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/applied_forces/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/freeenergyparameters.h"
  85 #include "gromacs/mdlib/md_support.h"
  86 #include "gromacs/mdlib/mdatoms.h"
  87 #include "gromacs/mdlib/mdoutf.h"
  88 #include "gromacs/mdlib/membed.h"
  89 #include "gromacs/mdlib/resethandler.h"
  90 #include "gromacs/mdlib/sighandler.h"
  91 #include "gromacs/mdlib/simulationsignal.h"
  92 #include "gromacs/mdlib/stat.h"
  93 #include "gromacs/mdlib/stophandler.h"
  94 #include "gromacs/mdlib/tgroup.h"
  95 #include "gromacs/mdlib/trajectory_writing.h"
  96 #include "gromacs/mdlib/update.h"
  97 #include "gromacs/mdlib/vcm.h"
  98 #include "gromacs/mdlib/vsite.h"
  99 #include "gromacs/mdrunutility/handlerestart.h"
 100 #include "gromacs/mdrunutility/multisim.h"
 101 #include "gromacs/mdrunutility/printtime.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/enerdata.h"
 107 #include "gromacs/mdtypes/energyhistory.h"
 108 #include "gromacs/mdtypes/forcebuffers.h"
 109 #include "gromacs/mdtypes/forcerec.h"
 110 #include "gromacs/mdtypes/group.h"
 111 #include "gromacs/mdtypes/inputrec.h"
 112 #include "gromacs/mdtypes/interaction_const.h"
 113 #include "gromacs/mdtypes/md_enums.h"
 114 #include "gromacs/mdtypes/mdatom.h"
 115 #include "gromacs/mdtypes/mdrunoptions.h"
 116 #include "gromacs/mdtypes/observableshistory.h"
 117 #include "gromacs/mdtypes/simulation_workload.h"
 118 #include "gromacs/mdtypes/state.h"
 119 #include "gromacs/mimic/communicator.h"
 120 #include "gromacs/mimic/utilities.h"
 121 #include "gromacs/pbcutil/pbc.h"
 122 #include "gromacs/pulling/pull.h"
 123 #include "gromacs/timing/wallcycle.h"
 124 #include "gromacs/timing/walltime_accounting.h"
 125 #include "gromacs/topology/atoms.h"
 126 #include "gromacs/topology/idef.h"
 127 #include "gromacs/topology/mtop_util.h"
 128 #include "gromacs/topology/topology.h"
 129 #include "gromacs/trajectory/trajectoryframe.h"
 130 #include "gromacs/utility/basedefinitions.h"
 131 #include "gromacs/utility/cstringutil.h"
 132 #include "gromacs/utility/fatalerror.h"
 133 #include "gromacs/utility/logger.h"
 134 #include "gromacs/utility/real.h"
 135
 136 #include "legacysimulator.h"
 137 #include "replicaexchange.h"
 138 #include "shellfc.h"
 139
 140 using gmx::SimulationSignaller;
 141
 142 void gmx::LegacySimulator::do_mimic()
 143 {
 144     t_inputrec*       ir = inputrec;
 145     int64_t           step, step_rel;
 146     double            t;
 147     bool              isLastStep               = false;
 148     bool              doFreeEnergyPerturbation = false;
 149     unsigned int      force_flags;
 150     tensor            force_vir, shake_vir, total_vir, pres;
 151     rvec              mu_tot;
 152     ForceBuffers      f;
 153     gmx_global_stat_t gstat;
 154     gmx_shellfc_t*    shellfc;
 155
 156     double cycles;
 157
 158     /* Domain decomposition could incorrectly miss a bonded
 159        interaction, but checking for that requires a global
 160        communication stage, which does not otherwise happen in DD
 161        code. So we do that alongside the first global energy reduction
 162        after a new DD is made. These variables handle whether the
 163        check happens, and the result it returns. */
 164     bool shouldCheckNumberOfBondedInteractions = false;
 165     int  totalNumberOfBondedInteractions       = -1;
 166
 167     SimulationSignals signals;
 168     // Most global communnication stages don't propagate mdrun
 169     // signals, and will use this object to achieve that.
 170     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 171
 172     if (ir->bExpanded)
 173     {
 174         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 175     }
 176     if (ir->bSimTemp)
 177     {
 178         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 179     }
 180     if (ir->bDoAwh)
 181     {
 182         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 183     }
 184     if (replExParams.exchangeInterval > 0)
 185     {
 186         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 187     }
 188     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 189     {
 190         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 191     }
 192     if (ir->bIMD)
 193     {
 194         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 195     }
 196     if (isMultiSim(ms))
 197     {
 198         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 199     }
 200     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](int i) {
 201             return i != eannNO;
 202         }))
 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     if (MASTER(cr))
 214     {
 215         MimicCommunicator::init();
 216         auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(top_global);
 217         MimicCommunicator::sendInitData(nonConstGlobalTopology, state_global->x);
 218         ir->nsteps = MimicCommunicator::getStepNumber();
 219     }
 220
 221     ir->nstxout_compressed         = 0;
 222     const SimulationGroups* groups = &top_global->groups;
 223     {
 224         auto nonConstGlobalTopology                          = const_cast<gmx_mtop_t*>(top_global);
 225         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 226     }
 227
 228     initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda);
 229
 230     const bool        simulationsShareState = false;
 231     gmx_mdoutf*       outf                  = init_mdoutf(fplog,
 232                                    nfile,
 233                                    fnm,
 234                                    mdrunOptions,
 235                                    cr,
 236                                    outputProvider,
 237                                    mdModulesNotifier,
 238                                    ir,
 239                                    top_global,
 240                                    oenv,
 241                                    wcycle,
 242                                    StartingBehavior::NewSimulation,
 243                                    simulationsShareState,
 244                                    ms);
 245     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
 246                                    top_global,
 247                                    ir,
 248                                    pull_work,
 249                                    mdoutf_get_fp_dhdl(outf),
 250                                    true,
 251                                    StartingBehavior::NewSimulation,
 252                                    simulationsShareState,
 253                                    mdModulesNotifier);
 254
 255     gstat = global_stat_init(ir);
 256
 257     /* Check for polarizable models and flexible constraints */
 258     shellfc = init_shell_flexcon(fplog,
 259                                  top_global,
 260                                  constr ? constr->numFlexibleConstraints() : 0,
 261                                  ir->nstcalcenergy,
 262                                  DOMAINDECOMP(cr),
 263                                  runScheduleWork->simulationWork.useGpuPme);
 264
 265     {
 266         double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
 267         if ((io > 2000) && MASTER(cr))
 268         {
 269             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 270         }
 271     }
 272
 273     // Local state only becomes valid now.
 274     std::unique_ptr<t_state> stateInstance;
 275     t_state*                 state;
 276
 277     gmx_localtop_t top(top_global->ffparams);
 278
 279     if (DOMAINDECOMP(cr))
 280     {
 281         stateInstance = std::make_unique<t_state>();
 282         state         = stateInstance.get();
 283         dd_init_local_state(cr->dd, state_global, state);
 284
 285         /* Distribute the charge groups over the nodes from the master node */
 286         dd_partition_system(fplog,
 287                             mdlog,
 288                             ir->init_step,
 289                             cr,
 290                             TRUE,
 291                             1,
 292                             state_global,
 293                             *top_global,
 294                             ir,
 295                             imdSession,
 296                             pull_work,
 297                             state,
 298                             &f,
 299                             mdAtoms,
 300                             &top,
 301                             fr,
 302                             vsite,
 303                             constr,
 304                             nrnb,
 305                             nullptr,
 306                             FALSE);
 307         shouldCheckNumberOfBondedInteractions = true;
 308         gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr->mpi_comm_mygroup);
 309     }
 310     else
 311     {
 312         state_change_natoms(state_global, state_global->natoms);
 313         /* Copy the pointer to the global state */
 314         state = state_global;
 315
 316         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 317     }
 318
 319     auto mdatoms = mdAtoms->mdatoms();
 320
 321     // NOTE: The global state is no longer used at this point.
 322     // But state_global is still used as temporary storage space for writing
 323     // the global state to file and potentially for replica exchange.
 324     // (Global topology should persist.)
 325
 326     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 327
 328     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 329     {
 330         doFreeEnergyPerturbation = true;
 331     }
 332
 333     {
 334         int cglo_flags =
 335                 (CGLO_GSTAT
 336                  | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 337         bool   bSumEkinhOld = false;
 338         t_vcm* vcm          = nullptr;
 339         compute_globals(gstat,
 340                         cr,
 341                         ir,
 342                         fr,
 343                         ekind,
 344                         makeConstArrayRef(state->x),
 345                         makeConstArrayRef(state->v),
 346                         state->box,
 347                         mdatoms,
 348                         nrnb,
 349                         vcm,
 350                         nullptr,
 351                         enerd,
 352                         force_vir,
 353                         shake_vir,
 354                         total_vir,
 355                         pres,
 356                         constr,
 357                         &nullSignaller,
 358                         state->box,
 359                         &totalNumberOfBondedInteractions,
 360                         &bSumEkinhOld,
 361                         cglo_flags);
 362     }
 363     checkNumberOfBondedInteractions(mdlog,
 364                                     cr,
 365                                     totalNumberOfBondedInteractions,
 366                                     top_global,
 367                                     &top,
 368                                     makeConstArrayRef(state->x),
 369                                     state->box,
 370                                     &shouldCheckNumberOfBondedInteractions);
 371
 372     if (MASTER(cr))
 373     {
 374         fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global->name));
 375         if (mdrunOptions.verbose)
 376         {
 377             fprintf(stderr,
 378                     "Calculated time to finish depends on nsteps from "
 379                     "run input file,\nwhich may not correspond to the time "
 380                     "needed to process input trajectory.\n\n");
 381         }
 382         fprintf(fplog, "\n");
 383     }
 384
 385     walltime_accounting_start_time(walltime_accounting);
 386     wallcycle_start(wcycle, ewcRUN);
 387     print_start(fplog, cr, walltime_accounting, "mdrun");
 388
 389     /***********************************************************
 390      *
 391      *             Loop over MD steps
 392      *
 393      ************************************************************/
 394
 395     if (constr)
 396     {
 397         GMX_LOG(mdlog.info)
 398                 .asParagraph()
 399                 .appendText(
 400                         "Simulations has constraints. Constraints will "
 401                         "be handled by CPMD.");
 402     }
 403
 404     GMX_LOG(mdlog.info)
 405             .asParagraph()
 406             .appendText(
 407                     "MiMiC does not report kinetic energy, total energy, temperature, virial and "
 408                     "pressure.");
 409
 410     step     = ir->init_step;
 411     step_rel = 0;
 412
 413     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 414             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 415             false,
 416             MASTER(cr),
 417             ir->nstlist,
 418             mdrunOptions.reproducible,
 419             nstglobalcomm,
 420             mdrunOptions.maximumHoursToRun,
 421             ir->nstlist == 0,
 422             fplog,
 423             step,
 424             bNS,
 425             walltime_accounting);
 426
 427     // we don't do counter resetting in rerun - finish will always be valid
 428     walltime_accounting_set_valid_finish(walltime_accounting);
 429
 430     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 431
 432     /* and stop now if we should */
 433     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 434     while (!isLastStep)
 435     {
 436         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 437         wallcycle_start(wcycle, ewcSTEP);
 438
 439         t = step;
 440
 441         if (MASTER(cr))
 442         {
 443             MimicCommunicator::getCoords(&state_global->x, state_global->natoms);
 444         }
 445
 446         if (ir->efep != efepNO)
 447         {
 448             state->lambda = currentLambdas(step, *(ir->fepvals), state_global->fep_state);
 449         }
 450
 451         if (MASTER(cr))
 452         {
 453             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 454             if (constructVsites && DOMAINDECOMP(cr))
 455             {
 456                 gmx_fatal(FARGS,
 457                           "Vsite recalculation with -rerun is not implemented with domain "
 458                           "decomposition, "
 459                           "use a single rank");
 460             }
 461         }
 462
 463         if (DOMAINDECOMP(cr))
 464         {
 465             /* Repartition the domain decomposition */
 466             const bool bMasterState = true;
 467             dd_partition_system(fplog,
 468                                 mdlog,
 469                                 step,
 470                                 cr,
 471                                 bMasterState,
 472                                 nstglobalcomm,
 473                                 state_global,
 474                                 *top_global,
 475                                 ir,
 476                                 imdSession,
 477                                 pull_work,
 478                                 state,
 479                                 &f,
 480                                 mdAtoms,
 481                                 &top,
 482                                 fr,
 483                                 vsite,
 484                                 constr,
 485                                 nrnb,
 486                                 wcycle,
 487                                 mdrunOptions.verbose);
 488             shouldCheckNumberOfBondedInteractions = true;
 489         }
 490
 491         if (MASTER(cr))
 492         {
 493             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 494         }
 495
 496         if (ir->efep != efepNO)
 497         {
 498             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 499         }
 500
 501         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 502                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
 503                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 504
 505         if (shellfc)
 506         {
 507             /* Now is the time to relax the shells */
 508             relax_shell_flexcon(fplog,
 509                                 cr,
 510                                 ms,
 511                                 mdrunOptions.verbose,
 512                                 enforcedRotation,
 513                                 step,
 514                                 ir,
 515                                 imdSession,
 516                                 pull_work,
 517                                 bNS,
 518                                 force_flags,
 519                                 &top,
 520                                 constr,
 521                                 enerd,
 522                                 state->natoms,
 523                                 state->x.arrayRefWithPadding(),
 524                                 state->v.arrayRefWithPadding(),
 525                                 state->box,
 526                                 state->lambda,
 527                                 &state->hist,
 528                                 &f.view(),
 529                                 force_vir,
 530                                 mdatoms,
 531                                 nrnb,
 532                                 wcycle,
 533                                 shellfc,
 534                                 fr,
 535                                 runScheduleWork,
 536                                 t,
 537                                 mu_tot,
 538                                 vsite,
 539                                 ddBalanceRegionHandler);
 540         }
 541         else
 542         {
 543             /* The coordinates (x) are shifted (to get whole molecules)
 544              * in do_force.
 545              * This is parallellized as well, and does communication too.
 546              * Check comments in sim_util.c
 547              */
 548             Awh*       awh = nullptr;
 549             gmx_edsam* ed  = nullptr;
 550             do_force(fplog,
 551                      cr,
 552                      ms,
 553                      ir,
 554                      awh,
 555                      enforcedRotation,
 556                      imdSession,
 557                      pull_work,
 558                      step,
 559                      nrnb,
 560                      wcycle,
 561                      &top,
 562                      state->box,
 563                      state->x.arrayRefWithPadding(),
 564                      &state->hist,
 565                      &f.view(),
 566                      force_vir,
 567                      mdatoms,
 568                      enerd,
 569                      state->lambda,
 570                      fr,
 571                      runScheduleWork,
 572                      vsite,
 573                      mu_tot,
 574                      t,
 575                      ed,
 576                      GMX_FORCE_NS | force_flags,
 577                      ddBalanceRegionHandler);
 578         }
 579
 580         /* Now we have the energies and forces corresponding to the
 581          * coordinates at time t.
 582          */
 583         {
 584             const bool isCheckpointingStep = false;
 585             const bool doRerun             = false;
 586             const bool bSumEkinhOld        = false;
 587             do_md_trajectory_writing(fplog,
 588                                      cr,
 589                                      nfile,
 590                                      fnm,
 591                                      step,
 592                                      step_rel,
 593                                      t,
 594                                      ir,
 595                                      state,
 596                                      state_global,
 597                                      observablesHistory,
 598                                      top_global,
 599                                      fr,
 600                                      outf,
 601                                      energyOutput,
 602                                      ekind,
 603                                      f.view().force(),
 604                                      isCheckpointingStep,
 605                                      doRerun,
 606                                      isLastStep,
 607                                      mdrunOptions.writeConfout,
 608                                      bSumEkinhOld);
 609         }
 610
 611         stopHandler->setSignal();
 612
 613         if (vsite != nullptr)
 614         {
 615             wallcycle_start(wcycle, ewcVSITECONSTR);
 616             vsite->construct(state->x, ir->delta_t, state->v, state->box);
 617             wallcycle_stop(wcycle, ewcVSITECONSTR);
 618         }
 619
 620         {
 621             const bool          doInterSimSignal = false;
 622             const bool          doIntraSimSignal = true;
 623             bool                bSumEkinhOld     = false;
 624             t_vcm*              vcm              = nullptr;
 625             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 626
 627             compute_globals(gstat,
 628                             cr,
 629                             ir,
 630                             fr,
 631                             ekind,
 632                             makeConstArrayRef(state->x),
 633                             makeConstArrayRef(state->v),
 634                             state->box,
 635                             mdatoms,
 636                             nrnb,
 637                             vcm,
 638                             wcycle,
 639                             enerd,
 640                             nullptr,
 641                             nullptr,
 642                             nullptr,
 643                             nullptr,
 644                             constr,
 645                             &signaller,
 646                             state->box,
 647                             &totalNumberOfBondedInteractions,
 648                             &bSumEkinhOld,
 649                             CGLO_GSTAT | CGLO_ENERGY
 650                                     | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
 651                                                                              : 0));
 652             checkNumberOfBondedInteractions(mdlog,
 653                                             cr,
 654                                             totalNumberOfBondedInteractions,
 655                                             top_global,
 656                                             &top,
 657                                             makeConstArrayRef(state->x),
 658                                             state->box,
 659                                             &shouldCheckNumberOfBondedInteractions);
 660         }
 661
 662         {
 663             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 664             gmx::ArrayRef<gmx::RVec>       ftemp;
 665             gmx::ArrayRef<const gmx::RVec> flocal = f.view().force();
 666             if (DOMAINDECOMP(cr))
 667             {
 668                 ftemp = gmx::makeArrayRef(fglobal);
 669                 dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl, flocal, ftemp);
 670             }
 671             else
 672             {
 673                 ftemp = f.view().force();
 674             }
 675
 676             if (MASTER(cr))
 677             {
 678                 MimicCommunicator::sendEnergies(enerd->term[F_EPOT]);
 679                 MimicCommunicator::sendForces(ftemp, state_global->natoms);
 680             }
 681         }
 682
 683
 684         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 685            the virial that should probably be addressed eventually. state->veta has better properies,
 686            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 687            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 688
 689         if (ir->efep != efepNO)
 690         {
 691             /* Sum up the foreign energy and dhdl terms for md and sd.
 692                Currently done every step so that dhdl is correct in the .edr */
 693             accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
 694         }
 695
 696         /* Output stuff */
 697         if (MASTER(cr))
 698         {
 699             const bool bCalcEnerStep = true;
 700             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 701                                              bCalcEnerStep,
 702                                              t,
 703                                              mdatoms->tmass,
 704                                              enerd,
 705                                              ir->fepvals,
 706                                              ir->expandedvals,
 707                                              state->box,
 708                                              PTCouplingArrays({ state->boxv,
 709                                                                 state->nosehoover_xi,
 710                                                                 state->nosehoover_vxi,
 711                                                                 state->nhpres_xi,
 712                                                                 state->nhpres_vxi }),
 713                                              state->fep_state,
 714                                              shake_vir,
 715                                              force_vir,
 716                                              total_vir,
 717                                              pres,
 718                                              ekind,
 719                                              mu_tot,
 720                                              constr);
 721
 722             const bool do_ene = true;
 723             const bool do_log = true;
 724             Awh*       awh    = nullptr;
 725             const bool do_dr  = ir->nstdisreout != 0;
 726             const bool do_or  = ir->nstorireout != 0;
 727
 728             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 729             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 730                                                do_ene,
 731                                                do_dr,
 732                                                do_or,
 733                                                do_log ? fplog : nullptr,
 734                                                step,
 735                                                t,
 736                                                fr->fcdata.get(),
 737                                                awh);
 738
 739             if (do_per_step(step, ir->nstlog))
 740             {
 741                 if (fflush(fplog) != 0)
 742                 {
 743                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 744                 }
 745             }
 746         }
 747
 748         /* Print the remaining wall clock time for the run */
 749         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 750         {
 751             if (shellfc)
 752             {
 753                 fprintf(stderr, "\n");
 754             }
 755             print_time(stderr, walltime_accounting, step, ir, cr);
 756         }
 757
 758         cycles = wallcycle_stop(wcycle, ewcSTEP);
 759         if (DOMAINDECOMP(cr) && wcycle)
 760         {
 761             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 762         }
 763
 764         /* increase the MD step number */
 765         step++;
 766         step_rel++;
 767     }
 768     /* End of main MD loop */
 769
 770     /* Closing TNG files can include compressing data. Therefore it is good to do that
 771      * before stopping the time measurements. */
 772     mdoutf_tng_close(outf);
 773
 774     /* Stop measuring walltime */
 775     walltime_accounting_end_time(walltime_accounting);
 776
 777     if (MASTER(cr))
 778     {
 779         MimicCommunicator::finalize();
 780     }
 781
 782     if (!thisRankHasDuty(cr, DUTY_PME))
 783     {
 784         /* Tell the PME only node to finish */
 785         gmx_pme_send_finish(cr);
 786     }
 787
 788     done_mdoutf(outf);
 789
 790     done_shellfc(fplog, shellfc, step_rel);
 791
 792     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 793 }