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_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/listed_forces.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/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/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 "legacysimulator.h"
 135 #include "replicaexchange.h"
 136 #include "shellfc.h"
 137
 138 using gmx::SimulationSignaller;
 139
 140 void gmx::LegacySimulator::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     unsigned int                force_flags;
 148     tensor                      force_vir, shake_vir, total_vir, pres;
 149     rvec                        mu_tot;
 150     PaddedHostVector<gmx::RVec> f{};
 151     gmx_global_stat_t           gstat;
 152     gmx_shellfc_t*              shellfc;
 153
 154     double cycles;
 155
 156     /* Domain decomposition could incorrectly miss a bonded
 157        interaction, but checking for that requires a global
 158        communication stage, which does not otherwise happen in DD
 159        code. So we do that alongside the first global energy reduction
 160        after a new DD is made. These variables handle whether the
 161        check happens, and the result it returns. */
 162     bool shouldCheckNumberOfBondedInteractions = false;
 163     int  totalNumberOfBondedInteractions       = -1;
 164
 165     SimulationSignals signals;
 166     // Most global communnication stages don't propagate mdrun
 167     // signals, and will use this object to achieve that.
 168     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 169
 170     if (ir->bExpanded)
 171     {
 172         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 173     }
 174     if (ir->bSimTemp)
 175     {
 176         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 177     }
 178     if (ir->bDoAwh)
 179     {
 180         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 181     }
 182     if (replExParams.exchangeInterval > 0)
 183     {
 184         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 185     }
 186     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 187     {
 188         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 189     }
 190     if (ir->bIMD)
 191     {
 192         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 193     }
 194     if (isMultiSim(ms))
 195     {
 196         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 197     }
 198     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
 199                     [](int i) { return i != eannNO; }))
 200     {
 201         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 202     }
 203
 204     /* Settings for rerun */
 205     ir->nstlist              = 1;
 206     ir->nstcalcenergy        = 1;
 207     int        nstglobalcomm = 1;
 208     const bool bNS           = true;
 209
 210     if (MASTER(cr))
 211     {
 212         MimicCommunicator::init();
 213         auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(top_global);
 214         MimicCommunicator::sendInitData(nonConstGlobalTopology, state_global->x);
 215         ir->nsteps = MimicCommunicator::getStepNumber();
 216     }
 217
 218     ir->nstxout_compressed         = 0;
 219     const SimulationGroups* groups = &top_global->groups;
 220     {
 221         auto nonConstGlobalTopology                          = const_cast<gmx_mtop_t*>(top_global);
 222         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 223     }
 224
 225     initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
 226
 227     const bool        simulationsShareState = false;
 228     gmx_mdoutf*       outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
 229                                    mdModulesNotifier, ir, top_global, oenv, wcycle,
 230                                    StartingBehavior::NewSimulation, simulationsShareState, ms);
 231     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
 232                                    mdoutf_get_fp_dhdl(outf), true, StartingBehavior::NewSimulation,
 233                                    mdModulesNotifier);
 234
 235     gstat = global_stat_init(ir);
 236
 237     /* Check for polarizable models and flexible constraints */
 238     shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
 239                                  ir->nstcalcenergy, DOMAINDECOMP(cr));
 240
 241     {
 242         double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
 243         if ((io > 2000) && MASTER(cr))
 244         {
 245             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 246         }
 247     }
 248
 249     // Local state only becomes valid now.
 250     std::unique_ptr<t_state> stateInstance;
 251     t_state*                 state;
 252
 253     gmx_localtop_t top(top_global->ffparams);
 254
 255     if (DOMAINDECOMP(cr))
 256     {
 257         stateInstance = std::make_unique<t_state>();
 258         state         = stateInstance.get();
 259         dd_init_local_state(cr->dd, state_global, state);
 260
 261         /* Distribute the charge groups over the nodes from the master node */
 262         dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
 263                             imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
 264                             nrnb, nullptr, FALSE);
 265         shouldCheckNumberOfBondedInteractions = true;
 266         gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr->mpi_comm_mygroup);
 267     }
 268     else
 269     {
 270         state_change_natoms(state_global, state_global->natoms);
 271         /* Copy the pointer to the global state */
 272         state = state_global;
 273
 274         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 275     }
 276
 277     auto mdatoms = mdAtoms->mdatoms();
 278
 279     // NOTE: The global state is no longer used at this point.
 280     // But state_global is still used as temporary storage space for writing
 281     // the global state to file and potentially for replica exchange.
 282     // (Global topology should persist.)
 283
 284     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 285
 286     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 287     {
 288         doFreeEnergyPerturbation = true;
 289     }
 290
 291     {
 292         int cglo_flags =
 293                 (CGLO_GSTAT
 294                  | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 295         bool   bSumEkinhOld = false;
 296         t_vcm* vcm          = nullptr;
 297         compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
 298                         makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
 299                         force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
 300                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 301     }
 302     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
 303                                     makeConstArrayRef(state->x), state->box,
 304                                     &shouldCheckNumberOfBondedInteractions);
 305
 306     if (MASTER(cr))
 307     {
 308         fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global->name));
 309         if (mdrunOptions.verbose)
 310         {
 311             fprintf(stderr,
 312                     "Calculated time to finish depends on nsteps from "
 313                     "run input file,\nwhich may not correspond to the time "
 314                     "needed to process input trajectory.\n\n");
 315         }
 316         fprintf(fplog, "\n");
 317     }
 318
 319     walltime_accounting_start_time(walltime_accounting);
 320     wallcycle_start(wcycle, ewcRUN);
 321     print_start(fplog, cr, walltime_accounting, "mdrun");
 322
 323     /***********************************************************
 324      *
 325      *             Loop over MD steps
 326      *
 327      ************************************************************/
 328
 329     if (constr)
 330     {
 331         GMX_LOG(mdlog.info)
 332                 .asParagraph()
 333                 .appendText(
 334                         "Simulations has constraints. Constraints will "
 335                         "be handled by CPMD.");
 336     }
 337
 338     GMX_LOG(mdlog.info)
 339             .asParagraph()
 340             .appendText(
 341                     "MiMiC does not report kinetic energy, total energy, temperature, virial and "
 342                     "pressure.");
 343
 344     step     = ir->init_step;
 345     step_rel = 0;
 346
 347     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 348             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false, MASTER(cr),
 349             ir->nstlist, mdrunOptions.reproducible, nstglobalcomm, mdrunOptions.maximumHoursToRun,
 350             ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 351
 352     // we don't do counter resetting in rerun - finish will always be valid
 353     walltime_accounting_set_valid_finish(walltime_accounting);
 354
 355     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 356
 357     /* and stop now if we should */
 358     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 359     while (!isLastStep)
 360     {
 361         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 362         wallcycle_start(wcycle, ewcSTEP);
 363
 364         t = step;
 365
 366         if (MASTER(cr))
 367         {
 368             MimicCommunicator::getCoords(&state_global->x, state_global->natoms);
 369         }
 370
 371         if (ir->efep != efepNO)
 372         {
 373             setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
 374         }
 375
 376         if (MASTER(cr))
 377         {
 378             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 379             if (constructVsites && DOMAINDECOMP(cr))
 380             {
 381                 gmx_fatal(FARGS,
 382                           "Vsite recalculation with -rerun is not implemented with domain "
 383                           "decomposition, "
 384                           "use a single rank");
 385             }
 386         }
 387
 388         if (DOMAINDECOMP(cr))
 389         {
 390             /* Repartition the domain decomposition */
 391             const bool bMasterState = true;
 392             dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
 393                                 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
 394                                 fr, vsite, constr, nrnb, wcycle, mdrunOptions.verbose);
 395             shouldCheckNumberOfBondedInteractions = true;
 396         }
 397
 398         if (MASTER(cr))
 399         {
 400             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 401         }
 402
 403         if (ir->efep != efepNO)
 404         {
 405             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 406         }
 407
 408         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 409                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
 410                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 411
 412         if (shellfc)
 413         {
 414             /* Now is the time to relax the shells */
 415             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
 416                                 imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
 417                                 state->natoms, state->x.arrayRefWithPadding(),
 418                                 state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
 419                                 f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, shellfc,
 420                                 fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
 421         }
 422         else
 423         {
 424             /* The coordinates (x) are shifted (to get whole molecules)
 425              * in do_force.
 426              * This is parallellized as well, and does communication too.
 427              * Check comments in sim_util.c
 428              */
 429             Awh*       awh = nullptr;
 430             gmx_edsam* ed  = nullptr;
 431             do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
 432                      wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
 433                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
 434                      vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
 435         }
 436
 437         /* Now we have the energies and forces corresponding to the
 438          * coordinates at time t.
 439          */
 440         {
 441             const bool isCheckpointingStep = false;
 442             const bool doRerun             = false;
 443             const bool bSumEkinhOld        = false;
 444             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
 445                                      state_global, observablesHistory, top_global, fr, outf,
 446                                      energyOutput, ekind, f, isCheckpointingStep, doRerun,
 447                                      isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
 448         }
 449
 450         stopHandler->setSignal();
 451
 452         if (vsite != nullptr)
 453         {
 454             wallcycle_start(wcycle, ewcVSITECONSTR);
 455             vsite->construct(state->x, ir->delta_t, state->v, state->box);
 456             wallcycle_stop(wcycle, ewcVSITECONSTR);
 457         }
 458
 459         {
 460             const bool          doInterSimSignal = false;
 461             const bool          doIntraSimSignal = true;
 462             bool                bSumEkinhOld     = false;
 463             t_vcm*              vcm              = nullptr;
 464             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 465
 466             compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
 467                             makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
 468                             enerd, nullptr, nullptr, nullptr, nullptr, constr, &signaller,
 469                             state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
 470                             CGLO_GSTAT | CGLO_ENERGY
 471                                     | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
 472                                                                              : 0));
 473             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
 474                                             &top, makeConstArrayRef(state->x), state->box,
 475                                             &shouldCheckNumberOfBondedInteractions);
 476         }
 477
 478         {
 479             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 480             gmx::ArrayRef<gmx::RVec>       ftemp;
 481             gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
 482             if (DOMAINDECOMP(cr))
 483             {
 484                 ftemp = gmx::makeArrayRef(fglobal);
 485                 dd_collect_vec(cr->dd, state, flocal, ftemp);
 486             }
 487             else
 488             {
 489                 ftemp = gmx::makeArrayRef(f);
 490             }
 491
 492             if (MASTER(cr))
 493             {
 494                 MimicCommunicator::sendEnergies(enerd->term[F_EPOT]);
 495                 MimicCommunicator::sendForces(ftemp, state_global->natoms);
 496             }
 497         }
 498
 499
 500         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 501            the virial that should probably be addressed eventually. state->veta has better properies,
 502            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 503            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 504
 505         if (ir->efep != efepNO)
 506         {
 507             /* Sum up the foreign energy and dhdl terms for md and sd.
 508                Currently done every step so that dhdl is correct in the .edr */
 509             accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
 510         }
 511
 512         /* Output stuff */
 513         if (MASTER(cr))
 514         {
 515             const bool bCalcEnerStep = true;
 516             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep, t,
 517                                              mdatoms->tmass, enerd, state, ir->fepvals,
 518                                              ir->expandedvals, state->box, shake_vir, force_vir,
 519                                              total_vir, pres, ekind, mu_tot, constr);
 520
 521             const bool do_ene = true;
 522             const bool do_log = true;
 523             Awh*       awh    = nullptr;
 524             const bool do_dr  = ir->nstdisreout != 0;
 525             const bool do_or  = ir->nstorireout != 0;
 526
 527             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 528             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
 529                                                do_log ? fplog : nullptr, step, t,
 530                                                &fr->listedForces->fcdata(), awh);
 531
 532             if (do_per_step(step, ir->nstlog))
 533             {
 534                 if (fflush(fplog) != 0)
 535                 {
 536                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 537                 }
 538             }
 539         }
 540
 541         /* Print the remaining wall clock time for the run */
 542         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 543         {
 544             if (shellfc)
 545             {
 546                 fprintf(stderr, "\n");
 547             }
 548             print_time(stderr, walltime_accounting, step, ir, cr);
 549         }
 550
 551         cycles = wallcycle_stop(wcycle, ewcSTEP);
 552         if (DOMAINDECOMP(cr) && wcycle)
 553         {
 554             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 555         }
 556
 557         /* increase the MD step number */
 558         step++;
 559         step_rel++;
 560     }
 561     /* End of main MD loop */
 562
 563     /* Closing TNG files can include compressing data. Therefore it is good to do that
 564      * before stopping the time measurements. */
 565     mdoutf_tng_close(outf);
 566
 567     /* Stop measuring walltime */
 568     walltime_accounting_end_time(walltime_accounting);
 569
 570     if (MASTER(cr))
 571     {
 572         MimicCommunicator::finalize();
 573     }
 574
 575     if (!thisRankHasDuty(cr, DUTY_PME))
 576     {
 577         /* Tell the PME only node to finish */
 578         gmx_pme_send_finish(cr);
 579     }
 580
 581     done_mdoutf(outf);
 582
 583     done_shellfc(fplog, shellfc, step_rel);
 584
 585     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 586 }