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/simulation_workload.h"
 119 #include "gromacs/mdtypes/state.h"
 120 #include "gromacs/mimic/communicator.h"
 121 #include "gromacs/mimic/utilities.h"
 122 #include "gromacs/pbcutil/pbc.h"
 123 #include "gromacs/pulling/pull.h"
 124 #include "gromacs/timing/wallcycle.h"
 125 #include "gromacs/timing/walltime_accounting.h"
 126 #include "gromacs/topology/atoms.h"
 127 #include "gromacs/topology/idef.h"
 128 #include "gromacs/topology/mtop_util.h"
 129 #include "gromacs/topology/topology.h"
 130 #include "gromacs/trajectory/trajectoryframe.h"
 131 #include "gromacs/utility/basedefinitions.h"
 132 #include "gromacs/utility/cstringutil.h"
 133 #include "gromacs/utility/fatalerror.h"
 134 #include "gromacs/utility/logger.h"
 135 #include "gromacs/utility/real.h"
 136
 137 #include "legacysimulator.h"
 138 #include "replicaexchange.h"
 139 #include "shellfc.h"
 140
 141 using gmx::SimulationSignaller;
 142
 143 void gmx::LegacySimulator::do_mimic()
 144 {
 145     const t_inputrec* ir = inputrec;
 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,
 232                        ir->efep,
 233                        ir->bSimTemp,
 234                        *ir->fepvals,
 235                        ir->simtempvals->temperatures,
 236                        gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
 237                        MASTER(cr),
 238                        &state_global->fep_state,
 239                        state_global->lambda);
 240
 241     const bool        simulationsShareState = false;
 242     gmx_mdoutf*       outf                  = init_mdoutf(fplog,
 243                                    nfile,
 244                                    fnm,
 245                                    mdrunOptions,
 246                                    cr,
 247                                    outputProvider,
 248                                    mdModulesNotifiers,
 249                                    ir,
 250                                    top_global,
 251                                    oenv,
 252                                    wcycle,
 253                                    StartingBehavior::NewSimulation,
 254                                    simulationsShareState,
 255                                    ms);
 256     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
 257                                    top_global,
 258                                    *ir,
 259                                    pull_work,
 260                                    mdoutf_get_fp_dhdl(outf),
 261                                    true,
 262                                    StartingBehavior::NewSimulation,
 263                                    simulationsShareState,
 264                                    mdModulesNotifiers);
 265
 266     gstat = global_stat_init(ir);
 267
 268     /* Check for polarizable models and flexible constraints */
 269     shellfc = init_shell_flexcon(fplog,
 270                                  top_global,
 271                                  constr ? constr->numFlexibleConstraints() : 0,
 272                                  ir->nstcalcenergy,
 273                                  DOMAINDECOMP(cr),
 274                                  runScheduleWork->simulationWork.useGpuPme);
 275
 276     {
 277         double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
 278         if ((io > 2000) && MASTER(cr))
 279         {
 280             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 281         }
 282     }
 283
 284     // Local state only becomes valid now.
 285     std::unique_ptr<t_state> stateInstance;
 286     t_state*                 state;
 287
 288     gmx_localtop_t top(top_global.ffparams);
 289
 290     if (DOMAINDECOMP(cr))
 291     {
 292         stateInstance = std::make_unique<t_state>();
 293         state         = stateInstance.get();
 294         dd_init_local_state(*cr->dd, state_global, state);
 295
 296         /* Distribute the charge groups over the nodes from the master node */
 297         dd_partition_system(fplog,
 298                             mdlog,
 299                             ir->init_step,
 300                             cr,
 301                             TRUE,
 302                             1,
 303                             state_global,
 304                             top_global,
 305                             *ir,
 306                             imdSession,
 307                             pull_work,
 308                             state,
 309                             &f,
 310                             mdAtoms,
 311                             &top,
 312                             fr,
 313                             vsite,
 314                             constr,
 315                             nrnb,
 316                             nullptr,
 317                             FALSE);
 318     }
 319     else
 320     {
 321         state_change_natoms(state_global, state_global->natoms);
 322         /* Copy the pointer to the global state */
 323         state = state_global;
 324
 325         mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 326     }
 327
 328     auto* mdatoms = mdAtoms->mdatoms();
 329
 330     // NOTE: The global state is no longer used at this point.
 331     // But state_global is still used as temporary storage space for writing
 332     // the global state to file and potentially for replica exchange.
 333     // (Global topology should persist.)
 334
 335     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 336
 337     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 338     {
 339         doFreeEnergyPerturbation = true;
 340     }
 341
 342     {
 343         int cglo_flags = CGLO_GSTAT;
 344         if (DOMAINDECOMP(cr) && dd_localTopologyChecker(*cr->dd).shouldCheckNumberOfBondedInteractions())
 345         {
 346             cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 347         }
 348         bool   bSumEkinhOld = false;
 349         t_vcm* vcm          = nullptr;
 350         compute_globals(gstat,
 351                         cr,
 352                         ir,
 353                         fr,
 354                         ekind,
 355                         makeConstArrayRef(state->x),
 356                         makeConstArrayRef(state->v),
 357                         state->box,
 358                         mdatoms,
 359                         nrnb,
 360                         vcm,
 361                         nullptr,
 362                         enerd,
 363                         force_vir,
 364                         shake_vir,
 365                         total_vir,
 366                         pres,
 367                         gmx::ArrayRef<real>{},
 368                         &nullSignaller,
 369                         state->box,
 370                         &bSumEkinhOld,
 371                         cglo_flags);
 372         if (DOMAINDECOMP(cr))
 373         {
 374             dd_localTopologyChecker(cr->dd)->checkNumberOfBondedInteractions(
 375                     &top, makeConstArrayRef(state->x), state->box);
 376         }
 377     }
 378
 379     if (MASTER(cr))
 380     {
 381         fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global.name));
 382         if (mdrunOptions.verbose)
 383         {
 384             fprintf(stderr,
 385                     "Calculated time to finish depends on nsteps from "
 386                     "run input file,\nwhich may not correspond to the time "
 387                     "needed to process input trajectory.\n\n");
 388         }
 389         fprintf(fplog, "\n");
 390     }
 391
 392     walltime_accounting_start_time(walltime_accounting);
 393     wallcycle_start(wcycle, WallCycleCounter::Run);
 394     print_start(fplog, cr, walltime_accounting, "mdrun");
 395
 396     /***********************************************************
 397      *
 398      *             Loop over MD steps
 399      *
 400      ************************************************************/
 401
 402     if (constr)
 403     {
 404         GMX_LOG(mdlog.info)
 405                 .asParagraph()
 406                 .appendText(
 407                         "Simulations has constraints. Constraints will "
 408                         "be handled by CPMD.");
 409     }
 410
 411     GMX_LOG(mdlog.info)
 412             .asParagraph()
 413             .appendText(
 414                     "MiMiC does not report kinetic energy, total energy, temperature, virial and "
 415                     "pressure.");
 416
 417     int64_t step     = ir->init_step;
 418     int64_t step_rel = 0;
 419
 420     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 421             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 422             false,
 423             MASTER(cr),
 424             ir->nstlist,
 425             mdrunOptions.reproducible,
 426             nstglobalcomm,
 427             mdrunOptions.maximumHoursToRun,
 428             ir->nstlist == 0,
 429             fplog,
 430             step,
 431             bNS,
 432             walltime_accounting);
 433
 434     // we don't do counter resetting in rerun - finish will always be valid
 435     walltime_accounting_set_valid_finish(walltime_accounting);
 436
 437     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 438
 439     /* and stop now if we should */
 440     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 441     while (!isLastStep)
 442     {
 443         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 444         wallcycle_start(wcycle, WallCycleCounter::Step);
 445
 446         t = step;
 447
 448         if (MASTER(cr))
 449         {
 450             MimicCommunicator::getCoords(&state_global->x, state_global->natoms);
 451         }
 452
 453         if (ir->efep != FreeEnergyPerturbationType::No)
 454         {
 455             state->lambda = currentLambdas(step, *(ir->fepvals), state_global->fep_state);
 456         }
 457
 458         if (MASTER(cr))
 459         {
 460             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 461             if (constructVsites && DOMAINDECOMP(cr))
 462             {
 463                 gmx_fatal(FARGS,
 464                           "Vsite recalculation with -rerun is not implemented with domain "
 465                           "decomposition, "
 466                           "use a single rank");
 467             }
 468             if (constructVsites)
 469             {
 470                 wallcycle_start(wcycle, WallCycleCounter::VsiteConstr);
 471                 vsite->construct(state->x, state->v, state->box, VSiteOperation::PositionsAndVelocities);
 472                 wallcycle_stop(wcycle, WallCycleCounter::VsiteConstr);
 473             }
 474         }
 475
 476         if (DOMAINDECOMP(cr))
 477         {
 478             /* Repartition the domain decomposition */
 479             const bool bMasterState = true;
 480             dd_partition_system(fplog,
 481                                 mdlog,
 482                                 step,
 483                                 cr,
 484                                 bMasterState,
 485                                 nstglobalcomm,
 486                                 state_global,
 487                                 top_global,
 488                                 *ir,
 489                                 imdSession,
 490                                 pull_work,
 491                                 state,
 492                                 &f,
 493                                 mdAtoms,
 494                                 &top,
 495                                 fr,
 496                                 vsite,
 497                                 constr,
 498                                 nrnb,
 499                                 wcycle,
 500                                 mdrunOptions.verbose);
 501         }
 502
 503         if (MASTER(cr))
 504         {
 505             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 506         }
 507
 508         if (ir->efep != FreeEnergyPerturbationType::No)
 509         {
 510             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 511         }
 512
 513         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 514                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
 515                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 516
 517         if (shellfc)
 518         {
 519             /* Now is the time to relax the shells */
 520             relax_shell_flexcon(fplog,
 521                                 cr,
 522                                 ms,
 523                                 mdrunOptions.verbose,
 524                                 enforcedRotation,
 525                                 step,
 526                                 ir,
 527                                 imdSession,
 528                                 pull_work,
 529                                 bNS,
 530                                 force_flags,
 531                                 &top,
 532                                 constr,
 533                                 enerd,
 534                                 state->natoms,
 535                                 state->x.arrayRefWithPadding(),
 536                                 state->v.arrayRefWithPadding(),
 537                                 state->box,
 538                                 state->lambda,
 539                                 &state->hist,
 540                                 &f.view(),
 541                                 force_vir,
 542                                 *mdatoms,
 543                                 nrnb,
 544                                 wcycle,
 545                                 shellfc,
 546                                 fr,
 547                                 runScheduleWork,
 548                                 t,
 549                                 mu_tot,
 550                                 vsite,
 551                                 ddBalanceRegionHandler);
 552         }
 553         else
 554         {
 555             /* The coordinates (x) are shifted (to get whole molecules)
 556              * in do_force.
 557              * This is parallellized as well, and does communication too.
 558              * Check comments in sim_util.c
 559              */
 560             Awh*       awh = nullptr;
 561             gmx_edsam* ed  = nullptr;
 562             do_force(fplog,
 563                      cr,
 564                      ms,
 565                      *ir,
 566                      awh,
 567                      enforcedRotation,
 568                      imdSession,
 569                      pull_work,
 570                      step,
 571                      nrnb,
 572                      wcycle,
 573                      &top,
 574                      state->box,
 575                      state->x.arrayRefWithPadding(),
 576                      &state->hist,
 577                      &f.view(),
 578                      force_vir,
 579                      mdatoms,
 580                      enerd,
 581                      state->lambda,
 582                      fr,
 583                      runScheduleWork,
 584                      vsite,
 585                      mu_tot,
 586                      t,
 587                      ed,
 588                      GMX_FORCE_NS | force_flags,
 589                      ddBalanceRegionHandler);
 590         }
 591
 592         /* Now we have the energies and forces corresponding to the
 593          * coordinates at time t.
 594          */
 595         {
 596             const bool isCheckpointingStep = false;
 597             const bool doRerun             = false;
 598             const bool bSumEkinhOld        = false;
 599             do_md_trajectory_writing(fplog,
 600                                      cr,
 601                                      nfile,
 602                                      fnm,
 603                                      step,
 604                                      step_rel,
 605                                      t,
 606                                      ir,
 607                                      state,
 608                                      state_global,
 609                                      observablesHistory,
 610                                      top_global,
 611                                      fr,
 612                                      outf,
 613                                      energyOutput,
 614                                      ekind,
 615                                      f.view().force(),
 616                                      isCheckpointingStep,
 617                                      doRerun,
 618                                      isLastStep,
 619                                      mdrunOptions.writeConfout,
 620                                      bSumEkinhOld);
 621         }
 622
 623         stopHandler->setSignal();
 624
 625         {
 626             const bool          doInterSimSignal = false;
 627             const bool          doIntraSimSignal = true;
 628             bool                bSumEkinhOld     = false;
 629             t_vcm*              vcm              = nullptr;
 630             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 631
 632             int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
 633             if (DOMAINDECOMP(cr) && dd_localTopologyChecker(*cr->dd).shouldCheckNumberOfBondedInteractions())
 634             {
 635                 cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 636             }
 637             compute_globals(gstat,
 638                             cr,
 639                             ir,
 640                             fr,
 641                             ekind,
 642                             makeConstArrayRef(state->x),
 643                             makeConstArrayRef(state->v),
 644                             state->box,
 645                             mdatoms,
 646                             nrnb,
 647                             vcm,
 648                             wcycle,
 649                             enerd,
 650                             nullptr,
 651                             nullptr,
 652                             nullptr,
 653                             nullptr,
 654                             constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
 655                             &signaller,
 656                             state->box,
 657                             &bSumEkinhOld,
 658                             cglo_flags);
 659             if (DOMAINDECOMP(cr))
 660             {
 661                 dd_localTopologyChecker(cr->dd)->checkNumberOfBondedInteractions(
 662                         &top, makeConstArrayRef(state->x), state->box);
 663             }
 664         }
 665
 666         {
 667             gmx::HostVector<gmx::RVec>     fglobal(top_global.natoms);
 668             gmx::ArrayRef<gmx::RVec>       ftemp;
 669             gmx::ArrayRef<const gmx::RVec> flocal = f.view().force();
 670             if (DOMAINDECOMP(cr))
 671             {
 672                 ftemp = gmx::makeArrayRef(fglobal);
 673                 dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl, flocal, ftemp);
 674             }
 675             else
 676             {
 677                 ftemp = f.view().force();
 678             }
 679
 680             if (MASTER(cr))
 681             {
 682                 MimicCommunicator::sendEnergies(enerd->term[F_EPOT]);
 683                 MimicCommunicator::sendForces(ftemp, state_global->natoms);
 684             }
 685         }
 686
 687
 688         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 689            the virial that should probably be addressed eventually. state->veta has better properies,
 690            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 691            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 692
 693         if (ir->efep != FreeEnergyPerturbationType::No)
 694         {
 695             /* Sum up the foreign energy and dhdl terms for md and sd.
 696                Currently done every step so that dhdl is correct in the .edr */
 697             accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
 698         }
 699
 700         /* Output stuff */
 701         if (MASTER(cr))
 702         {
 703             const bool bCalcEnerStep = true;
 704             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 705                                              bCalcEnerStep,
 706                                              t,
 707                                              mdatoms->tmass,
 708                                              enerd,
 709                                              ir->fepvals.get(),
 710                                              ir->expandedvals.get(),
 711                                              state->box,
 712                                              PTCouplingArrays({ state->boxv,
 713                                                                 state->nosehoover_xi,
 714                                                                 state->nosehoover_vxi,
 715                                                                 state->nhpres_xi,
 716                                                                 state->nhpres_vxi }),
 717                                              state->fep_state,
 718                                              total_vir,
 719                                              pres,
 720                                              ekind,
 721                                              mu_tot,
 722                                              constr);
 723
 724             const bool do_ene = true;
 725             const bool do_log = true;
 726             Awh*       awh    = nullptr;
 727             const bool do_dr  = ir->nstdisreout != 0;
 728             const bool do_or  = ir->nstorireout != 0;
 729
 730             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 731             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 732                                                do_ene,
 733                                                do_dr,
 734                                                do_or,
 735                                                do_log ? fplog : nullptr,
 736                                                step,
 737                                                t,
 738                                                fr->fcdata.get(),
 739                                                awh);
 740
 741             if (do_per_step(step, ir->nstlog))
 742             {
 743                 if (fflush(fplog) != 0)
 744                 {
 745                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 746                 }
 747             }
 748         }
 749
 750         /* Print the remaining wall clock time for the run */
 751         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 752         {
 753             if (shellfc)
 754             {
 755                 fprintf(stderr, "\n");
 756             }
 757             print_time(stderr, walltime_accounting, step, ir, cr);
 758         }
 759
 760         cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
 761         if (DOMAINDECOMP(cr) && wcycle)
 762         {
 763             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 764         }
 765
 766         /* increase the MD step number */
 767         step++;
 768         step_rel++;
 769     }
 770     /* End of main MD loop */
 771
 772     /* Closing TNG files can include compressing data. Therefore it is good to do that
 773      * before stopping the time measurements. */
 774     mdoutf_tng_close(outf);
 775
 776     /* Stop measuring walltime */
 777     walltime_accounting_end_time(walltime_accounting);
 778
 779     if (MASTER(cr))
 780     {
 781         MimicCommunicator::finalize();
 782     }
 783
 784     if (!thisRankHasDuty(cr, DUTY_PME))
 785     {
 786         /* Tell the PME only node to finish */
 787         gmx_pme_send_finish(cr);
 788     }
 789
 790     done_mdoutf(outf);
 791
 792     done_shellfc(fplog, shellfc, step_rel);
 793
 794     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 795 }