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 (DOMAINDECOMP(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                                  DOMAINDECOMP(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     // Local state only becomes valid now.
 288     std::unique_ptr<t_state> stateInstance;
 289     t_state*                 state;
 290
 291     gmx_localtop_t top(top_global.ffparams);
 292
 293     if (DOMAINDECOMP(cr))
 294     {
 295         stateInstance = std::make_unique<t_state>();
 296         state         = stateInstance.get();
 297         dd_init_local_state(*cr->dd, state_global, state);
 298
 299         /* Distribute the charge groups over the nodes from the master node */
 300         dd_partition_system(fplog,
 301                             mdlog,
 302                             ir->init_step,
 303                             cr,
 304                             TRUE,
 305                             1,
 306                             state_global,
 307                             top_global,
 308                             *ir,
 309                             imdSession,
 310                             pull_work,
 311                             state,
 312                             &f,
 313                             mdAtoms,
 314                             &top,
 315                             fr,
 316                             vsite,
 317                             constr,
 318                             nrnb,
 319                             nullptr,
 320                             FALSE);
 321     }
 322     else
 323     {
 324         state_change_natoms(state_global, state_global->natoms);
 325         /* Copy the pointer to the global state */
 326         state = state_global;
 327
 328         mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 329     }
 330
 331     auto* mdatoms = mdAtoms->mdatoms();
 332
 333     // NOTE: The global state is no longer used at this point.
 334     // But state_global is still used as temporary storage space for writing
 335     // the global state to file and potentially for replica exchange.
 336     // (Global topology should persist.)
 337
 338     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 339     fr->longRangeNonbondeds->updateAfterPartition(*mdatoms);
 340
 341     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 342     {
 343         doFreeEnergyPerturbation = true;
 344     }
 345
 346     int64_t step     = ir->init_step;
 347     int64_t step_rel = 0;
 348
 349     {
 350         int cglo_flags = CGLO_GSTAT;
 351         if (DOMAINDECOMP(cr) && dd_localTopologyChecker(*cr->dd).shouldCheckNumberOfBondedInteractions())
 352         {
 353             cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 354         }
 355         bool   bSumEkinhOld = false;
 356         t_vcm* vcm          = nullptr;
 357         compute_globals(gstat,
 358                         cr,
 359                         ir,
 360                         fr,
 361                         ekind,
 362                         makeConstArrayRef(state->x),
 363                         makeConstArrayRef(state->v),
 364                         state->box,
 365                         mdatoms,
 366                         nrnb,
 367                         vcm,
 368                         nullptr,
 369                         enerd,
 370                         force_vir,
 371                         shake_vir,
 372                         total_vir,
 373                         pres,
 374                         gmx::ArrayRef<real>{},
 375                         &nullSignaller,
 376                         state->box,
 377                         &bSumEkinhOld,
 378                         cglo_flags,
 379                         step,
 380                         &observablesReducer);
 381         if (DOMAINDECOMP(cr))
 382         {
 383             dd_localTopologyChecker(cr->dd)->checkNumberOfBondedInteractions(
 384                     &top, makeConstArrayRef(state->x), state->box);
 385         }
 386     }
 387
 388     if (MASTER(cr))
 389     {
 390         fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global.name));
 391         if (mdrunOptions.verbose)
 392         {
 393             fprintf(stderr,
 394                     "Calculated time to finish depends on nsteps from "
 395                     "run input file,\nwhich may not correspond to the time "
 396                     "needed to process input trajectory.\n\n");
 397         }
 398         fprintf(fplog, "\n");
 399     }
 400
 401     walltime_accounting_start_time(walltime_accounting);
 402     wallcycle_start(wcycle, WallCycleCounter::Run);
 403     print_start(fplog, cr, walltime_accounting, "mdrun");
 404
 405     /***********************************************************
 406      *
 407      *             Loop over MD steps
 408      *
 409      ************************************************************/
 410
 411     if (constr)
 412     {
 413         GMX_LOG(mdlog.info)
 414                 .asParagraph()
 415                 .appendText(
 416                         "Simulations has constraints. Constraints will "
 417                         "be handled by CPMD.");
 418     }
 419
 420     GMX_LOG(mdlog.info)
 421             .asParagraph()
 422             .appendText(
 423                     "MiMiC does not report kinetic energy, total energy, temperature, virial and "
 424                     "pressure.");
 425
 426     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 427             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 428             false,
 429             MASTER(cr),
 430             ir->nstlist,
 431             mdrunOptions.reproducible,
 432             nstglobalcomm,
 433             mdrunOptions.maximumHoursToRun,
 434             ir->nstlist == 0,
 435             fplog,
 436             step,
 437             bNS,
 438             walltime_accounting);
 439
 440     // we don't do counter resetting in rerun - finish will always be valid
 441     walltime_accounting_set_valid_finish(walltime_accounting);
 442
 443     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 444
 445     /* and stop now if we should */
 446     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 447     while (!isLastStep)
 448     {
 449         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 450         wallcycle_start(wcycle, WallCycleCounter::Step);
 451
 452         t = step;
 453
 454         if (MASTER(cr))
 455         {
 456             MimicCommunicator::getCoords(state_global->x, state_global->natoms);
 457         }
 458
 459         if (ir->efep != FreeEnergyPerturbationType::No)
 460         {
 461             state->lambda = currentLambdas(step, *(ir->fepvals), state_global->fep_state);
 462         }
 463
 464         if (MASTER(cr))
 465         {
 466             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 467             if (constructVsites && DOMAINDECOMP(cr))
 468             {
 469                 gmx_fatal(FARGS,
 470                           "Vsite recalculation with -rerun is not implemented with domain "
 471                           "decomposition, "
 472                           "use a single rank");
 473             }
 474             if (constructVsites)
 475             {
 476                 wallcycle_start(wcycle, WallCycleCounter::VsiteConstr);
 477                 vsite->construct(state->x, state->v, state->box, VSiteOperation::PositionsAndVelocities);
 478                 wallcycle_stop(wcycle, WallCycleCounter::VsiteConstr);
 479             }
 480         }
 481
 482         if (DOMAINDECOMP(cr))
 483         {
 484             /* Repartition the domain decomposition */
 485             const bool bMasterState = true;
 486             dd_partition_system(fplog,
 487                                 mdlog,
 488                                 step,
 489                                 cr,
 490                                 bMasterState,
 491                                 nstglobalcomm,
 492                                 state_global,
 493                                 top_global,
 494                                 *ir,
 495                                 imdSession,
 496                                 pull_work,
 497                                 state,
 498                                 &f,
 499                                 mdAtoms,
 500                                 &top,
 501                                 fr,
 502                                 vsite,
 503                                 constr,
 504                                 nrnb,
 505                                 wcycle,
 506                                 mdrunOptions.verbose);
 507         }
 508
 509         if (MASTER(cr))
 510         {
 511             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 512         }
 513
 514         if (ir->efep != FreeEnergyPerturbationType::No)
 515         {
 516             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 517         }
 518
 519         fr->longRangeNonbondeds->updateAfterPartition(*mdatoms);
 520
 521         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 522                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
 523                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 524
 525         if (shellfc)
 526         {
 527             /* Now is the time to relax the shells */
 528             relax_shell_flexcon(fplog,
 529                                 cr,
 530                                 ms,
 531                                 mdrunOptions.verbose,
 532                                 enforcedRotation,
 533                                 step,
 534                                 ir,
 535                                 imdSession,
 536                                 pull_work,
 537                                 bNS,
 538                                 force_flags,
 539                                 &top,
 540                                 constr,
 541                                 enerd,
 542                                 state->natoms,
 543                                 state->x.arrayRefWithPadding(),
 544                                 state->v.arrayRefWithPadding(),
 545                                 state->box,
 546                                 state->lambda,
 547                                 &state->hist,
 548                                 &f.view(),
 549                                 force_vir,
 550                                 *mdatoms,
 551                                 fr->longRangeNonbondeds.get(),
 552                                 nrnb,
 553                                 wcycle,
 554                                 shellfc,
 555                                 fr,
 556                                 runScheduleWork,
 557                                 t,
 558                                 mu_tot,
 559                                 vsite,
 560                                 ddBalanceRegionHandler);
 561         }
 562         else
 563         {
 564             /* The coordinates (x) are shifted (to get whole molecules)
 565              * in do_force.
 566              * This is parallellized as well, and does communication too.
 567              * Check comments in sim_util.c
 568              */
 569             Awh*       awh = nullptr;
 570             gmx_edsam* ed  = nullptr;
 571             do_force(fplog,
 572                      cr,
 573                      ms,
 574                      *ir,
 575                      awh,
 576                      enforcedRotation,
 577                      imdSession,
 578                      pull_work,
 579                      step,
 580                      nrnb,
 581                      wcycle,
 582                      &top,
 583                      state->box,
 584                      state->x.arrayRefWithPadding(),
 585                      &state->hist,
 586                      &f.view(),
 587                      force_vir,
 588                      mdatoms,
 589                      enerd,
 590                      state->lambda,
 591                      fr,
 592                      runScheduleWork,
 593                      vsite,
 594                      mu_tot,
 595                      t,
 596                      ed,
 597                      fr->longRangeNonbondeds.get(),
 598                      GMX_FORCE_NS | force_flags,
 599                      ddBalanceRegionHandler);
 600         }
 601
 602         /* Now we have the energies and forces corresponding to the
 603          * coordinates at time t.
 604          */
 605         {
 606             const bool isCheckpointingStep = false;
 607             const bool doRerun             = false;
 608             const bool bSumEkinhOld        = false;
 609             do_md_trajectory_writing(fplog,
 610                                      cr,
 611                                      nfile,
 612                                      fnm,
 613                                      step,
 614                                      step_rel,
 615                                      t,
 616                                      ir,
 617                                      state,
 618                                      state_global,
 619                                      observablesHistory,
 620                                      top_global,
 621                                      fr,
 622                                      outf,
 623                                      energyOutput,
 624                                      ekind,
 625                                      f.view().force(),
 626                                      isCheckpointingStep,
 627                                      doRerun,
 628                                      isLastStep,
 629                                      mdrunOptions.writeConfout,
 630                                      bSumEkinhOld);
 631         }
 632
 633         stopHandler->setSignal();
 634
 635         {
 636             const bool          doInterSimSignal = false;
 637             const bool          doIntraSimSignal = true;
 638             bool                bSumEkinhOld     = false;
 639             t_vcm*              vcm              = nullptr;
 640             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 641
 642             int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
 643             if (DOMAINDECOMP(cr) && dd_localTopologyChecker(*cr->dd).shouldCheckNumberOfBondedInteractions())
 644             {
 645                 cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 646             }
 647             compute_globals(gstat,
 648                             cr,
 649                             ir,
 650                             fr,
 651                             ekind,
 652                             makeConstArrayRef(state->x),
 653                             makeConstArrayRef(state->v),
 654                             state->box,
 655                             mdatoms,
 656                             nrnb,
 657                             vcm,
 658                             wcycle,
 659                             enerd,
 660                             nullptr,
 661                             nullptr,
 662                             nullptr,
 663                             nullptr,
 664                             constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
 665                             &signaller,
 666                             state->box,
 667                             &bSumEkinhOld,
 668                             cglo_flags,
 669                             step,
 670                             &observablesReducer);
 671             if (DOMAINDECOMP(cr))
 672             {
 673                 dd_localTopologyChecker(cr->dd)->checkNumberOfBondedInteractions(
 674                         &top, makeConstArrayRef(state->x), state->box);
 675             }
 676         }
 677
 678         {
 679             gmx::HostVector<gmx::RVec>     fglobal(top_global.natoms);
 680             gmx::ArrayRef<gmx::RVec>       ftemp;
 681             gmx::ArrayRef<const gmx::RVec> flocal = f.view().force();
 682             if (DOMAINDECOMP(cr))
 683             {
 684                 ftemp = gmx::makeArrayRef(fglobal);
 685                 dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl, flocal, ftemp);
 686             }
 687             else
 688             {
 689                 ftemp = f.view().force();
 690             }
 691
 692             if (MASTER(cr))
 693             {
 694                 MimicCommunicator::sendEnergies(enerd->term[F_EPOT]);
 695                 MimicCommunicator::sendForces(ftemp, state_global->natoms);
 696             }
 697         }
 698
 699
 700         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 701            the virial that should probably be addressed eventually. state->veta has better properies,
 702            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 703            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 704
 705         if (ir->efep != FreeEnergyPerturbationType::No)
 706         {
 707             /* Sum up the foreign energy and dhdl terms for md and sd.
 708                Currently done every step so that dhdl is correct in the .edr */
 709             accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
 710         }
 711
 712         /* Output stuff */
 713         if (MASTER(cr))
 714         {
 715             const bool bCalcEnerStep = true;
 716             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 717                                              bCalcEnerStep,
 718                                              t,
 719                                              mdatoms->tmass,
 720                                              enerd,
 721                                              ir->fepvals.get(),
 722                                              ir->expandedvals.get(),
 723                                              state->box,
 724                                              PTCouplingArrays({ state->boxv,
 725                                                                 state->nosehoover_xi,
 726                                                                 state->nosehoover_vxi,
 727                                                                 state->nhpres_xi,
 728                                                                 state->nhpres_vxi }),
 729                                              state->fep_state,
 730                                              total_vir,
 731                                              pres,
 732                                              ekind,
 733                                              mu_tot,
 734                                              constr);
 735
 736             const bool do_ene = true;
 737             const bool do_log = true;
 738             Awh*       awh    = nullptr;
 739             const bool do_dr  = ir->nstdisreout != 0;
 740             const bool do_or  = ir->nstorireout != 0;
 741
 742             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 743             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 744                                                do_ene,
 745                                                do_dr,
 746                                                do_or,
 747                                                do_log ? fplog : nullptr,
 748                                                step,
 749                                                t,
 750                                                fr->fcdata.get(),
 751                                                awh);
 752
 753             if (do_per_step(step, ir->nstlog))
 754             {
 755                 if (fflush(fplog) != 0)
 756                 {
 757                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 758                 }
 759             }
 760         }
 761
 762         /* Print the remaining wall clock time for the run */
 763         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 764         {
 765             if (shellfc)
 766             {
 767                 fprintf(stderr, "\n");
 768             }
 769             print_time(stderr, walltime_accounting, step, ir, cr);
 770         }
 771
 772         cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
 773         if (DOMAINDECOMP(cr) && wcycle)
 774         {
 775             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 776         }
 777
 778         /* increase the MD step number */
 779         step++;
 780         step_rel++;
 781     }
 782     /* End of main MD loop */
 783
 784     /* Closing TNG files can include compressing data. Therefore it is good to do that
 785      * before stopping the time measurements. */
 786     mdoutf_tng_close(outf);
 787
 788     /* Stop measuring walltime */
 789     walltime_accounting_end_time(walltime_accounting);
 790
 791     if (MASTER(cr))
 792     {
 793         MimicCommunicator::finalize();
 794     }
 795
 796     if (!thisRankHasDuty(cr, DUTY_PME))
 797     {
 798         /* Tell the PME only node to finish */
 799         gmx_pme_send_finish(cr);
 800     }
 801
 802     done_mdoutf(outf);
 803
 804     done_shellfc(fplog, shellfc, step_rel);
 805
 806     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 807 }