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     const 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     SimulationSignals signals;
 159     // Most global communnication stages don't propagate mdrun
 160     // signals, and will use this object to achieve that.
 161     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 162
 163     if (ir->bExpanded)
 164     {
 165         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 166     }
 167     if (ir->bSimTemp)
 168     {
 169         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 170     }
 171     if (ir->bDoAwh)
 172     {
 173         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 174     }
 175     if (replExParams.exchangeInterval > 0)
 176     {
 177         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 178     }
 179     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 180     {
 181         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 182     }
 183     if (ir->bIMD)
 184     {
 185         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 186     }
 187     if (isMultiSim(ms))
 188     {
 189         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 190     }
 191     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](SimulatedAnnealing i) {
 192             return i != SimulatedAnnealing::No;
 193         }))
 194     {
 195         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 196     }
 197
 198     /* Settings for rerun */
 199     {
 200         // TODO: Avoid changing inputrec (#3854)
 201         auto* nonConstInputrec               = const_cast<t_inputrec*>(inputrec);
 202         nonConstInputrec->nstlist            = 1;
 203         nonConstInputrec->nstcalcenergy      = 1;
 204         nonConstInputrec->nstxout_compressed = 0;
 205     }
 206     int        nstglobalcomm = 1;
 207     const bool bNS           = true;
 208
 209     if (MASTER(cr))
 210     {
 211         MimicCommunicator::init();
 212         auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(&top_global);
 213         MimicCommunicator::sendInitData(nonConstGlobalTopology, state_global->x);
 214         // TODO: Avoid changing inputrec (#3854)
 215         auto* nonConstInputrec   = const_cast<t_inputrec*>(inputrec);
 216         nonConstInputrec->nsteps = MimicCommunicator::getStepNumber();
 217     }
 218     if (DOMAINDECOMP(cr))
 219     {
 220         // TODO: Avoid changing inputrec (#3854)
 221         auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
 222         gmx_bcast(sizeof(ir->nsteps), &nonConstInputrec->nsteps, cr->mpi_comm_mygroup);
 223     }
 224
 225     const SimulationGroups* groups = &top_global.groups;
 226     {
 227         auto nonConstGlobalTopology                          = const_cast<gmx_mtop_t*>(&top_global);
 228         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
 229     }
 230
 231     initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda);
 232
 233     const bool        simulationsShareState = false;
 234     gmx_mdoutf*       outf                  = init_mdoutf(fplog,
 235                                    nfile,
 236                                    fnm,
 237                                    mdrunOptions,
 238                                    cr,
 239                                    outputProvider,
 240                                    mdModulesNotifier,
 241                                    ir,
 242                                    top_global,
 243                                    oenv,
 244                                    wcycle,
 245                                    StartingBehavior::NewSimulation,
 246                                    simulationsShareState,
 247                                    ms);
 248     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
 249                                    top_global,
 250                                    *ir,
 251                                    pull_work,
 252                                    mdoutf_get_fp_dhdl(outf),
 253                                    true,
 254                                    StartingBehavior::NewSimulation,
 255                                    simulationsShareState,
 256                                    mdModulesNotifier);
 257
 258     gstat = global_stat_init(ir);
 259
 260     /* Check for polarizable models and flexible constraints */
 261     shellfc = init_shell_flexcon(fplog,
 262                                  top_global,
 263                                  constr ? constr->numFlexibleConstraints() : 0,
 264                                  ir->nstcalcenergy,
 265                                  DOMAINDECOMP(cr),
 266                                  runScheduleWork->simulationWork.useGpuPme);
 267
 268     {
 269         double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
 270         if ((io > 2000) && MASTER(cr))
 271         {
 272             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 273         }
 274     }
 275
 276     // Local state only becomes valid now.
 277     std::unique_ptr<t_state> stateInstance;
 278     t_state*                 state;
 279
 280     gmx_localtop_t top(top_global.ffparams);
 281
 282     if (DOMAINDECOMP(cr))
 283     {
 284         stateInstance = std::make_unique<t_state>();
 285         state         = stateInstance.get();
 286         dd_init_local_state(*cr->dd, state_global, state);
 287
 288         /* Distribute the charge groups over the nodes from the master node */
 289         dd_partition_system(fplog,
 290                             mdlog,
 291                             ir->init_step,
 292                             cr,
 293                             TRUE,
 294                             1,
 295                             state_global,
 296                             top_global,
 297                             *ir,
 298                             imdSession,
 299                             pull_work,
 300                             state,
 301                             &f,
 302                             mdAtoms,
 303                             &top,
 304                             fr,
 305                             vsite,
 306                             constr,
 307                             nrnb,
 308                             nullptr,
 309                             FALSE);
 310     }
 311     else
 312     {
 313         state_change_natoms(state_global, state_global->natoms);
 314         /* Copy the pointer to the global state */
 315         state = state_global;
 316
 317         mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 318     }
 319
 320     auto mdatoms = mdAtoms->mdatoms();
 321
 322     // NOTE: The global state is no longer used at this point.
 323     // But state_global is still used as temporary storage space for writing
 324     // the global state to file and potentially for replica exchange.
 325     // (Global topology should persist.)
 326
 327     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 328
 329     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 330     {
 331         doFreeEnergyPerturbation = true;
 332     }
 333
 334     {
 335         int cglo_flags = CGLO_GSTAT;
 336         if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
 337         {
 338             cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 339         }
 340         bool   bSumEkinhOld = false;
 341         t_vcm* vcm          = nullptr;
 342         compute_globals(gstat,
 343                         cr,
 344                         ir,
 345                         fr,
 346                         ekind,
 347                         makeConstArrayRef(state->x),
 348                         makeConstArrayRef(state->v),
 349                         state->box,
 350                         mdatoms,
 351                         nrnb,
 352                         vcm,
 353                         nullptr,
 354                         enerd,
 355                         force_vir,
 356                         shake_vir,
 357                         total_vir,
 358                         pres,
 359                         gmx::ArrayRef<real>{},
 360                         &nullSignaller,
 361                         state->box,
 362                         &bSumEkinhOld,
 363                         cglo_flags);
 364         if (DOMAINDECOMP(cr))
 365         {
 366             checkNumberOfBondedInteractions(
 367                     mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
 368         }
 369     }
 370
 371     if (MASTER(cr))
 372     {
 373         fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global.name));
 374         if (mdrunOptions.verbose)
 375         {
 376             fprintf(stderr,
 377                     "Calculated time to finish depends on nsteps from "
 378                     "run input file,\nwhich may not correspond to the time "
 379                     "needed to process input trajectory.\n\n");
 380         }
 381         fprintf(fplog, "\n");
 382     }
 383
 384     walltime_accounting_start_time(walltime_accounting);
 385     wallcycle_start(wcycle, ewcRUN);
 386     print_start(fplog, cr, walltime_accounting, "mdrun");
 387
 388     /***********************************************************
 389      *
 390      *             Loop over MD steps
 391      *
 392      ************************************************************/
 393
 394     if (constr)
 395     {
 396         GMX_LOG(mdlog.info)
 397                 .asParagraph()
 398                 .appendText(
 399                         "Simulations has constraints. Constraints will "
 400                         "be handled by CPMD.");
 401     }
 402
 403     GMX_LOG(mdlog.info)
 404             .asParagraph()
 405             .appendText(
 406                     "MiMiC does not report kinetic energy, total energy, temperature, virial and "
 407                     "pressure.");
 408
 409     step     = ir->init_step;
 410     step_rel = 0;
 411
 412     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 413             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 414             false,
 415             MASTER(cr),
 416             ir->nstlist,
 417             mdrunOptions.reproducible,
 418             nstglobalcomm,
 419             mdrunOptions.maximumHoursToRun,
 420             ir->nstlist == 0,
 421             fplog,
 422             step,
 423             bNS,
 424             walltime_accounting);
 425
 426     // we don't do counter resetting in rerun - finish will always be valid
 427     walltime_accounting_set_valid_finish(walltime_accounting);
 428
 429     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 430
 431     /* and stop now if we should */
 432     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 433     while (!isLastStep)
 434     {
 435         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 436         wallcycle_start(wcycle, ewcSTEP);
 437
 438         t = step;
 439
 440         if (MASTER(cr))
 441         {
 442             MimicCommunicator::getCoords(&state_global->x, state_global->natoms);
 443         }
 444
 445         if (ir->efep != FreeEnergyPerturbationType::No)
 446         {
 447             state->lambda = currentLambdas(step, *(ir->fepvals), state_global->fep_state);
 448         }
 449
 450         if (MASTER(cr))
 451         {
 452             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 453             if (constructVsites && DOMAINDECOMP(cr))
 454             {
 455                 gmx_fatal(FARGS,
 456                           "Vsite recalculation with -rerun is not implemented with domain "
 457                           "decomposition, "
 458                           "use a single rank");
 459             }
 460             if (constructVsites)
 461             {
 462                 wallcycle_start(wcycle, ewcVSITECONSTR);
 463                 vsite->construct(state->x, state->v, state->box, VSiteOperation::PositionsAndVelocities);
 464                 wallcycle_stop(wcycle, ewcVSITECONSTR);
 465             }
 466         }
 467
 468         if (DOMAINDECOMP(cr))
 469         {
 470             /* Repartition the domain decomposition */
 471             const bool bMasterState = true;
 472             dd_partition_system(fplog,
 473                                 mdlog,
 474                                 step,
 475                                 cr,
 476                                 bMasterState,
 477                                 nstglobalcomm,
 478                                 state_global,
 479                                 top_global,
 480                                 *ir,
 481                                 imdSession,
 482                                 pull_work,
 483                                 state,
 484                                 &f,
 485                                 mdAtoms,
 486                                 &top,
 487                                 fr,
 488                                 vsite,
 489                                 constr,
 490                                 nrnb,
 491                                 wcycle,
 492                                 mdrunOptions.verbose);
 493         }
 494
 495         if (MASTER(cr))
 496         {
 497             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 498         }
 499
 500         if (ir->efep != FreeEnergyPerturbationType::No)
 501         {
 502             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 503         }
 504
 505         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 506                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
 507                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 508
 509         if (shellfc)
 510         {
 511             /* Now is the time to relax the shells */
 512             relax_shell_flexcon(fplog,
 513                                 cr,
 514                                 ms,
 515                                 mdrunOptions.verbose,
 516                                 enforcedRotation,
 517                                 step,
 518                                 ir,
 519                                 imdSession,
 520                                 pull_work,
 521                                 bNS,
 522                                 force_flags,
 523                                 &top,
 524                                 constr,
 525                                 enerd,
 526                                 state->natoms,
 527                                 state->x.arrayRefWithPadding(),
 528                                 state->v.arrayRefWithPadding(),
 529                                 state->box,
 530                                 state->lambda,
 531                                 &state->hist,
 532                                 &f.view(),
 533                                 force_vir,
 534                                 *mdatoms,
 535                                 nrnb,
 536                                 wcycle,
 537                                 shellfc,
 538                                 fr,
 539                                 runScheduleWork,
 540                                 t,
 541                                 mu_tot,
 542                                 vsite,
 543                                 ddBalanceRegionHandler);
 544         }
 545         else
 546         {
 547             /* The coordinates (x) are shifted (to get whole molecules)
 548              * in do_force.
 549              * This is parallellized as well, and does communication too.
 550              * Check comments in sim_util.c
 551              */
 552             Awh*       awh = nullptr;
 553             gmx_edsam* ed  = nullptr;
 554             do_force(fplog,
 555                      cr,
 556                      ms,
 557                      *ir,
 558                      awh,
 559                      enforcedRotation,
 560                      imdSession,
 561                      pull_work,
 562                      step,
 563                      nrnb,
 564                      wcycle,
 565                      &top,
 566                      state->box,
 567                      state->x.arrayRefWithPadding(),
 568                      &state->hist,
 569                      &f.view(),
 570                      force_vir,
 571                      mdatoms,
 572                      enerd,
 573                      state->lambda,
 574                      fr,
 575                      runScheduleWork,
 576                      vsite,
 577                      mu_tot,
 578                      t,
 579                      ed,
 580                      GMX_FORCE_NS | force_flags,
 581                      ddBalanceRegionHandler);
 582         }
 583
 584         /* Now we have the energies and forces corresponding to the
 585          * coordinates at time t.
 586          */
 587         {
 588             const bool isCheckpointingStep = false;
 589             const bool doRerun             = false;
 590             const bool bSumEkinhOld        = false;
 591             do_md_trajectory_writing(fplog,
 592                                      cr,
 593                                      nfile,
 594                                      fnm,
 595                                      step,
 596                                      step_rel,
 597                                      t,
 598                                      ir,
 599                                      state,
 600                                      state_global,
 601                                      observablesHistory,
 602                                      top_global,
 603                                      fr,
 604                                      outf,
 605                                      energyOutput,
 606                                      ekind,
 607                                      f.view().force(),
 608                                      isCheckpointingStep,
 609                                      doRerun,
 610                                      isLastStep,
 611                                      mdrunOptions.writeConfout,
 612                                      bSumEkinhOld);
 613         }
 614
 615         stopHandler->setSignal();
 616
 617         {
 618             const bool          doInterSimSignal = false;
 619             const bool          doIntraSimSignal = true;
 620             bool                bSumEkinhOld     = false;
 621             t_vcm*              vcm              = nullptr;
 622             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 623
 624             int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
 625             if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
 626             {
 627                 cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 628             }
 629             compute_globals(gstat,
 630                             cr,
 631                             ir,
 632                             fr,
 633                             ekind,
 634                             makeConstArrayRef(state->x),
 635                             makeConstArrayRef(state->v),
 636                             state->box,
 637                             mdatoms,
 638                             nrnb,
 639                             vcm,
 640                             wcycle,
 641                             enerd,
 642                             nullptr,
 643                             nullptr,
 644                             nullptr,
 645                             nullptr,
 646                             constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
 647                             &signaller,
 648                             state->box,
 649                             &bSumEkinhOld,
 650                             cglo_flags);
 651             if (DOMAINDECOMP(cr))
 652             {
 653                 checkNumberOfBondedInteractions(
 654                         mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
 655             }
 656         }
 657
 658         {
 659             gmx::HostVector<gmx::RVec>     fglobal(top_global.natoms);
 660             gmx::ArrayRef<gmx::RVec>       ftemp;
 661             gmx::ArrayRef<const gmx::RVec> flocal = f.view().force();
 662             if (DOMAINDECOMP(cr))
 663             {
 664                 ftemp = gmx::makeArrayRef(fglobal);
 665                 dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl, flocal, ftemp);
 666             }
 667             else
 668             {
 669                 ftemp = f.view().force();
 670             }
 671
 672             if (MASTER(cr))
 673             {
 674                 MimicCommunicator::sendEnergies(enerd->term[F_EPOT]);
 675                 MimicCommunicator::sendForces(ftemp, state_global->natoms);
 676             }
 677         }
 678
 679
 680         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 681            the virial that should probably be addressed eventually. state->veta has better properies,
 682            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 683            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 684
 685         if (ir->efep != FreeEnergyPerturbationType::No)
 686         {
 687             /* Sum up the foreign energy and dhdl terms for md and sd.
 688                Currently done every step so that dhdl is correct in the .edr */
 689             accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
 690         }
 691
 692         /* Output stuff */
 693         if (MASTER(cr))
 694         {
 695             const bool bCalcEnerStep = true;
 696             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 697                                              bCalcEnerStep,
 698                                              t,
 699                                              mdatoms->tmass,
 700                                              enerd,
 701                                              ir->fepvals.get(),
 702                                              ir->expandedvals.get(),
 703                                              state->box,
 704                                              PTCouplingArrays({ state->boxv,
 705                                                                 state->nosehoover_xi,
 706                                                                 state->nosehoover_vxi,
 707                                                                 state->nhpres_xi,
 708                                                                 state->nhpres_vxi }),
 709                                              state->fep_state,
 710                                              shake_vir,
 711                                              force_vir,
 712                                              total_vir,
 713                                              pres,
 714                                              ekind,
 715                                              mu_tot,
 716                                              constr);
 717
 718             const bool do_ene = true;
 719             const bool do_log = true;
 720             Awh*       awh    = nullptr;
 721             const bool do_dr  = ir->nstdisreout != 0;
 722             const bool do_or  = ir->nstorireout != 0;
 723
 724             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 725             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 726                                                do_ene,
 727                                                do_dr,
 728                                                do_or,
 729                                                do_log ? fplog : nullptr,
 730                                                step,
 731                                                t,
 732                                                fr->fcdata.get(),
 733                                                awh);
 734
 735             if (do_per_step(step, ir->nstlog))
 736             {
 737                 if (fflush(fplog) != 0)
 738                 {
 739                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 740                 }
 741             }
 742         }
 743
 744         /* Print the remaining wall clock time for the run */
 745         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 746         {
 747             if (shellfc)
 748             {
 749                 fprintf(stderr, "\n");
 750             }
 751             print_time(stderr, walltime_accounting, step, ir, cr);
 752         }
 753
 754         cycles = wallcycle_stop(wcycle, ewcSTEP);
 755         if (DOMAINDECOMP(cr) && wcycle)
 756         {
 757             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 758         }
 759
 760         /* increase the MD step number */
 761         step++;
 762         step_rel++;
 763     }
 764     /* End of main MD loop */
 765
 766     /* Closing TNG files can include compressing data. Therefore it is good to do that
 767      * before stopping the time measurements. */
 768     mdoutf_tng_close(outf);
 769
 770     /* Stop measuring walltime */
 771     walltime_accounting_end_time(walltime_accounting);
 772
 773     if (MASTER(cr))
 774     {
 775         MimicCommunicator::finalize();
 776     }
 777
 778     if (!thisRankHasDuty(cr, DUTY_PME))
 779     {
 780         /* Tell the PME only node to finish */
 781         gmx_pme_send_finish(cr);
 782     }
 783
 784     done_mdoutf(outf);
 785
 786     done_shellfc(fplog, shellfc, step_rel);
 787
 788     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 789 }