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     /* Domain decomposition could incorrectly miss a bonded
 159        interaction, but checking for that requires a global
 160        communication stage, which does not otherwise happen in DD
 161        code. So we do that alongside the first global energy reduction
 162        after a new DD is made. These variables handle whether the
 163        check happens, and the result it returns. */
 164     bool shouldCheckNumberOfBondedInteractions = false;
 165     int  totalNumberOfBondedInteractions       = -1;
 166
 167     SimulationSignals signals;
 168     // Most global communnication stages don't propagate mdrun
 169     // signals, and will use this object to achieve that.
 170     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 171
 172     if (ir->bExpanded)
 173     {
 174         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 175     }
 176     if (ir->bSimTemp)
 177     {
 178         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 179     }
 180     if (ir->bDoAwh)
 181     {
 182         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 183     }
 184     if (replExParams.exchangeInterval > 0)
 185     {
 186         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 187     }
 188     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 189     {
 190         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 191     }
 192     if (ir->bIMD)
 193     {
 194         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 195     }
 196     if (isMultiSim(ms))
 197     {
 198         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 199     }
 200     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](SimulatedAnnealing i) {
 201             return i != SimulatedAnnealing::No;
 202         }))
 203     {
 204         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 205     }
 206
 207     /* Settings for rerun */
 208     {
 209         // TODO: Avoid changing inputrec (#3854)
 210         auto* nonConstInputrec               = const_cast<t_inputrec*>(inputrec);
 211         nonConstInputrec->nstlist            = 1;
 212         nonConstInputrec->nstcalcenergy      = 1;
 213         nonConstInputrec->nstxout_compressed = 0;
 214     }
 215     int        nstglobalcomm = 1;
 216     const bool bNS           = true;
 217
 218     if (MASTER(cr))
 219     {
 220         MimicCommunicator::init();
 221         auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(top_global);
 222         MimicCommunicator::sendInitData(nonConstGlobalTopology, state_global->x);
 223         // TODO: Avoid changing inputrec (#3854)
 224         auto* nonConstInputrec   = const_cast<t_inputrec*>(inputrec);
 225         nonConstInputrec->nsteps = MimicCommunicator::getStepNumber();
 226     }
 227     if (DOMAINDECOMP(cr))
 228     {
 229         // TODO: Avoid changing inputrec (#3854)
 230         auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
 231         gmx_bcast(sizeof(ir->nsteps), &nonConstInputrec->nsteps, cr->mpi_comm_mygroup);
 232     }
 233
 234     const SimulationGroups* groups = &top_global->groups;
 235     {
 236         auto nonConstGlobalTopology                          = const_cast<gmx_mtop_t*>(top_global);
 237         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 238     }
 239
 240     initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda);
 241
 242     const bool        simulationsShareState = false;
 243     gmx_mdoutf*       outf                  = init_mdoutf(fplog,
 244                                    nfile,
 245                                    fnm,
 246                                    mdrunOptions,
 247                                    cr,
 248                                    outputProvider,
 249                                    mdModulesNotifier,
 250                                    ir,
 251                                    top_global,
 252                                    oenv,
 253                                    wcycle,
 254                                    StartingBehavior::NewSimulation,
 255                                    simulationsShareState,
 256                                    ms);
 257     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
 258                                    top_global,
 259                                    ir,
 260                                    pull_work,
 261                                    mdoutf_get_fp_dhdl(outf),
 262                                    true,
 263                                    StartingBehavior::NewSimulation,
 264                                    simulationsShareState,
 265                                    mdModulesNotifier);
 266
 267     gstat = global_stat_init(ir);
 268
 269     /* Check for polarizable models and flexible constraints */
 270     shellfc = init_shell_flexcon(fplog,
 271                                  top_global,
 272                                  constr ? constr->numFlexibleConstraints() : 0,
 273                                  ir->nstcalcenergy,
 274                                  DOMAINDECOMP(cr),
 275                                  runScheduleWork->simulationWork.useGpuPme);
 276
 277     {
 278         double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
 279         if ((io > 2000) && MASTER(cr))
 280         {
 281             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 282         }
 283     }
 284
 285     // Local state only becomes valid now.
 286     std::unique_ptr<t_state> stateInstance;
 287     t_state*                 state;
 288
 289     gmx_localtop_t top(top_global->ffparams);
 290
 291     if (DOMAINDECOMP(cr))
 292     {
 293         stateInstance = std::make_unique<t_state>();
 294         state         = stateInstance.get();
 295         dd_init_local_state(cr->dd, state_global, state);
 296
 297         /* Distribute the charge groups over the nodes from the master node */
 298         dd_partition_system(fplog,
 299                             mdlog,
 300                             ir->init_step,
 301                             cr,
 302                             TRUE,
 303                             1,
 304                             state_global,
 305                             *top_global,
 306                             ir,
 307                             imdSession,
 308                             pull_work,
 309                             state,
 310                             &f,
 311                             mdAtoms,
 312                             &top,
 313                             fr,
 314                             vsite,
 315                             constr,
 316                             nrnb,
 317                             nullptr,
 318                             FALSE);
 319         shouldCheckNumberOfBondedInteractions = true;
 320     }
 321     else
 322     {
 323         state_change_natoms(state_global, state_global->natoms);
 324         /* Copy the pointer to the global state */
 325         state = state_global;
 326
 327         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 328     }
 329
 330     auto mdatoms = mdAtoms->mdatoms();
 331
 332     // NOTE: The global state is no longer used at this point.
 333     // But state_global is still used as temporary storage space for writing
 334     // the global state to file and potentially for replica exchange.
 335     // (Global topology should persist.)
 336
 337     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 338
 339     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 340     {
 341         doFreeEnergyPerturbation = true;
 342     }
 343
 344     {
 345         int cglo_flags =
 346                 (CGLO_GSTAT
 347                  | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 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                         &totalNumberOfBondedInteractions,
 371                         &bSumEkinhOld,
 372                         cglo_flags);
 373     }
 374     checkNumberOfBondedInteractions(mdlog,
 375                                     cr,
 376                                     totalNumberOfBondedInteractions,
 377                                     top_global,
 378                                     &top,
 379                                     makeConstArrayRef(state->x),
 380                                     state->box,
 381                                     &shouldCheckNumberOfBondedInteractions);
 382
 383     if (MASTER(cr))
 384     {
 385         fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global->name));
 386         if (mdrunOptions.verbose)
 387         {
 388             fprintf(stderr,
 389                     "Calculated time to finish depends on nsteps from "
 390                     "run input file,\nwhich may not correspond to the time "
 391                     "needed to process input trajectory.\n\n");
 392         }
 393         fprintf(fplog, "\n");
 394     }
 395
 396     walltime_accounting_start_time(walltime_accounting);
 397     wallcycle_start(wcycle, ewcRUN);
 398     print_start(fplog, cr, walltime_accounting, "mdrun");
 399
 400     /***********************************************************
 401      *
 402      *             Loop over MD steps
 403      *
 404      ************************************************************/
 405
 406     if (constr)
 407     {
 408         GMX_LOG(mdlog.info)
 409                 .asParagraph()
 410                 .appendText(
 411                         "Simulations has constraints. Constraints will "
 412                         "be handled by CPMD.");
 413     }
 414
 415     GMX_LOG(mdlog.info)
 416             .asParagraph()
 417             .appendText(
 418                     "MiMiC does not report kinetic energy, total energy, temperature, virial and "
 419                     "pressure.");
 420
 421     step     = ir->init_step;
 422     step_rel = 0;
 423
 424     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 425             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 426             false,
 427             MASTER(cr),
 428             ir->nstlist,
 429             mdrunOptions.reproducible,
 430             nstglobalcomm,
 431             mdrunOptions.maximumHoursToRun,
 432             ir->nstlist == 0,
 433             fplog,
 434             step,
 435             bNS,
 436             walltime_accounting);
 437
 438     // we don't do counter resetting in rerun - finish will always be valid
 439     walltime_accounting_set_valid_finish(walltime_accounting);
 440
 441     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 442
 443     /* and stop now if we should */
 444     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 445     while (!isLastStep)
 446     {
 447         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 448         wallcycle_start(wcycle, ewcSTEP);
 449
 450         t = step;
 451
 452         if (MASTER(cr))
 453         {
 454             MimicCommunicator::getCoords(&state_global->x, state_global->natoms);
 455         }
 456
 457         if (ir->efep != FreeEnergyPerturbationType::No)
 458         {
 459             state->lambda = currentLambdas(step, *(ir->fepvals), state_global->fep_state);
 460         }
 461
 462         if (MASTER(cr))
 463         {
 464             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 465             if (constructVsites && DOMAINDECOMP(cr))
 466             {
 467                 gmx_fatal(FARGS,
 468                           "Vsite recalculation with -rerun is not implemented with domain "
 469                           "decomposition, "
 470                           "use a single rank");
 471             }
 472             if (constructVsites)
 473             {
 474                 wallcycle_start(wcycle, ewcVSITECONSTR);
 475                 vsite->construct(state->x, state->v, state->box, VSiteOperation::PositionsAndVelocities);
 476                 wallcycle_stop(wcycle, ewcVSITECONSTR);
 477             }
 478         }
 479
 480         if (DOMAINDECOMP(cr))
 481         {
 482             /* Repartition the domain decomposition */
 483             const bool bMasterState = true;
 484             dd_partition_system(fplog,
 485                                 mdlog,
 486                                 step,
 487                                 cr,
 488                                 bMasterState,
 489                                 nstglobalcomm,
 490                                 state_global,
 491                                 *top_global,
 492                                 ir,
 493                                 imdSession,
 494                                 pull_work,
 495                                 state,
 496                                 &f,
 497                                 mdAtoms,
 498                                 &top,
 499                                 fr,
 500                                 vsite,
 501                                 constr,
 502                                 nrnb,
 503                                 wcycle,
 504                                 mdrunOptions.verbose);
 505             shouldCheckNumberOfBondedInteractions = true;
 506         }
 507
 508         if (MASTER(cr))
 509         {
 510             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 511         }
 512
 513         if (ir->efep != FreeEnergyPerturbationType::No)
 514         {
 515             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 516         }
 517
 518         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 519                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
 520                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 521
 522         if (shellfc)
 523         {
 524             /* Now is the time to relax the shells */
 525             relax_shell_flexcon(fplog,
 526                                 cr,
 527                                 ms,
 528                                 mdrunOptions.verbose,
 529                                 enforcedRotation,
 530                                 step,
 531                                 ir,
 532                                 imdSession,
 533                                 pull_work,
 534                                 bNS,
 535                                 force_flags,
 536                                 &top,
 537                                 constr,
 538                                 enerd,
 539                                 state->natoms,
 540                                 state->x.arrayRefWithPadding(),
 541                                 state->v.arrayRefWithPadding(),
 542                                 state->box,
 543                                 state->lambda,
 544                                 &state->hist,
 545                                 &f.view(),
 546                                 force_vir,
 547                                 mdatoms,
 548                                 nrnb,
 549                                 wcycle,
 550                                 shellfc,
 551                                 fr,
 552                                 runScheduleWork,
 553                                 t,
 554                                 mu_tot,
 555                                 vsite,
 556                                 ddBalanceRegionHandler);
 557         }
 558         else
 559         {
 560             /* The coordinates (x) are shifted (to get whole molecules)
 561              * in do_force.
 562              * This is parallellized as well, and does communication too.
 563              * Check comments in sim_util.c
 564              */
 565             Awh*       awh = nullptr;
 566             gmx_edsam* ed  = nullptr;
 567             do_force(fplog,
 568                      cr,
 569                      ms,
 570                      *ir,
 571                      awh,
 572                      enforcedRotation,
 573                      imdSession,
 574                      pull_work,
 575                      step,
 576                      nrnb,
 577                      wcycle,
 578                      &top,
 579                      state->box,
 580                      state->x.arrayRefWithPadding(),
 581                      &state->hist,
 582                      &f.view(),
 583                      force_vir,
 584                      mdatoms,
 585                      enerd,
 586                      state->lambda,
 587                      fr,
 588                      runScheduleWork,
 589                      vsite,
 590                      mu_tot,
 591                      t,
 592                      ed,
 593                      GMX_FORCE_NS | force_flags,
 594                      ddBalanceRegionHandler);
 595         }
 596
 597         /* Now we have the energies and forces corresponding to the
 598          * coordinates at time t.
 599          */
 600         {
 601             const bool isCheckpointingStep = false;
 602             const bool doRerun             = false;
 603             const bool bSumEkinhOld        = false;
 604             do_md_trajectory_writing(fplog,
 605                                      cr,
 606                                      nfile,
 607                                      fnm,
 608                                      step,
 609                                      step_rel,
 610                                      t,
 611                                      ir,
 612                                      state,
 613                                      state_global,
 614                                      observablesHistory,
 615                                      top_global,
 616                                      fr,
 617                                      outf,
 618                                      energyOutput,
 619                                      ekind,
 620                                      f.view().force(),
 621                                      isCheckpointingStep,
 622                                      doRerun,
 623                                      isLastStep,
 624                                      mdrunOptions.writeConfout,
 625                                      bSumEkinhOld);
 626         }
 627
 628         stopHandler->setSignal();
 629
 630         {
 631             const bool          doInterSimSignal = false;
 632             const bool          doIntraSimSignal = true;
 633             bool                bSumEkinhOld     = false;
 634             t_vcm*              vcm              = nullptr;
 635             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 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                             &totalNumberOfBondedInteractions,
 658                             &bSumEkinhOld,
 659                             CGLO_GSTAT | CGLO_ENERGY
 660                                     | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
 661                                                                              : 0));
 662             checkNumberOfBondedInteractions(mdlog,
 663                                             cr,
 664                                             totalNumberOfBondedInteractions,
 665                                             top_global,
 666                                             &top,
 667                                             makeConstArrayRef(state->x),
 668                                             state->box,
 669                                             &shouldCheckNumberOfBondedInteractions);
 670         }
 671
 672         {
 673             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 674             gmx::ArrayRef<gmx::RVec>       ftemp;
 675             gmx::ArrayRef<const gmx::RVec> flocal = f.view().force();
 676             if (DOMAINDECOMP(cr))
 677             {
 678                 ftemp = gmx::makeArrayRef(fglobal);
 679                 dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl, flocal, ftemp);
 680             }
 681             else
 682             {
 683                 ftemp = f.view().force();
 684             }
 685
 686             if (MASTER(cr))
 687             {
 688                 MimicCommunicator::sendEnergies(enerd->term[F_EPOT]);
 689                 MimicCommunicator::sendForces(ftemp, state_global->natoms);
 690             }
 691         }
 692
 693
 694         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 695            the virial that should probably be addressed eventually. state->veta has better properies,
 696            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 697            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 698
 699         if (ir->efep != FreeEnergyPerturbationType::No)
 700         {
 701             /* Sum up the foreign energy and dhdl terms for md and sd.
 702                Currently done every step so that dhdl is correct in the .edr */
 703             accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
 704         }
 705
 706         /* Output stuff */
 707         if (MASTER(cr))
 708         {
 709             const bool bCalcEnerStep = true;
 710             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 711                                              bCalcEnerStep,
 712                                              t,
 713                                              mdatoms->tmass,
 714                                              enerd,
 715                                              ir->fepvals.get(),
 716                                              ir->expandedvals.get(),
 717                                              state->box,
 718                                              PTCouplingArrays({ state->boxv,
 719                                                                 state->nosehoover_xi,
 720                                                                 state->nosehoover_vxi,
 721                                                                 state->nhpres_xi,
 722                                                                 state->nhpres_vxi }),
 723                                              state->fep_state,
 724                                              shake_vir,
 725                                              force_vir,
 726                                              total_vir,
 727                                              pres,
 728                                              ekind,
 729                                              mu_tot,
 730                                              constr);
 731
 732             const bool do_ene = true;
 733             const bool do_log = true;
 734             Awh*       awh    = nullptr;
 735             const bool do_dr  = ir->nstdisreout != 0;
 736             const bool do_or  = ir->nstorireout != 0;
 737
 738             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 739             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 740                                                do_ene,
 741                                                do_dr,
 742                                                do_or,
 743                                                do_log ? fplog : nullptr,
 744                                                step,
 745                                                t,
 746                                                fr->fcdata.get(),
 747                                                awh);
 748
 749             if (do_per_step(step, ir->nstlog))
 750             {
 751                 if (fflush(fplog) != 0)
 752                 {
 753                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 754                 }
 755             }
 756         }
 757
 758         /* Print the remaining wall clock time for the run */
 759         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 760         {
 761             if (shellfc)
 762             {
 763                 fprintf(stderr, "\n");
 764             }
 765             print_time(stderr, walltime_accounting, step, ir, cr);
 766         }
 767
 768         cycles = wallcycle_stop(wcycle, ewcSTEP);
 769         if (DOMAINDECOMP(cr) && wcycle)
 770         {
 771             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 772         }
 773
 774         /* increase the MD step number */
 775         step++;
 776         step_rel++;
 777     }
 778     /* End of main MD loop */
 779
 780     /* Closing TNG files can include compressing data. Therefore it is good to do that
 781      * before stopping the time measurements. */
 782     mdoutf_tng_close(outf);
 783
 784     /* Stop measuring walltime */
 785     walltime_accounting_end_time(walltime_accounting);
 786
 787     if (MASTER(cr))
 788     {
 789         MimicCommunicator::finalize();
 790     }
 791
 792     if (!thisRankHasDuty(cr, DUTY_PME))
 793     {
 794         /* Tell the PME only node to finish */
 795         gmx_pme_send_finish(cr);
 796     }
 797
 798     done_mdoutf(outf);
 799
 800     done_shellfc(fplog, shellfc, step_rel);
 801
 802     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 803 }