src/gromacs/mdrun/mimic.cpp

   1 /*
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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/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 "legacysimulator.h"
 136 #include "replicaexchange.h"
 137 #include "shellfc.h"
 138
 139 using gmx::SimulationSignaller;
 140
 141 void gmx::LegacySimulator::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     unsigned int                force_flags;
 149     tensor                      force_vir, shake_vir, total_vir, pres;
 150     rvec                        mu_tot;
 151     PaddedHostVector<gmx::RVec> f{};
 152     gmx_global_stat_t           gstat;
 153     gmx_shellfc_t*              shellfc;
 154
 155     double cycles;
 156
 157     /* Domain decomposition could incorrectly miss a bonded
 158        interaction, but checking for that requires a global
 159        communication stage, which does not otherwise happen in DD
 160        code. So we do that alongside the first global energy reduction
 161        after a new DD is made. These variables handle whether the
 162        check happens, and the result it returns. */
 163     bool shouldCheckNumberOfBondedInteractions = false;
 164     int  totalNumberOfBondedInteractions       = -1;
 165
 166     SimulationSignals signals;
 167     // Most global communnication stages don't propagate mdrun
 168     // signals, and will use this object to achieve that.
 169     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 170
 171     if (ir->bExpanded)
 172     {
 173         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 174     }
 175     if (ir->bSimTemp)
 176     {
 177         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 178     }
 179     if (ir->bDoAwh)
 180     {
 181         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 182     }
 183     if (replExParams.exchangeInterval > 0)
 184     {
 185         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 186     }
 187     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 188     {
 189         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 190     }
 191     if (ir->bIMD)
 192     {
 193         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 194     }
 195     if (isMultiSim(ms))
 196     {
 197         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 198     }
 199     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
 200                     [](int i) { return i != eannNO; }))
 201     {
 202         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 203     }
 204
 205     /* Settings for rerun */
 206     ir->nstlist              = 1;
 207     ir->nstcalcenergy        = 1;
 208     int        nstglobalcomm = 1;
 209     const bool bNS           = true;
 210
 211     if (MASTER(cr))
 212     {
 213         MimicCommunicator::init();
 214         auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(top_global);
 215         MimicCommunicator::sendInitData(nonConstGlobalTopology, state_global->x);
 216         ir->nsteps = MimicCommunicator::getStepNumber();
 217     }
 218
 219     ir->nstxout_compressed         = 0;
 220     const SimulationGroups* groups = &top_global->groups;
 221     {
 222         auto nonConstGlobalTopology                          = const_cast<gmx_mtop_t*>(top_global);
 223         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 224     }
 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->mpi_comm_mygroup);
 268     }
 269     else
 270     {
 271         state_change_natoms(state_global, state_global->natoms);
 272         /* Copy the pointer to the global state */
 273         state = state_global;
 274
 275         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 276     }
 277
 278     auto mdatoms = mdAtoms->mdatoms();
 279
 280     // NOTE: The global state is no longer used at this point.
 281     // But state_global is still used as temporary storage space for writing
 282     // the global state to file and potentially for replica exchange.
 283     // (Global topology should persist.)
 284
 285     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 286
 287     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 288     {
 289         doFreeEnergyPerturbation = true;
 290     }
 291
 292     {
 293         int cglo_flags =
 294                 (CGLO_GSTAT
 295                  | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 296         bool   bSumEkinhOld = false;
 297         t_vcm* vcm          = nullptr;
 298         compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
 299                         makeConstArrayRef(state->v), state->box, state->lambda[efptVDW], mdatoms, nrnb,
 300                         vcm, nullptr, enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
 301                         state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 302     }
 303     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
 304                                     makeConstArrayRef(state->x), state->box,
 305                                     &shouldCheckNumberOfBondedInteractions);
 306
 307     if (MASTER(cr))
 308     {
 309         fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global->name));
 310         if (mdrunOptions.verbose)
 311         {
 312             fprintf(stderr,
 313                     "Calculated time to finish depends on nsteps from "
 314                     "run input file,\nwhich may not correspond to the time "
 315                     "needed to process input trajectory.\n\n");
 316         }
 317         fprintf(fplog, "\n");
 318     }
 319
 320     walltime_accounting_start_time(walltime_accounting);
 321     wallcycle_start(wcycle, ewcRUN);
 322     print_start(fplog, cr, walltime_accounting, "mdrun");
 323
 324     /***********************************************************
 325      *
 326      *             Loop over MD steps
 327      *
 328      ************************************************************/
 329
 330     if (constr)
 331     {
 332         GMX_LOG(mdlog.info)
 333                 .asParagraph()
 334                 .appendText(
 335                         "Simulations has constraints. Constraints will "
 336                         "be handled by CPMD.");
 337     }
 338
 339     GMX_LOG(mdlog.info)
 340             .asParagraph()
 341             .appendText(
 342                     "MiMiC does not report kinetic energy, total energy, temperature, virial and "
 343                     "pressure.");
 344
 345     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 346             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false, MASTER(cr),
 347             ir->nstlist, mdrunOptions.reproducible, nstglobalcomm, mdrunOptions.maximumHoursToRun,
 348             ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 349
 350     // we don't do counter resetting in rerun - finish will always be valid
 351     walltime_accounting_set_valid_finish(walltime_accounting);
 352
 353     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 354
 355     step     = ir->init_step;
 356     step_rel = 0;
 357
 358     /* and stop now if we should */
 359     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 360     while (!isLastStep)
 361     {
 362         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 363         wallcycle_start(wcycle, ewcSTEP);
 364
 365         t = step;
 366
 367         if (MASTER(cr))
 368         {
 369             MimicCommunicator::getCoords(&state_global->x, state_global->natoms);
 370         }
 371
 372         if (ir->efep != efepNO)
 373         {
 374             setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
 375         }
 376
 377         if (MASTER(cr))
 378         {
 379             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 380             if (constructVsites && DOMAINDECOMP(cr))
 381             {
 382                 gmx_fatal(FARGS,
 383                           "Vsite recalculation with -rerun is not implemented with domain "
 384                           "decomposition, "
 385                           "use a single rank");
 386             }
 387         }
 388
 389         if (DOMAINDECOMP(cr))
 390         {
 391             /* Repartition the domain decomposition */
 392             const bool bMasterState = true;
 393             dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
 394                                 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
 395                                 fr, vsite, constr, nrnb, wcycle, mdrunOptions.verbose);
 396             shouldCheckNumberOfBondedInteractions = true;
 397         }
 398
 399         if (MASTER(cr))
 400         {
 401             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 402         }
 403
 404         if (ir->efep != efepNO)
 405         {
 406             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 407         }
 408
 409         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 410                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
 411                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 412
 413         if (shellfc)
 414         {
 415             /* Now is the time to relax the shells */
 416             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
 417                                 imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
 418                                 state->natoms, state->x.arrayRefWithPadding(),
 419                                 state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
 420                                 f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, shellfc,
 421                                 fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
 422         }
 423         else
 424         {
 425             /* The coordinates (x) are shifted (to get whole molecules)
 426              * in do_force.
 427              * This is parallellized as well, and does communication too.
 428              * Check comments in sim_util.c
 429              */
 430             Awh*       awh = nullptr;
 431             gmx_edsam* ed  = nullptr;
 432             do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
 433                      wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
 434                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, fr,
 435                      runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
 436                      ddBalanceRegionHandler);
 437         }
 438
 439         /* Now we have the energies and forces corresponding to the
 440          * coordinates at time t.
 441          */
 442         {
 443             const bool isCheckpointingStep = false;
 444             const bool doRerun             = false;
 445             const bool bSumEkinhOld        = false;
 446             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
 447                                      state_global, observablesHistory, top_global, fr, outf,
 448                                      energyOutput, ekind, f, isCheckpointingStep, doRerun,
 449                                      isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
 450         }
 451
 452         stopHandler->setSignal();
 453
 454         if (vsite != nullptr)
 455         {
 456             wallcycle_start(wcycle, ewcVSITECONSTR);
 457             vsite->construct(state->x, ir->delta_t, state->v, state->box);
 458             wallcycle_stop(wcycle, ewcVSITECONSTR);
 459         }
 460
 461         {
 462             const bool          doInterSimSignal = false;
 463             const bool          doIntraSimSignal = true;
 464             bool                bSumEkinhOld     = false;
 465             t_vcm*              vcm              = nullptr;
 466             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 467
 468             compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
 469                             makeConstArrayRef(state->v), state->box, state->lambda[efptVDW], mdatoms,
 470                             nrnb, vcm, wcycle, enerd, nullptr, nullptr, nullptr, nullptr, constr,
 471                             &signaller, state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
 472                             CGLO_GSTAT | CGLO_ENERGY
 473                                     | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
 474                                                                              : 0));
 475             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
 476                                             &top, makeConstArrayRef(state->x), state->box,
 477                                             &shouldCheckNumberOfBondedInteractions);
 478         }
 479
 480         {
 481             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 482             gmx::ArrayRef<gmx::RVec>       ftemp;
 483             gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
 484             if (DOMAINDECOMP(cr))
 485             {
 486                 ftemp = gmx::makeArrayRef(fglobal);
 487                 dd_collect_vec(cr->dd, state, flocal, ftemp);
 488             }
 489             else
 490             {
 491                 ftemp = gmx::makeArrayRef(f);
 492             }
 493
 494             if (MASTER(cr))
 495             {
 496                 MimicCommunicator::sendEnergies(enerd->term[F_EPOT]);
 497                 MimicCommunicator::sendForces(ftemp, state_global->natoms);
 498             }
 499         }
 500
 501
 502         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 503            the virial that should probably be addressed eventually. state->veta has better properies,
 504            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 505            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 506
 507         if (ir->efep != efepNO)
 508         {
 509             /* Sum up the foreign energy and dhdl terms for md and sd.
 510                Currently done every step so that dhdl is correct in the .edr */
 511             sum_dhdl(enerd, state->lambda, *ir->fepvals);
 512         }
 513
 514         /* Output stuff */
 515         if (MASTER(cr))
 516         {
 517             const bool bCalcEnerStep = true;
 518             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep, t,
 519                                              mdatoms->tmass, enerd, state, ir->fepvals,
 520                                              ir->expandedvals, state->box, shake_vir, force_vir,
 521                                              total_vir, pres, ekind, mu_tot, constr);
 522
 523             const bool do_ene = true;
 524             const bool do_log = true;
 525             Awh*       awh    = nullptr;
 526             const bool do_dr  = ir->nstdisreout != 0;
 527             const bool do_or  = ir->nstorireout != 0;
 528
 529             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 530             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
 531                                                do_log ? fplog : nullptr, step, t, fcd, awh);
 532
 533             if (do_per_step(step, ir->nstlog))
 534             {
 535                 if (fflush(fplog) != 0)
 536                 {
 537                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 538                 }
 539             }
 540         }
 541
 542         /* Print the remaining wall clock time for the run */
 543         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 544         {
 545             if (shellfc)
 546             {
 547                 fprintf(stderr, "\n");
 548             }
 549             print_time(stderr, walltime_accounting, step, ir, cr);
 550         }
 551
 552         cycles = wallcycle_stop(wcycle, ewcSTEP);
 553         if (DOMAINDECOMP(cr) && wcycle)
 554         {
 555             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 556         }
 557
 558         /* increase the MD step number */
 559         step++;
 560         step_rel++;
 561     }
 562     /* End of main MD loop */
 563
 564     /* Closing TNG files can include compressing data. Therefore it is good to do that
 565      * before stopping the time measurements. */
 566     mdoutf_tng_close(outf);
 567
 568     /* Stop measuring walltime */
 569     walltime_accounting_end_time(walltime_accounting);
 570
 571     if (MASTER(cr))
 572     {
 573         MimicCommunicator::finalize();
 574     }
 575
 576     if (!thisRankHasDuty(cr, DUTY_PME))
 577     {
 578         /* Tell the PME only node to finish */
 579         gmx_pme_send_finish(cr);
 580     }
 581
 582     done_mdoutf(outf);
 583
 584     done_shellfc(fplog, shellfc, step_rel);
 585
 586     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 587 }