if (ir->efep != efepNO)
 553         {
 554             /* Sum up the foreign energy and dhdl terms for md and sd.
 555                Currently done every step so that dhdl is correct in the .edr */
 556             sum_dhdl(enerd, state->lambda, ir->fepvals);
 557         }
 558
 559         /* Output stuff */
 560         if (MASTER(cr))
 561         {
 562             const bool bCalcEnerStep = true;
 563             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep,
 564                                              t, mdatoms->tmass, enerd, state,
 565                                              ir->fepvals, ir->expandedvals, state->box,
 566                                              shake_vir, force_vir, total_vir, pres,
 567                                              ekind, mu_tot, constr);
 568
 569             const bool do_ene = true;
 570             const bool do_log = true;
 571             Awh       *awh    = nullptr;
 572             const bool do_dr  = ir->nstdisreout != 0;
 573             const bool do_or  = ir->nstorireout != 0;
 574
 575             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
 576                                                do_log ? fplog : nullptr,
 577                                                step, t,
 578                                                eprNORMAL, fcd, groups, &(ir->opts), awh);
 579
 580             if (do_per_step(step, ir->nstlog))
 581             {
 582                 if (fflush(fplog) != 0)
 583                 {
 584                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 585                 }
 586             }
 587         }
 588
 589         /* Print the remaining wall clock time for the run */
 590         if (isMasterSimMasterRank(ms, MASTER(cr)) &&
 591             (mdrunOptions.verbose || gmx_got_usr_signal()))
 592         {
 593             if (shellfc)
 594             {
 595                 fprintf(stderr, "\n");
 596             }
 597             print_time(stderr, walltime_accounting, step, ir, cr);
 598         }
 599
 600         cycles = wallcycle_stop(wcycle, ewcSTEP);
 601         if (DOMAINDECOMP(cr) && wcycle)
 602         {
 603             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 604         }
 605
 606         /* increase the MD step number */
 607         step++;
 608         step_rel++;
 609     }
 610     /* End of main MD loop */
 611
 612     /* Closing TNG files can include compressing data. Therefore it is good to do that
 613      * before stopping the time measurements. */
 614     mdoutf_tng_close(outf);
 615
 616     /* Stop measuring walltime */
 617     walltime_accounting_end_time(walltime_accounting);
 618
 619     if (MASTER(cr))
 620     {
 621         mimicCommunicator.finalize();
 622     }
 623
 624     if (!thisRankHasDuty(cr, DUTY_PME))
 625     {
 626         /* Tell the PME only node to finish */
 627         gmx_pme_send_finish(cr);
 628     }
 629
 630     done_mdoutf(outf);
 631
 632     done_shellfc(fplog, shellfc, step_rel);
 633
 634     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 635 }