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/localtopologychecker.h"
  61 #include "gromacs/domdec/mdsetup.h"
  62 #include "gromacs/domdec/partition.h"
  63 #include "gromacs/essentialdynamics/edsam.h"
  64 #include "gromacs/ewald/pme_load_balancing.h"
  65 #include "gromacs/ewald/pme_pp.h"
  66 #include "gromacs/fileio/trxio.h"
  67 #include "gromacs/gmxlib/network.h"
  68 #include "gromacs/gmxlib/nrnb.h"
  69 #include "gromacs/gpu_utils/gpu_utils.h"
  70 #include "gromacs/listed_forces/listed_forces.h"
  71 #include "gromacs/math/functions.h"
  72 #include "gromacs/math/utilities.h"
  73 #include "gromacs/math/vec.h"
  74 #include "gromacs/math/vectypes.h"
  75 #include "gromacs/mdlib/checkpointhandler.h"
  76 #include "gromacs/mdlib/compute_io.h"
  77 #include "gromacs/mdlib/constr.h"
  78 #include "gromacs/mdlib/ebin.h"
  79 #include "gromacs/mdlib/enerdata_utils.h"
  80 #include "gromacs/mdlib/energyoutput.h"
  81 #include "gromacs/mdlib/expanded.h"
  82 #include "gromacs/mdlib/force.h"
  83 #include "gromacs/mdlib/force_flags.h"
  84 #include "gromacs/mdlib/forcerec.h"
  85 #include "gromacs/mdlib/freeenergyparameters.h"
  86 #include "gromacs/mdlib/md_support.h"
  87 #include "gromacs/mdlib/mdatoms.h"
  88 #include "gromacs/mdlib/mdoutf.h"
  89 #include "gromacs/mdlib/membed.h"
  90 #include "gromacs/mdlib/resethandler.h"
  91 #include "gromacs/mdlib/sighandler.h"
  92 #include "gromacs/mdlib/simulationsignal.h"
  93 #include "gromacs/mdlib/stat.h"
  94 #include "gromacs/mdlib/stophandler.h"
  95 #include "gromacs/mdlib/tgroup.h"
  96 #include "gromacs/mdlib/trajectory_writing.h"
  97 #include "gromacs/mdlib/update.h"
  98 #include "gromacs/mdlib/vcm.h"
  99 #include "gromacs/mdlib/vsite.h"
 100 #include "gromacs/mdrunutility/handlerestart.h"
 101 #include "gromacs/mdrunutility/multisim.h"
 102 #include "gromacs/mdrunutility/printtime.h"
 103 #include "gromacs/mdtypes/awh_history.h"
 104 #include "gromacs/mdtypes/awh_params.h"
 105 #include "gromacs/mdtypes/commrec.h"
 106 #include "gromacs/mdtypes/df_history.h"
 107 #include "gromacs/mdtypes/enerdata.h"
 108 #include "gromacs/mdtypes/energyhistory.h"
 109 #include "gromacs/mdtypes/forcebuffers.h"
 110 #include "gromacs/mdtypes/forcerec.h"
 111 #include "gromacs/mdtypes/group.h"
 112 #include "gromacs/mdtypes/inputrec.h"
 113 #include "gromacs/mdtypes/interaction_const.h"
 114 #include "gromacs/mdtypes/md_enums.h"
 115 #include "gromacs/mdtypes/mdatom.h"
 116 #include "gromacs/mdtypes/mdrunoptions.h"
 117 #include "gromacs/mdtypes/observableshistory.h"
 118 #include "gromacs/mdtypes/observablesreducer.h"
 119 #include "gromacs/mdtypes/simulation_workload.h"
 120 #include "gromacs/mdtypes/state.h"
 121 #include "gromacs/mimic/communicator.h"
 122 #include "gromacs/mimic/utilities.h"
 123 #include "gromacs/pbcutil/pbc.h"
 124 #include "gromacs/pulling/pull.h"
 125 #include "gromacs/timing/wallcycle.h"
 126 #include "gromacs/timing/walltime_accounting.h"
 127 #include "gromacs/topology/atoms.h"
 128 #include "gromacs/topology/idef.h"
 129 #include "gromacs/topology/mtop_util.h"
 130 #include "gromacs/topology/topology.h"
 131 #include "gromacs/trajectory/trajectoryframe.h"
 132 #include "gromacs/utility/basedefinitions.h"
 133 #include "gromacs/utility/cstringutil.h"
 134 #include "gromacs/utility/fatalerror.h"
 135 #include "gromacs/utility/logger.h"
 136 #include "gromacs/utility/real.h"
 137
 138 #include "legacysimulator.h"
 139 #include "replicaexchange.h"
 140 #include "shellfc.h"
 141
 142 using gmx::SimulationSignaller;
 143
 144 void gmx::LegacySimulator::do_mimic()
 145 {
 146     const t_inputrec* ir = inputrec;
 147     double            t;
 148     bool              isLastStep               = false;
 149     bool              doFreeEnergyPerturbation = false;
 150     unsigned int      force_flags;
 151     tensor            force_vir, shake_vir, total_vir, pres;
 152     rvec              mu_tot;
 153     ForceBuffers      f;
 154     gmx_global_stat_t gstat;
 155     gmx_shellfc_t*    shellfc;
 156
 157     double cycles;
 158
 159     SimulationSignals signals;
 160     // Most global communnication stages don't propagate mdrun
 161     // signals, and will use this object to achieve that.
 162     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 163
 164     if (ir->bExpanded)
 165     {
 166         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 167     }
 168     if (ir->bSimTemp)
 169     {
 170         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 171     }
 172     if (ir->bDoAwh)
 173     {
 174         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 175     }
 176     if (replExParams.exchangeInterval > 0)
 177     {
 178         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 179     }
 180     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 181     {
 182         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 183     }
 184     if (ir->bIMD)
 185     {
 186         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 187     }
 188     if (isMultiSim(ms))
 189     {
 190         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 191     }
 192     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](SimulatedAnnealing i) {
 193             return i != SimulatedAnnealing::No;
 194         }))
 195     {
 196         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 197     }
 198
 199     /* Settings for rerun */
 200     {
 201         // TODO: Avoid changing inputrec (#3854)
 202         auto* nonConstInputrec               = const_cast<t_inputrec*>(inputrec);
 203         nonConstInputrec->nstlist            = 1;
 204         nonConstInputrec->nstcalcenergy      = 1;
 205         nonConstInputrec->nstxout_compressed = 0;
 206     }
 207     int        nstglobalcomm = 1;
 208     const bool bNS           = true;
 209
 210     ObservablesReducer observablesReducer = observablesReducerBuilder->build();
 211
 212     if (MASTER(cr))
 213     {
 214         MimicCommunicator::init();
 215         auto* nonConstGlobalTopology = const_cast<gmx_mtop_t*>(&top_global);
 216         MimicCommunicator::sendInitData(nonConstGlobalTopology, state_global->x);
 217         // TODO: Avoid changing inputrec (#3854)
 218         auto* nonConstInputrec   = const_cast<t_inputrec*>(inputrec);
 219         nonConstInputrec->nsteps = MimicCommunicator::getStepNumber();
 220     }
 221     if (haveDDAtomOrdering(*cr))
 222     {
 223         // TODO: Avoid changing inputrec (#3854)
 224         auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
 225         gmx_bcast(sizeof(ir->nsteps), &nonConstInputrec->nsteps, cr->mpi_comm_mygroup);
 226     }
 227
 228     const SimulationGroups* groups = &top_global.groups;
 229     {
 230         auto* nonConstGlobalTopology                         = const_cast<gmx_mtop_t*>(&top_global);
 231         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
 232     }
 233
 234     initialize_lambdas(fplog,
 235                        ir->efep,
 236                        ir->bSimTemp,
 237                        *ir->fepvals,
 238                        ir->simtempvals->temperatures,
 239                        gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
 240                        MASTER(cr),
 241                        &state_global->fep_state,
 242                        state_global->lambda);
 243
 244     const bool        simulationsShareState = false;
 245     gmx_mdoutf*       outf                  = init_mdoutf(fplog,
 246                                    nfile,
 247                                    fnm,
 248                                    mdrunOptions,
 249                                    cr,
 250                                    outputProvider,
 251                                    mdModulesNotifiers,
 252                                    ir,
 253                                    top_global,
 254                                    oenv,
 255                                    wcycle,
 256                                    StartingBehavior::NewSimulation,
 257                                    simulationsShareState,
 258                                    ms);
 259     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
 260                                    top_global,
 261                                    *ir,
 262                                    pull_work,
 263                                    mdoutf_get_fp_dhdl(outf),
 264                                    true,
 265                                    StartingBehavior::NewSimulation,
 266                                    simulationsShareState,
 267                                    mdModulesNotifiers);
 268
 269     gstat = global_stat_init(ir);
 270
 271     /* Check for polarizable models and flexible constraints */
 272     shellfc = init_shell_flexcon(fplog,
 273                                  top_global,
 274                                  constr ? constr->numFlexibleConstraints() : 0,
 275                                  ir->nstcalcenergy,
 276                                  haveDDAtomOrdering(*cr),
 277                                  runScheduleWork->simulationWork.useGpuPme);
 278
 279     {
 280         double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
 281         if ((io > 2000) && MASTER(cr))
 282         {
 283             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 284         }
 285     }
 286
 287     if (haveDDAtomOrdering(*cr))
 288     {
 289         // Local state only becomes valid now.
 290         dd_init_local_state(*cr->dd, state_global, state);
 291
 292         /* Distribute the charge groups over the nodes from the master node */
 293         dd_partition_system(fplog,
 294                             mdlog,
 295                             ir->init_step,
 296                             cr,
 297                             TRUE,
 298                             1,
 299                             state_global,
 300                             top_global,
 301                             *ir,
 302                             imdSession,
 303                             pull_work,
 304                             state,
 305                             &f,
 306                             mdAtoms,
 307                             top,
 308                             fr,
 309                             vsite,
 310                             constr,
 311                             nrnb,
 312                             nullptr,
 313                             FALSE);
 314     }
 315     else
 316     {
 317         state_change_natoms(state_global, state_global->natoms);
 318         mdAlgorithmsSetupAtomData(cr, *ir, top_global, top, fr, &f, mdAtoms, constr, vsite, shellfc);
 319     }
 320
 321     auto* mdatoms = mdAtoms->mdatoms();
 322
 323     // NOTE: The global state is no longer used at this point.
 324     // But state_global is still used as temporary storage space for writing
 325     // the global state to file and potentially for replica exchange.
 326     // (Global topology should persist.)
 327
 328     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 329     fr->longRangeNonbondeds->updateAfterPartition(*mdatoms);
 330
 331     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 332     {
 333         doFreeEnergyPerturbation = true;
 334     }
 335
 336     int64_t step     = ir->init_step;
 337     int64_t step_rel = 0;
 338
 339     {
 340         int    cglo_flags   = CGLO_GSTAT;
 341         bool   bSumEkinhOld = false;
 342         t_vcm* vcm          = nullptr;
 343         compute_globals(gstat,
 344                         cr,
 345                         ir,
 346                         fr,
 347                         ekind,
 348                         makeConstArrayRef(state->x),
 349                         makeConstArrayRef(state->v),
 350                         state->box,
 351                         mdatoms,
 352                         nrnb,
 353                         vcm,
 354                         nullptr,
 355                         enerd,
 356                         force_vir,
 357                         shake_vir,
 358                         total_vir,
 359                         pres,
 360                         &nullSignaller,
 361                         state->box,
 362                         &bSumEkinhOld,
 363                         cglo_flags,
 364                         step,
 365                         &observablesReducer);
 366         // Clean up after pre-step use of compute_globals()
 367         observablesReducer.markAsReadyToReduce();
 368     }
 369
 370     if (MASTER(cr))
 371     {
 372         fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global.name));
 373         if (mdrunOptions.verbose)
 374         {
 375             fprintf(stderr,
 376                     "Calculated time to finish depends on nsteps from "
 377                     "run input file,\nwhich may not correspond to the time "
 378                     "needed to process input trajectory.\n\n");
 379         }
 380         fprintf(fplog, "\n");
 381     }
 382
 383     walltime_accounting_start_time(walltime_accounting);
 384     wallcycle_start(wcycle, WallCycleCounter::Run);
 385     print_start(fplog, cr, walltime_accounting, "mdrun");
 386
 387     /***********************************************************
 388      *
 389      *             Loop over MD steps
 390      *
 391      ************************************************************/
 392
 393     if (constr)
 394     {
 395         GMX_LOG(mdlog.info)
 396                 .asParagraph()
 397                 .appendText(
 398                         "Simulations has constraints. Constraints will "
 399                         "be handled by CPMD.");
 400     }
 401
 402     GMX_LOG(mdlog.info)
 403             .asParagraph()
 404             .appendText(
 405                     "MiMiC does not report kinetic energy, total energy, temperature, virial and "
 406                     "pressure.");
 407
 408     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 409             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 410             false,
 411             MASTER(cr),
 412             ir->nstlist,
 413             mdrunOptions.reproducible,
 414             nstglobalcomm,
 415             mdrunOptions.maximumHoursToRun,
 416             ir->nstlist == 0,
 417             fplog,
 418             step,
 419             bNS,
 420             walltime_accounting);
 421
 422     // we don't do counter resetting in rerun - finish will always be valid
 423     walltime_accounting_set_valid_finish(walltime_accounting);
 424
 425     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 426
 427     /* and stop now if we should */
 428     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 429     while (!isLastStep)
 430     {
 431         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 432         wallcycle_start(wcycle, WallCycleCounter::Step);
 433
 434         t = step;
 435
 436         if (MASTER(cr))
 437         {
 438             MimicCommunicator::getCoords(state_global->x, state_global->natoms);
 439         }
 440
 441         if (ir->efep != FreeEnergyPerturbationType::No)
 442         {
 443             state->lambda = currentLambdas(step, *(ir->fepvals), state_global->fep_state);
 444         }
 445
 446         if (MASTER(cr))
 447         {
 448             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 449             if (constructVsites && haveDDAtomOrdering(*cr))
 450             {
 451                 gmx_fatal(FARGS,
 452                           "Vsite recalculation with -rerun is not implemented with domain "
 453                           "decomposition, "
 454                           "use a single rank");
 455             }
 456             if (constructVsites)
 457             {
 458                 wallcycle_start(wcycle, WallCycleCounter::VsiteConstr);
 459                 vsite->construct(state->x, state->v, state->box, VSiteOperation::PositionsAndVelocities);
 460                 wallcycle_stop(wcycle, WallCycleCounter::VsiteConstr);
 461             }
 462         }
 463
 464         if (haveDDAtomOrdering(*cr))
 465         {
 466             /* Repartition the domain decomposition */
 467             const bool bMasterState = true;
 468             dd_partition_system(fplog,
 469                                 mdlog,
 470                                 step,
 471                                 cr,
 472                                 bMasterState,
 473                                 nstglobalcomm,
 474                                 state_global,
 475                                 top_global,
 476                                 *ir,
 477                                 imdSession,
 478                                 pull_work,
 479                                 state,
 480                                 &f,
 481                                 mdAtoms,
 482                                 top,
 483                                 fr,
 484                                 vsite,
 485                                 constr,
 486                                 nrnb,
 487                                 wcycle,
 488                                 mdrunOptions.verbose);
 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 != FreeEnergyPerturbationType::No)
 497         {
 498             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 499         }
 500
 501         fr->longRangeNonbondeds->updateAfterPartition(*mdatoms);
 502
 503         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 504                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
 505                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 506
 507         if (shellfc)
 508         {
 509             /* Now is the time to relax the shells */
 510             relax_shell_flexcon(fplog,
 511                                 cr,
 512                                 ms,
 513                                 mdrunOptions.verbose,
 514                                 enforcedRotation,
 515                                 step,
 516                                 ir,
 517                                 imdSession,
 518                                 pull_work,
 519                                 bNS,
 520                                 force_flags,
 521                                 top,
 522                                 constr,
 523                                 enerd,
 524                                 state->natoms,
 525                                 state->x.arrayRefWithPadding(),
 526                                 state->v.arrayRefWithPadding(),
 527                                 state->box,
 528                                 state->lambda,
 529                                 &state->hist,
 530                                 &f.view(),
 531                                 force_vir,
 532                                 *mdatoms,
 533                                 fr->longRangeNonbondeds.get(),
 534                                 nrnb,
 535                                 wcycle,
 536                                 shellfc,
 537                                 fr,
 538                                 runScheduleWork,
 539                                 t,
 540                                 mu_tot,
 541                                 vsite,
 542                                 ddBalanceRegionHandler);
 543         }
 544         else
 545         {
 546             /* The coordinates (x) are shifted (to get whole molecules)
 547              * in do_force.
 548              * This is parallellized as well, and does communication too.
 549              * Check comments in sim_util.c
 550              */
 551             Awh*       awh = nullptr;
 552             gmx_edsam* ed  = nullptr;
 553             do_force(fplog,
 554                      cr,
 555                      ms,
 556                      *ir,
 557                      awh,
 558                      enforcedRotation,
 559                      imdSession,
 560                      pull_work,
 561                      step,
 562                      nrnb,
 563                      wcycle,
 564                      top,
 565                      state->box,
 566                      state->x.arrayRefWithPadding(),
 567                      &state->hist,
 568                      &f.view(),
 569                      force_vir,
 570                      mdatoms,
 571                      enerd,
 572                      state->lambda,
 573                      fr,
 574                      runScheduleWork,
 575                      vsite,
 576                      mu_tot,
 577                      t,
 578                      ed,
 579                      fr->longRangeNonbondeds.get(),
 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             compute_globals(gstat,
 626                             cr,
 627                             ir,
 628                             fr,
 629                             ekind,
 630                             makeConstArrayRef(state->x),
 631                             makeConstArrayRef(state->v),
 632                             state->box,
 633                             mdatoms,
 634                             nrnb,
 635                             vcm,
 636                             wcycle,
 637                             enerd,
 638                             nullptr,
 639                             nullptr,
 640                             nullptr,
 641                             nullptr,
 642                             &signaller,
 643                             state->box,
 644                             &bSumEkinhOld,
 645                             cglo_flags,
 646                             step,
 647                             &observablesReducer);
 648         }
 649
 650         {
 651             gmx::HostVector<gmx::RVec>     fglobal(top_global.natoms);
 652             gmx::ArrayRef<gmx::RVec>       ftemp;
 653             gmx::ArrayRef<const gmx::RVec> flocal = f.view().force();
 654             if (haveDDAtomOrdering(*cr))
 655             {
 656                 ftemp = gmx::makeArrayRef(fglobal);
 657                 dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl, flocal, ftemp);
 658             }
 659             else
 660             {
 661                 ftemp = f.view().force();
 662             }
 663
 664             if (MASTER(cr))
 665             {
 666                 MimicCommunicator::sendEnergies(enerd->term[F_EPOT]);
 667                 MimicCommunicator::sendForces(ftemp, state_global->natoms);
 668             }
 669         }
 670
 671
 672         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 673            the virial that should probably be addressed eventually. state->veta has better properies,
 674            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 675            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 676
 677         if (ir->efep != FreeEnergyPerturbationType::No)
 678         {
 679             /* Sum up the foreign energy and dhdl terms for md and sd.
 680                Currently done every step so that dhdl is correct in the .edr */
 681             accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
 682         }
 683
 684         /* Output stuff */
 685         if (MASTER(cr))
 686         {
 687             const bool bCalcEnerStep = true;
 688             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 689                                              bCalcEnerStep,
 690                                              t,
 691                                              mdatoms->tmass,
 692                                              enerd,
 693                                              ir->fepvals.get(),
 694                                              state->box,
 695                                              PTCouplingArrays({ state->boxv,
 696                                                                 state->nosehoover_xi,
 697                                                                 state->nosehoover_vxi,
 698                                                                 state->nhpres_xi,
 699                                                                 state->nhpres_vxi }),
 700                                              state->fep_state,
 701                                              total_vir,
 702                                              pres,
 703                                              ekind,
 704                                              mu_tot,
 705                                              constr);
 706
 707             const bool do_ene = true;
 708             const bool do_log = true;
 709             Awh*       awh    = nullptr;
 710             const bool do_dr  = ir->nstdisreout != 0;
 711             const bool do_or  = ir->nstorireout != 0;
 712
 713             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 714             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 715                                                do_ene,
 716                                                do_dr,
 717                                                do_or,
 718                                                do_log ? fplog : nullptr,
 719                                                step,
 720                                                t,
 721                                                fr->fcdata.get(),
 722                                                awh);
 723
 724             if (do_per_step(step, ir->nstlog))
 725             {
 726                 if (fflush(fplog) != 0)
 727                 {
 728                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 729                 }
 730             }
 731         }
 732
 733         /* Print the remaining wall clock time for the run */
 734         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 735         {
 736             if (shellfc)
 737             {
 738                 fprintf(stderr, "\n");
 739             }
 740             print_time(stderr, walltime_accounting, step, ir, cr);
 741         }
 742
 743         cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
 744         if (haveDDAtomOrdering(*cr) && wcycle)
 745         {
 746             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 747         }
 748
 749         /* increase the MD step number */
 750         step++;
 751         step_rel++;
 752         observablesReducer.markAsReadyToReduce();
 753     }
 754     /* End of main MD loop */
 755
 756     /* Closing TNG files can include compressing data. Therefore it is good to do that
 757      * before stopping the time measurements. */
 758     mdoutf_tng_close(outf);
 759
 760     /* Stop measuring walltime */
 761     walltime_accounting_end_time(walltime_accounting);
 762
 763     if (MASTER(cr))
 764     {
 765         MimicCommunicator::finalize();
 766     }
 767
 768     if (!thisRankHasDuty(cr, DUTY_PME))
 769     {
 770         /* Tell the PME only node to finish */
 771         gmx_pme_send_finish(cr);
 772     }
 773
 774     done_mdoutf(outf);
 775
 776     done_shellfc(fplog, shellfc, step_rel);
 777
 778     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 779 }