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
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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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/domdec.h"
  57 #include "gromacs/domdec/domdec_network.h"
  58 #include "gromacs/domdec/domdec_struct.h"
  59 #include "gromacs/domdec/partition.h"
  60 #include "gromacs/essentialdynamics/edsam.h"
  61 #include "gromacs/ewald/pme.h"
  62 #include "gromacs/ewald/pme_load_balancing.h"
  63 #include "gromacs/fileio/trxio.h"
  64 #include "gromacs/gmxlib/network.h"
  65 #include "gromacs/gmxlib/nrnb.h"
  66 #include "gromacs/gpu_utils/gpu_utils.h"
  67 #include "gromacs/imd/imd.h"
  68 #include "gromacs/listed_forces/manage_threading.h"
  69 #include "gromacs/math/functions.h"
  70 #include "gromacs/math/utilities.h"
  71 #include "gromacs/math/vec.h"
  72 #include "gromacs/math/vectypes.h"
  73 #include "gromacs/mdlib/checkpointhandler.h"
  74 #include "gromacs/mdlib/compute_io.h"
  75 #include "gromacs/mdlib/constr.h"
  76 #include "gromacs/mdlib/ebin.h"
  77 #include "gromacs/mdlib/expanded.h"
  78 #include "gromacs/mdlib/force.h"
  79 #include "gromacs/mdlib/force_flags.h"
  80 #include "gromacs/mdlib/forcerec.h"
  81 #include "gromacs/mdlib/md_support.h"
  82 #include "gromacs/mdlib/mdatoms.h"
  83 #include "gromacs/mdlib/mdebin.h"
  84 #include "gromacs/mdlib/mdoutf.h"
  85 #include "gromacs/mdlib/mdrun.h"
  86 #include "gromacs/mdlib/mdsetup.h"
  87 #include "gromacs/mdlib/membed.h"
  88 #include "gromacs/mdlib/nb_verlet.h"
  89 #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
  90 #include "gromacs/mdlib/ns.h"
  91 #include "gromacs/mdlib/resethandler.h"
  92 #include "gromacs/mdlib/shellfc.h"
  93 #include "gromacs/mdlib/sighandler.h"
  94 #include "gromacs/mdlib/sim_util.h"
  95 #include "gromacs/mdlib/simulationsignal.h"
  96 #include "gromacs/mdlib/stophandler.h"
  97 #include "gromacs/mdlib/tgroup.h"
  98 #include "gromacs/mdlib/trajectory_writing.h"
  99 #include "gromacs/mdlib/update.h"
 100 #include "gromacs/mdlib/vcm.h"
 101 #include "gromacs/mdlib/vsite.h"
 102 #include "gromacs/mdtypes/awh_history.h"
 103 #include "gromacs/mdtypes/awh_params.h"
 104 #include "gromacs/mdtypes/commrec.h"
 105 #include "gromacs/mdtypes/df_history.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/observableshistory.h"
 115 #include "gromacs/mdtypes/state.h"
 116 #include "gromacs/mimic/MimicCommunicator.h"
 117 #include "gromacs/mimic/MimicUtils.h"
 118 #include "gromacs/pbcutil/mshift.h"
 119 #include "gromacs/pbcutil/pbc.h"
 120 #include "gromacs/pulling/pull.h"
 121 #include "gromacs/swap/swapcoords.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 "integrator.h"
 137 #include "replicaexchange.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     gmx_enerdata_t          *enerd;
 153     PaddedVector<gmx::RVec>  f {};
 154     gmx_global_stat_t        gstat;
 155     t_graph                 *graph = nullptr;
 156     gmx_groups_t            *groups;
 157     gmx_shellfc_t           *shellfc;
 158
 159     double                   cycles;
 160
 161     /* Domain decomposition could incorrectly miss a bonded
 162        interaction, but checking for that requires a global
 163        communication stage, which does not otherwise happen in DD
 164        code. So we do that alongside the first global energy reduction
 165        after a new DD is made. These variables handle whether the
 166        check happens, and the result it returns. */
 167     bool              shouldCheckNumberOfBondedInteractions = false;
 168     int               totalNumberOfBondedInteractions       = -1;
 169
 170     SimulationSignals signals;
 171     // Most global communnication stages don't propagate mdrun
 172     // signals, and will use this object to achieve that.
 173     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 174
 175     if (ir->bExpanded)
 176     {
 177         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 178     }
 179     if (ir->bSimTemp)
 180     {
 181         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 182     }
 183     if (ir->bDoAwh)
 184     {
 185         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 186     }
 187     if (replExParams.exchangeInterval > 0)
 188     {
 189         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 190     }
 191     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 192     {
 193         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 194     }
 195     if (ir->bIMD)
 196     {
 197         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 198     }
 199     if (isMultiSim(ms))
 200     {
 201         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 202     }
 203     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
 204                     [](int i){return i != eannNO; }))
 205     {
 206         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 207     }
 208
 209     /* Settings for rerun */
 210     ir->nstlist       = 1;
 211     ir->nstcalcenergy = 1;
 212     int        nstglobalcomm = 1;
 213     const bool bNS           = true;
 214
 215     // Communicator to interact with MiMiC
 216     MimicCommunicator mimicCommunicator {};
 217     if (MASTER(cr))
 218     {
 219         mimicCommunicator.init();
 220         mimicCommunicator.sendInitData(top_global, state_global->x);
 221         ir->nsteps = mimicCommunicator.getStepNumber();
 222     }
 223
 224     ir->nstxout_compressed                   = 0;
 225     groups                                   = &top_global->groups;
 226     top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 227
 228     initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
 229     init_nrnb(nrnb);
 230
 231     gmx_mdoutf *outf   = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle);
 232     t_mdebin   *mdebin = init_mdebin(mdrunOptions.continuationOptions.appendFiles ? nullptr : mdoutf_get_fp_ene(outf),
 233                                      top_global, ir, mdoutf_get_fp_dhdl(outf), true);
 234
 235     /* Energy terms and groups */
 236     snew(enerd, 1);
 237     init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
 238                   enerd);
 239
 240     /* Kinetic energy data */
 241     std::unique_ptr<gmx_ekindata_t> eKinData = std::make_unique<gmx_ekindata_t>();
 242     gmx_ekindata_t                 *ekind    = eKinData.get();
 243     init_ekindata(fplog, top_global, &(ir->opts), ekind);
 244     /* Copy the cos acceleration to the groups struct */
 245     ekind->cosacc.cos_accel = ir->cos_accel;
 246
 247     gstat = global_stat_init(ir);
 248
 249     /* Check for polarizable models and flexible constraints */
 250     shellfc = init_shell_flexcon(fplog,
 251                                  top_global, constr ? constr->numFlexibleConstraints() : 0,
 252                                  ir->nstcalcenergy, DOMAINDECOMP(cr));
 253
 254     {
 255         double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
 256         if ((io > 2000) && MASTER(cr))
 257         {
 258             fprintf(stderr,
 259                     "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
 260                     io);
 261         }
 262     }
 263
 264     // Local state only becomes valid now.
 265     std::unique_ptr<t_state> stateInstance;
 266     t_state *                state;
 267
 268     if (DOMAINDECOMP(cr))
 269     {
 270         dd_init_local_top(*top_global, &top);
 271
 272         stateInstance = std::make_unique<t_state>();
 273         state         = stateInstance.get();
 274         dd_init_local_state(cr->dd, state_global, state);
 275
 276         /* Distribute the charge groups over the nodes from the master node */
 277         dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
 278                             state_global, *top_global, ir,
 279                             state, &f, mdAtoms, &top, fr,
 280                             vsite, constr,
 281                             nrnb, nullptr, FALSE);
 282         shouldCheckNumberOfBondedInteractions = true;
 283         gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr);
 284     }
 285     else
 286     {
 287         state_change_natoms(state_global, state_global->natoms);
 288         /* We need to allocate one element extra, since we might use
 289          * (unaligned) 4-wide SIMD loads to access rvec entries.
 290          */
 291         f.resizeWithPadding(state_global->natoms);
 292         /* Copy the pointer to the global state */
 293         state = state_global;
 294
 295         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
 296                                   &graph, mdAtoms, constr, vsite, shellfc);
 297     }
 298
 299     auto mdatoms = mdAtoms->mdatoms();
 300
 301     // NOTE: The global state is no longer used at this point.
 302     // But state_global is still used as temporary storage space for writing
 303     // the global state to file and potentially for replica exchange.
 304     // (Global topology should persist.)
 305
 306     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 307
 308     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 309     {
 310         doFreeEnergyPerturbation = true;
 311     }
 312
 313     {
 314         int    cglo_flags = (CGLO_INITIALIZATION | CGLO_GSTAT |
 315                              (shouldCheckNumberOfBondedInteractions ?
 316                               CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 317         bool   bSumEkinhOld = false;
 318         t_vcm *vcm          = nullptr;
 319         compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 320                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
 321                         constr, &nullSignaller, state->box,
 322                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 323     }
 324     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 325                                     top_global, &top, state,
 326                                     &shouldCheckNumberOfBondedInteractions);
 327
 328     if (MASTER(cr))
 329     {
 330         fprintf(stderr, "starting MiMiC MD run '%s'\n\n",
 331                 *(top_global->name));
 332         if (mdrunOptions.verbose)
 333         {
 334             fprintf(stderr, "Calculated time to finish depends on nsteps from "
 335                     "run input file,\nwhich may not correspond to the time "
 336                     "needed to process input trajectory.\n\n");
 337         }
 338         fprintf(fplog, "\n");
 339     }
 340
 341     walltime_accounting_start_time(walltime_accounting);
 342     wallcycle_start(wcycle, ewcRUN);
 343     print_start(fplog, cr, walltime_accounting, "mdrun");
 344
 345     /***********************************************************
 346      *
 347      *             Loop over MD steps
 348      *
 349      ************************************************************/
 350
 351     if (constr)
 352     {
 353         GMX_LOG(mdlog.info).asParagraph().
 354             appendText("Simulations has constraints. Constraints will "
 355                        "be handled by CPMD.");
 356     }
 357
 358     GMX_LOG(mdlog.info).asParagraph().
 359         appendText("MiMiC does not report kinetic energy, total energy, temperature, virial and pressure.");
 360
 361     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 362                 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
 363                 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
 364                 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 365
 366     // we don't do counter resetting in rerun - finish will always be valid
 367     walltime_accounting_set_valid_finish(walltime_accounting);
 368
 369     DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion   =
 370         (DOMAINDECOMP(cr) ?
 371          DdOpenBalanceRegionBeforeForceComputation::yes :
 372          DdOpenBalanceRegionBeforeForceComputation::no);
 373     DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion  =
 374         (DOMAINDECOMP(cr) ?
 375          DdCloseBalanceRegionAfterForceComputation::yes :
 376          DdCloseBalanceRegionAfterForceComputation::no);
 377
 378     step     = ir->init_step;
 379     step_rel = 0;
 380
 381     /* and stop now if we should */
 382     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 383     while (!isLastStep)
 384     {
 385         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 386         wallcycle_start(wcycle, ewcSTEP);
 387
 388         t = step;
 389
 390         if (MASTER(cr))
 391         {
 392             mimicCommunicator.getCoords(&state_global->x, state_global->natoms);
 393         }
 394
 395         if (ir->efep != efepNO)
 396         {
 397             setCurrentLambdasLocal(step, ir->fepvals, lam0, state);
 398         }
 399
 400         if (MASTER(cr))
 401         {
 402             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 403             if (constructVsites && DOMAINDECOMP(cr))
 404             {
 405                 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
 406                           "use a single rank");
 407             }
 408         }
 409
 410         if (DOMAINDECOMP(cr))
 411         {
 412             /* Repartition the domain decomposition */
 413             const bool bMasterState = true;
 414             dd_partition_system(fplog, mdlog, step, cr,
 415                                 bMasterState, nstglobalcomm,
 416                                 state_global, *top_global, ir,
 417                                 state, &f, mdAtoms, &top, fr,
 418                                 vsite, constr,
 419                                 nrnb, wcycle,
 420                                 mdrunOptions.verbose);
 421             shouldCheckNumberOfBondedInteractions = true;
 422         }
 423
 424         if (MASTER(cr))
 425         {
 426             print_ebin_header(fplog, step, t); /* can we improve the information printed here? */
 427         }
 428
 429         if (ir->efep != efepNO)
 430         {
 431             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 432         }
 433
 434         force_flags = (GMX_FORCE_STATECHANGED |
 435                        GMX_FORCE_DYNAMICBOX |
 436                        GMX_FORCE_ALLFORCES |
 437                        GMX_FORCE_VIRIAL |  // TODO: Get rid of this once #2649 is solved
 438                        GMX_FORCE_ENERGY |
 439                        (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 440
 441         if (shellfc)
 442         {
 443             /* Now is the time to relax the shells */
 444             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
 445                                 enforcedRotation, step,
 446                                 ir, bNS, force_flags, &top,
 447                                 constr, enerd, fcd,
 448                                 state, f.arrayRefWithPadding(), force_vir, mdatoms,
 449                                 nrnb, wcycle, graph, groups,
 450                                 shellfc, fr, ppForceWorkload, t, mu_tot,
 451                                 vsite,
 452                                 ddOpenBalanceRegion, ddCloseBalanceRegion);
 453         }
 454         else
 455         {
 456             /* The coordinates (x) are shifted (to get whole molecules)
 457              * in do_force.
 458              * This is parallellized as well, and does communication too.
 459              * Check comments in sim_util.c
 460              */
 461             Awh       *awh = nullptr;
 462             gmx_edsam *ed  = nullptr;
 463             do_force(fplog, cr, ms, ir, awh, enforcedRotation,
 464                      step, nrnb, wcycle, &top, groups,
 465                      state->box, state->x.arrayRefWithPadding(), &state->hist,
 466                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
 467                      state->lambda, graph,
 468                      fr, ppForceWorkload, vsite, mu_tot, t, ed,
 469                      GMX_FORCE_NS | force_flags,
 470                      ddOpenBalanceRegion, ddCloseBalanceRegion);
 471         }
 472
 473         /* Now we have the energies and forces corresponding to the
 474          * coordinates at time t.
 475          */
 476         {
 477             const bool isCheckpointingStep = false;
 478             const bool doRerun             = false;
 479             const bool bSumEkinhOld        = false;
 480             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
 481                                      ir, state, state_global, observablesHistory,
 482                                      top_global, fr,
 483                                      outf, mdebin, ekind, f,
 484                                      isCheckpointingStep, doRerun, isLastStep,
 485                                      mdrunOptions.writeConfout,
 486                                      bSumEkinhOld);
 487         }
 488
 489         stopHandler->setSignal();
 490
 491         if (graph)
 492         {
 493             /* Need to unshift here */
 494             unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 495         }
 496
 497         if (vsite != nullptr)
 498         {
 499             wallcycle_start(wcycle, ewcVSITECONSTR);
 500             if (graph != nullptr)
 501             {
 502                 shift_self(graph, state->box, as_rvec_array(state->x.data()));
 503             }
 504             construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
 505                              top.idef.iparams, top.idef.il,
 506                              fr->ePBC, fr->bMolPBC, cr, state->box);
 507
 508             if (graph != nullptr)
 509             {
 510                 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 511             }
 512             wallcycle_stop(wcycle, ewcVSITECONSTR);
 513         }
 514
 515         {
 516             const bool          doInterSimSignal = false;
 517             const bool          doIntraSimSignal = true;
 518             bool                bSumEkinhOld     = false;
 519             t_vcm              *vcm              = nullptr;
 520             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 521
 522             compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 523                             wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
 524                             constr, &signaller,
 525                             state->box,
 526                             &totalNumberOfBondedInteractions, &bSumEkinhOld,
 527                             CGLO_GSTAT | CGLO_ENERGY
 528                             | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
 529                             );
 530             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 531                                             top_global, &top, state,
 532                                             &shouldCheckNumberOfBondedInteractions);
 533         }
 534
 535         {
 536             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 537             gmx::ArrayRef<gmx::RVec>       ftemp;
 538             gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
 539             if (DOMAINDECOMP(cr))
 540             {
 541                 ftemp = gmx::makeArrayRef(fglobal);
 542                 dd_collect_vec(cr->dd, state, flocal, ftemp);
 543             }
 544             else
 545             {
 546                 ftemp = gmx::makeArrayRef(f);
 547             }
 548
 549             if (MASTER(cr))
 550             {
 551                 mimicCommunicator.sendEnergies(enerd->term[F_EPOT]);
 552                 mimicCommunicator.sendForces(ftemp, state_global->natoms);
 553             }
 554         }
 555
 556
 557
 558         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 559            the virial that should probably be addressed eventually. state->veta has better properies,
 560            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 561            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 562
 563         if (ir->efep != efepNO)
 564         {
 565             /* Sum up the foreign energy and dhdl terms for md and sd.
 566                Currently done every step so that dhdl is correct in the .edr */
 567             sum_dhdl(enerd, state->lambda, ir->fepvals);
 568         }
 569
 570         /* Output stuff */
 571         if (MASTER(cr))
 572         {
 573             const bool bCalcEnerStep = true;
 574             upd_mdebin(mdebin, doFreeEnergyPerturbation, bCalcEnerStep,
 575                        t, mdatoms->tmass, enerd, state,
 576                        ir->fepvals, ir->expandedvals, state->box,
 577                        shake_vir, force_vir, total_vir, pres,
 578                        ekind, mu_tot, constr);
 579
 580             const bool do_ene = true;
 581             const bool do_log = true;
 582             Awh       *awh    = nullptr;
 583             const bool do_dr  = ir->nstdisreout != 0;
 584             const bool do_or  = ir->nstorireout != 0;
 585
 586             print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : nullptr,
 587                        step, t,
 588                        eprNORMAL, mdebin, fcd, groups, &(ir->opts), awh);
 589
 590             if (do_per_step(step, ir->nstlog))
 591             {
 592                 if (fflush(fplog) != 0)
 593                 {
 594                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 595                 }
 596             }
 597         }
 598
 599         /* Print the remaining wall clock time for the run */
 600         if (isMasterSimMasterRank(ms, cr) &&
 601             (mdrunOptions.verbose || gmx_got_usr_signal()))
 602         {
 603             if (shellfc)
 604             {
 605                 fprintf(stderr, "\n");
 606             }
 607             print_time(stderr, walltime_accounting, step, ir, cr);
 608         }
 609
 610         cycles = wallcycle_stop(wcycle, ewcSTEP);
 611         if (DOMAINDECOMP(cr) && wcycle)
 612         {
 613             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 614         }
 615
 616         /* increase the MD step number */
 617         step++;
 618         step_rel++;
 619     }
 620     /* End of main MD loop */
 621
 622     /* Closing TNG files can include compressing data. Therefore it is good to do that
 623      * before stopping the time measurements. */
 624     mdoutf_tng_close(outf);
 625
 626     /* Stop measuring walltime */
 627     walltime_accounting_end_time(walltime_accounting);
 628
 629     if (MASTER(cr))
 630     {
 631         mimicCommunicator.finalize();
 632     }
 633
 634     if (!thisRankHasDuty(cr, DUTY_PME))
 635     {
 636         /* Tell the PME only node to finish */
 637         gmx_pme_send_finish(cr);
 638     }
 639
 640     done_mdebin(mdebin);
 641     done_mdoutf(outf);
 642
 643     done_shellfc(fplog, shellfc, step_rel);
 644
 645     // Clean up swapcoords
 646     if (ir->eSwapCoords != eswapNO)
 647     {
 648         finish_swapcoords(ir->swap);
 649     }
 650
 651     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 652
 653     destroy_enerdata(enerd);
 654     sfree(enerd);
 655 }