src/gromacs/mdrun/mimic.cpp

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  35
  36 /*! \internal \file
  37  *
  38  * \brief Declares the loop for MiMiC QM/MM
  39  *
  40  * \author Viacheslav Bolnykh <v.bolnykh@hpc-leap.eu>
  41  * \ingroup module_mdrun
  42  */
  43 #include "gmxpre.h"
  44
  45 #include <cinttypes>
  46 #include <cmath>
  47 #include <cstdio>
  48 #include <cstdlib>
  49
  50 #include <algorithm>
  51 #include <memory>
  52
  53 #include "gromacs/applied_forces/awh/awh.h"
  54 #include "gromacs/commandline/filenm.h"
  55 #include "gromacs/domdec/collect.h"
  56 #include "gromacs/domdec/dlbtiming.h"
  57 #include "gromacs/domdec/domdec.h"
  58 #include "gromacs/domdec/domdec_network.h"
  59 #include "gromacs/domdec/domdec_struct.h"
  60 #include "gromacs/domdec/mdsetup.h"
  61 #include "gromacs/domdec/partition.h"
  62 #include "gromacs/essentialdynamics/edsam.h"
  63 #include "gromacs/ewald/pme_load_balancing.h"
  64 #include "gromacs/ewald/pme_pp.h"
  65 #include "gromacs/fileio/trxio.h"
  66 #include "gromacs/gmxlib/network.h"
  67 #include "gromacs/gmxlib/nrnb.h"
  68 #include "gromacs/gpu_utils/gpu_utils.h"
  69 #include "gromacs/listed_forces/listed_forces.h"
  70 #include "gromacs/math/functions.h"
  71 #include "gromacs/math/utilities.h"
  72 #include "gromacs/math/vec.h"
  73 #include "gromacs/math/vectypes.h"
  74 #include "gromacs/mdlib/checkpointhandler.h"
  75 #include "gromacs/mdlib/compute_io.h"
  76 #include "gromacs/mdlib/constr.h"
  77 #include "gromacs/mdlib/ebin.h"
  78 #include "gromacs/mdlib/enerdata_utils.h"
  79 #include "gromacs/mdlib/energyoutput.h"
  80 #include "gromacs/mdlib/expanded.h"
  81 #include "gromacs/mdlib/force.h"
  82 #include "gromacs/mdlib/force_flags.h"
  83 #include "gromacs/mdlib/forcerec.h"
  84 #include "gromacs/mdlib/freeenergyparameters.h"
  85 #include "gromacs/mdlib/md_support.h"
  86 #include "gromacs/mdlib/mdatoms.h"
  87 #include "gromacs/mdlib/mdoutf.h"
  88 #include "gromacs/mdlib/membed.h"
  89 #include "gromacs/mdlib/resethandler.h"
  90 #include "gromacs/mdlib/sighandler.h"
  91 #include "gromacs/mdlib/simulationsignal.h"
  92 #include "gromacs/mdlib/stat.h"
  93 #include "gromacs/mdlib/stophandler.h"
  94 #include "gromacs/mdlib/tgroup.h"
  95 #include "gromacs/mdlib/trajectory_writing.h"
  96 #include "gromacs/mdlib/update.h"
  97 #include "gromacs/mdlib/vcm.h"
  98 #include "gromacs/mdlib/vsite.h"
  99 #include "gromacs/mdrunutility/handlerestart.h"
 100 #include "gromacs/mdrunutility/multisim.h"
 101 #include "gromacs/mdrunutility/printtime.h"
 102 #include "gromacs/mdtypes/awh_history.h"
 103 #include "gromacs/mdtypes/awh_params.h"
 104 #include "gromacs/mdtypes/commrec.h"
 105 #include "gromacs/mdtypes/df_history.h"
 106 #include "gromacs/mdtypes/enerdata.h"
 107 #include "gromacs/mdtypes/energyhistory.h"
 108 #include "gromacs/mdtypes/forcebuffers.h"
 109 #include "gromacs/mdtypes/forcerec.h"
 110 #include "gromacs/mdtypes/group.h"
 111 #include "gromacs/mdtypes/inputrec.h"
 112 #include "gromacs/mdtypes/interaction_const.h"
 113 #include "gromacs/mdtypes/md_enums.h"
 114 #include "gromacs/mdtypes/mdatom.h"
 115 #include "gromacs/mdtypes/mdrunoptions.h"
 116 #include "gromacs/mdtypes/observableshistory.h"
 117 #include "gromacs/mdtypes/simulation_workload.h"
 118 #include "gromacs/mdtypes/state.h"
 119 #include "gromacs/mimic/communicator.h"
 120 #include "gromacs/mimic/utilities.h"
 121 #include "gromacs/pbcutil/pbc.h"
 122 #include "gromacs/pulling/pull.h"
 123 #include "gromacs/timing/wallcycle.h"
 124 #include "gromacs/timing/walltime_accounting.h"
 125 #include "gromacs/topology/atoms.h"
 126 #include "gromacs/topology/idef.h"
 127 #include "gromacs/topology/mtop_util.h"
 128 #include "gromacs/topology/topology.h"
 129 #include "gromacs/trajectory/trajectoryframe.h"
 130 #include "gromacs/utility/basedefinitions.h"
 131 #include "gromacs/utility/cstringutil.h"
 132 #include "gromacs/utility/fatalerror.h"
 133 #include "gromacs/utility/logger.h"
 134 #include "gromacs/utility/real.h"
 135
 136 #include "legacysimulator.h"
 137 #include "replicaexchange.h"
 138 #include "shellfc.h"
 139
 140 using gmx::SimulationSignaller;
 141
 142 void gmx::LegacySimulator::do_mimic()
 143 {
 144     const t_inputrec* ir = inputrec;
 145     int64_t           step, step_rel;
 146     double            t;
 147     bool              isLastStep               = false;
 148     bool              doFreeEnergyPerturbation = false;
 149     unsigned int      force_flags;
 150     tensor            force_vir, shake_vir, total_vir, pres;
 151     rvec              mu_tot;
 152     ForceBuffers      f;
 153     gmx_global_stat_t gstat;
 154     gmx_shellfc_t*    shellfc;
 155
 156     double cycles;
 157
 158     SimulationSignals signals;
 159     // Most global communnication stages don't propagate mdrun
 160     // signals, and will use this object to achieve that.
 161     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 162
 163     if (ir->bExpanded)
 164     {
 165         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 166     }
 167     if (ir->bSimTemp)
 168     {
 169         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 170     }
 171     if (ir->bDoAwh)
 172     {
 173         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 174     }
 175     if (replExParams.exchangeInterval > 0)
 176     {
 177         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 178     }
 179     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 180     {
 181         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 182     }
 183     if (ir->bIMD)
 184     {
 185         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 186     }
 187     if (isMultiSim(ms))
 188     {
 189         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 190     }
 191     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](SimulatedAnnealing i) {
 192             return i != SimulatedAnnealing::No;
 193         }))
 194     {
 195         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 196     }
 197
 198     /* Settings for rerun */
 199     {
 200         // TODO: Avoid changing inputrec (#3854)
 201         auto* nonConstInputrec               = const_cast<t_inputrec*>(inputrec);
 202         nonConstInputrec->nstlist            = 1;
 203         nonConstInputrec->nstcalcenergy      = 1;
 204         nonConstInputrec->nstxout_compressed = 0;
 205     }
 206     int        nstglobalcomm = 1;
 207     const bool bNS           = true;
 208
 209     if (MASTER(cr))
 210     {
 211         MimicCommunicator::init();
 212         auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(&top_global);
 213         MimicCommunicator::sendInitData(nonConstGlobalTopology, state_global->x);
 214         // TODO: Avoid changing inputrec (#3854)
 215         auto* nonConstInputrec   = const_cast<t_inputrec*>(inputrec);
 216         nonConstInputrec->nsteps = MimicCommunicator::getStepNumber();
 217     }
 218     if (DOMAINDECOMP(cr))
 219     {
 220         // TODO: Avoid changing inputrec (#3854)
 221         auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
 222         gmx_bcast(sizeof(ir->nsteps), &nonConstInputrec->nsteps, cr->mpi_comm_mygroup);
 223     }
 224
 225     const SimulationGroups* groups = &top_global.groups;
 226     {
 227         auto nonConstGlobalTopology                          = const_cast<gmx_mtop_t*>(&top_global);
 228         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
 229     }
 230
 231     initialize_lambdas(fplog,
 232                        *ir,
 233                        gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
 234                        MASTER(cr),
 235                        &state_global->fep_state,
 236                        state_global->lambda);
 237
 238     const bool        simulationsShareState = false;
 239     gmx_mdoutf*       outf                  = init_mdoutf(fplog,
 240                                    nfile,
 241                                    fnm,
 242                                    mdrunOptions,
 243                                    cr,
 244                                    outputProvider,
 245                                    mdModulesNotifiers,
 246                                    ir,
 247                                    top_global,
 248                                    oenv,
 249                                    wcycle,
 250                                    StartingBehavior::NewSimulation,
 251                                    simulationsShareState,
 252                                    ms);
 253     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
 254                                    top_global,
 255                                    *ir,
 256                                    pull_work,
 257                                    mdoutf_get_fp_dhdl(outf),
 258                                    true,
 259                                    StartingBehavior::NewSimulation,
 260                                    simulationsShareState,
 261                                    mdModulesNotifiers);
 262
 263     gstat = global_stat_init(ir);
 264
 265     /* Check for polarizable models and flexible constraints */
 266     shellfc = init_shell_flexcon(fplog,
 267                                  top_global,
 268                                  constr ? constr->numFlexibleConstraints() : 0,
 269                                  ir->nstcalcenergy,
 270                                  DOMAINDECOMP(cr),
 271                                  runScheduleWork->simulationWork.useGpuPme);
 272
 273     {
 274         double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
 275         if ((io > 2000) && MASTER(cr))
 276         {
 277             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 278         }
 279     }
 280
 281     // Local state only becomes valid now.
 282     std::unique_ptr<t_state> stateInstance;
 283     t_state*                 state;
 284
 285     gmx_localtop_t top(top_global.ffparams);
 286
 287     if (DOMAINDECOMP(cr))
 288     {
 289         stateInstance = std::make_unique<t_state>();
 290         state         = stateInstance.get();
 291         dd_init_local_state(*cr->dd, state_global, state);
 292
 293         /* Distribute the charge groups over the nodes from the master node */
 294         dd_partition_system(fplog,
 295                             mdlog,
 296                             ir->init_step,
 297                             cr,
 298                             TRUE,
 299                             1,
 300                             state_global,
 301                             top_global,
 302                             *ir,
 303                             imdSession,
 304                             pull_work,
 305                             state,
 306                             &f,
 307                             mdAtoms,
 308                             &top,
 309                             fr,
 310                             vsite,
 311                             constr,
 312                             nrnb,
 313                             nullptr,
 314                             FALSE);
 315     }
 316     else
 317     {
 318         state_change_natoms(state_global, state_global->natoms);
 319         /* Copy the pointer to the global state */
 320         state = state_global;
 321
 322         mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 323     }
 324
 325     auto mdatoms = mdAtoms->mdatoms();
 326
 327     // NOTE: The global state is no longer used at this point.
 328     // But state_global is still used as temporary storage space for writing
 329     // the global state to file and potentially for replica exchange.
 330     // (Global topology should persist.)
 331
 332     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 333
 334     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 335     {
 336         doFreeEnergyPerturbation = true;
 337     }
 338
 339     {
 340         int cglo_flags = CGLO_GSTAT;
 341         if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
 342         {
 343             cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 344         }
 345         bool   bSumEkinhOld = false;
 346         t_vcm* vcm          = nullptr;
 347         compute_globals(gstat,
 348                         cr,
 349                         ir,
 350                         fr,
 351                         ekind,
 352                         makeConstArrayRef(state->x),
 353                         makeConstArrayRef(state->v),
 354                         state->box,
 355                         mdatoms,
 356                         nrnb,
 357                         vcm,
 358                         nullptr,
 359                         enerd,
 360                         force_vir,
 361                         shake_vir,
 362                         total_vir,
 363                         pres,
 364                         gmx::ArrayRef<real>{},
 365                         &nullSignaller,
 366                         state->box,
 367                         &bSumEkinhOld,
 368                         cglo_flags);
 369         if (DOMAINDECOMP(cr))
 370         {
 371             checkNumberOfBondedInteractions(
 372                     mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
 373         }
 374     }
 375
 376     if (MASTER(cr))
 377     {
 378         fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global.name));
 379         if (mdrunOptions.verbose)
 380         {
 381             fprintf(stderr,
 382                     "Calculated time to finish depends on nsteps from "
 383                     "run input file,\nwhich may not correspond to the time "
 384                     "needed to process input trajectory.\n\n");
 385         }
 386         fprintf(fplog, "\n");
 387     }
 388
 389     walltime_accounting_start_time(walltime_accounting);
 390     wallcycle_start(wcycle, ewcRUN);
 391     print_start(fplog, cr, walltime_accounting, "mdrun");
 392
 393     /***********************************************************
 394      *
 395      *             Loop over MD steps
 396      *
 397      ************************************************************/
 398
 399     if (constr)
 400     {
 401         GMX_LOG(mdlog.info)
 402                 .asParagraph()
 403                 .appendText(
 404                         "Simulations has constraints. Constraints will "
 405                         "be handled by CPMD.");
 406     }
 407
 408     GMX_LOG(mdlog.info)
 409             .asParagraph()
 410             .appendText(
 411                     "MiMiC does not report kinetic energy, total energy, temperature, virial and "
 412                     "pressure.");
 413
 414     step     = ir->init_step;
 415     step_rel = 0;
 416
 417     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 418             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 419             false,
 420             MASTER(cr),
 421             ir->nstlist,
 422             mdrunOptions.reproducible,
 423             nstglobalcomm,
 424             mdrunOptions.maximumHoursToRun,
 425             ir->nstlist == 0,
 426             fplog,
 427             step,
 428             bNS,
 429             walltime_accounting);
 430
 431     // we don't do counter resetting in rerun - finish will always be valid
 432     walltime_accounting_set_valid_finish(walltime_accounting);
 433
 434     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 435
 436     /* and stop now if we should */
 437     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 438     while (!isLastStep)
 439     {
 440         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 441         wallcycle_start(wcycle, ewcSTEP);
 442
 443         t = step;
 444
 445         if (MASTER(cr))
 446         {
 447             MimicCommunicator::getCoords(&state_global->x, state_global->natoms);
 448         }
 449
 450         if (ir->efep != FreeEnergyPerturbationType::No)
 451         {
 452             state->lambda = currentLambdas(step, *(ir->fepvals), state_global->fep_state);
 453         }
 454
 455         if (MASTER(cr))
 456         {
 457             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 458             if (constructVsites && DOMAINDECOMP(cr))
 459             {
 460                 gmx_fatal(FARGS,
 461                           "Vsite recalculation with -rerun is not implemented with domain "
 462                           "decomposition, "
 463                           "use a single rank");
 464             }
 465             if (constructVsites)
 466             {
 467                 wallcycle_start(wcycle, ewcVSITECONSTR);
 468                 vsite->construct(state->x, state->v, state->box, VSiteOperation::PositionsAndVelocities);
 469                 wallcycle_stop(wcycle, ewcVSITECONSTR);
 470             }
 471         }
 472
 473         if (DOMAINDECOMP(cr))
 474         {
 475             /* Repartition the domain decomposition */
 476             const bool bMasterState = true;
 477             dd_partition_system(fplog,
 478                                 mdlog,
 479                                 step,
 480                                 cr,
 481                                 bMasterState,
 482                                 nstglobalcomm,
 483                                 state_global,
 484                                 top_global,
 485                                 *ir,
 486                                 imdSession,
 487                                 pull_work,
 488                                 state,
 489                                 &f,
 490                                 mdAtoms,
 491                                 &top,
 492                                 fr,
 493                                 vsite,
 494                                 constr,
 495                                 nrnb,
 496                                 wcycle,
 497                                 mdrunOptions.verbose);
 498         }
 499
 500         if (MASTER(cr))
 501         {
 502             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 503         }
 504
 505         if (ir->efep != FreeEnergyPerturbationType::No)
 506         {
 507             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 508         }
 509
 510         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 511                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
 512                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 513
 514         if (shellfc)
 515         {
 516             /* Now is the time to relax the shells */
 517             relax_shell_flexcon(fplog,
 518                                 cr,
 519                                 ms,
 520                                 mdrunOptions.verbose,
 521                                 enforcedRotation,
 522                                 step,
 523                                 ir,
 524                                 imdSession,
 525                                 pull_work,
 526                                 bNS,
 527                                 force_flags,
 528                                 &top,
 529                                 constr,
 530                                 enerd,
 531                                 state->natoms,
 532                                 state->x.arrayRefWithPadding(),
 533                                 state->v.arrayRefWithPadding(),
 534                                 state->box,
 535                                 state->lambda,
 536                                 &state->hist,
 537                                 &f.view(),
 538                                 force_vir,
 539                                 *mdatoms,
 540                                 nrnb,
 541                                 wcycle,
 542                                 shellfc,
 543                                 fr,
 544                                 runScheduleWork,
 545                                 t,
 546                                 mu_tot,
 547                                 vsite,
 548                                 ddBalanceRegionHandler);
 549         }
 550         else
 551         {
 552             /* The coordinates (x) are shifted (to get whole molecules)
 553              * in do_force.
 554              * This is parallellized as well, and does communication too.
 555              * Check comments in sim_util.c
 556              */
 557             Awh*       awh = nullptr;
 558             gmx_edsam* ed  = nullptr;
 559             do_force(fplog,
 560                      cr,
 561                      ms,
 562                      *ir,
 563                      awh,
 564                      enforcedRotation,
 565                      imdSession,
 566                      pull_work,
 567                      step,
 568                      nrnb,
 569                      wcycle,
 570                      &top,
 571                      state->box,
 572                      state->x.arrayRefWithPadding(),
 573                      &state->hist,
 574                      &f.view(),
 575                      force_vir,
 576                      mdatoms,
 577                      enerd,
 578                      state->lambda,
 579                      fr,
 580                      runScheduleWork,
 581                      vsite,
 582                      mu_tot,
 583                      t,
 584                      ed,
 585                      GMX_FORCE_NS | force_flags,
 586                      ddBalanceRegionHandler);
 587         }
 588
 589         /* Now we have the energies and forces corresponding to the
 590          * coordinates at time t.
 591          */
 592         {
 593             const bool isCheckpointingStep = false;
 594             const bool doRerun             = false;
 595             const bool bSumEkinhOld        = false;
 596             do_md_trajectory_writing(fplog,
 597                                      cr,
 598                                      nfile,
 599                                      fnm,
 600                                      step,
 601                                      step_rel,
 602                                      t,
 603                                      ir,
 604                                      state,
 605                                      state_global,
 606                                      observablesHistory,
 607                                      top_global,
 608                                      fr,
 609                                      outf,
 610                                      energyOutput,
 611                                      ekind,
 612                                      f.view().force(),
 613                                      isCheckpointingStep,
 614                                      doRerun,
 615                                      isLastStep,
 616                                      mdrunOptions.writeConfout,
 617                                      bSumEkinhOld);
 618         }
 619
 620         stopHandler->setSignal();
 621
 622         {
 623             const bool          doInterSimSignal = false;
 624             const bool          doIntraSimSignal = true;
 625             bool                bSumEkinhOld     = false;
 626             t_vcm*              vcm              = nullptr;
 627             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 628
 629             int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
 630             if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
 631             {
 632                 cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 633             }
 634             compute_globals(gstat,
 635                             cr,
 636                             ir,
 637                             fr,
 638                             ekind,
 639                             makeConstArrayRef(state->x),
 640                             makeConstArrayRef(state->v),
 641                             state->box,
 642                             mdatoms,
 643                             nrnb,
 644                             vcm,
 645                             wcycle,
 646                             enerd,
 647                             nullptr,
 648                             nullptr,
 649                             nullptr,
 650                             nullptr,
 651                             constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
 652                             &signaller,
 653                             state->box,
 654                             &bSumEkinhOld,
 655                             cglo_flags);
 656             if (DOMAINDECOMP(cr))
 657             {
 658                 checkNumberOfBondedInteractions(
 659                         mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
 660             }
 661         }
 662
 663         {
 664             gmx::HostVector<gmx::RVec>     fglobal(top_global.natoms);
 665             gmx::ArrayRef<gmx::RVec>       ftemp;
 666             gmx::ArrayRef<const gmx::RVec> flocal = f.view().force();
 667             if (DOMAINDECOMP(cr))
 668             {
 669                 ftemp = gmx::makeArrayRef(fglobal);
 670                 dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl, flocal, ftemp);
 671             }
 672             else
 673             {
 674                 ftemp = f.view().force();
 675             }
 676
 677             if (MASTER(cr))
 678             {
 679                 MimicCommunicator::sendEnergies(enerd->term[F_EPOT]);
 680                 MimicCommunicator::sendForces(ftemp, state_global->natoms);
 681             }
 682         }
 683
 684
 685         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 686            the virial that should probably be addressed eventually. state->veta has better properies,
 687            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 688            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 689
 690         if (ir->efep != FreeEnergyPerturbationType::No)
 691         {
 692             /* Sum up the foreign energy and dhdl terms for md and sd.
 693                Currently done every step so that dhdl is correct in the .edr */
 694             accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
 695         }
 696
 697         /* Output stuff */
 698         if (MASTER(cr))
 699         {
 700             const bool bCalcEnerStep = true;
 701             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 702                                              bCalcEnerStep,
 703                                              t,
 704                                              mdatoms->tmass,
 705                                              enerd,
 706                                              ir->fepvals.get(),
 707                                              ir->expandedvals.get(),
 708                                              state->box,
 709                                              PTCouplingArrays({ state->boxv,
 710                                                                 state->nosehoover_xi,
 711                                                                 state->nosehoover_vxi,
 712                                                                 state->nhpres_xi,
 713                                                                 state->nhpres_vxi }),
 714                                              state->fep_state,
 715                                              shake_vir,
 716                                              force_vir,
 717                                              total_vir,
 718                                              pres,
 719                                              ekind,
 720                                              mu_tot,
 721                                              constr);
 722
 723             const bool do_ene = true;
 724             const bool do_log = true;
 725             Awh*       awh    = nullptr;
 726             const bool do_dr  = ir->nstdisreout != 0;
 727             const bool do_or  = ir->nstorireout != 0;
 728
 729             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 730             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 731                                                do_ene,
 732                                                do_dr,
 733                                                do_or,
 734                                                do_log ? fplog : nullptr,
 735                                                step,
 736                                                t,
 737                                                fr->fcdata.get(),
 738                                                awh);
 739
 740             if (do_per_step(step, ir->nstlog))
 741             {
 742                 if (fflush(fplog) != 0)
 743                 {
 744                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 745                 }
 746             }
 747         }
 748
 749         /* Print the remaining wall clock time for the run */
 750         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 751         {
 752             if (shellfc)
 753             {
 754                 fprintf(stderr, "\n");
 755             }
 756             print_time(stderr, walltime_accounting, step, ir, cr);
 757         }
 758
 759         cycles = wallcycle_stop(wcycle, ewcSTEP);
 760         if (DOMAINDECOMP(cr) && wcycle)
 761         {
 762             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 763         }
 764
 765         /* increase the MD step number */
 766         step++;
 767         step_rel++;
 768     }
 769     /* End of main MD loop */
 770
 771     /* Closing TNG files can include compressing data. Therefore it is good to do that
 772      * before stopping the time measurements. */
 773     mdoutf_tng_close(outf);
 774
 775     /* Stop measuring walltime */
 776     walltime_accounting_end_time(walltime_accounting);
 777
 778     if (MASTER(cr))
 779     {
 780         MimicCommunicator::finalize();
 781     }
 782
 783     if (!thisRankHasDuty(cr, DUTY_PME))
 784     {
 785         /* Tell the PME only node to finish */
 786         gmx_pme_send_finish(cr);
 787     }
 788
 789     done_mdoutf(outf);
 790
 791     done_shellfc(fplog, shellfc, step_rel);
 792
 793     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 794 }