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     int64_t           step, step_rel;
 147     double            t;
 148     bool              isLastStep               = false;
 149     bool              doFreeEnergyPerturbation = false;
 150     unsigned int      force_flags;
 151     tensor            force_vir, shake_vir, total_vir, pres;
 152     rvec              mu_tot;
 153     ForceBuffers      f;
 154     gmx_global_stat_t gstat;
 155     gmx_shellfc_t*    shellfc;
 156
 157     double cycles;
 158
 159     SimulationSignals signals;
 160     // Most global communnication stages don't propagate mdrun
 161     // signals, and will use this object to achieve that.
 162     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 163
 164     if (ir->bExpanded)
 165     {
 166         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 167     }
 168     if (ir->bSimTemp)
 169     {
 170         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 171     }
 172     if (ir->bDoAwh)
 173     {
 174         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 175     }
 176     if (replExParams.exchangeInterval > 0)
 177     {
 178         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 179     }
 180     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 181     {
 182         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 183     }
 184     if (ir->bIMD)
 185     {
 186         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 187     }
 188     if (isMultiSim(ms))
 189     {
 190         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 191     }
 192     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](SimulatedAnnealing i) {
 193             return i != SimulatedAnnealing::No;
 194         }))
 195     {
 196         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 197     }
 198
 199     /* Settings for rerun */
 200     {
 201         // TODO: Avoid changing inputrec (#3854)
 202         auto* nonConstInputrec               = const_cast<t_inputrec*>(inputrec);
 203         nonConstInputrec->nstlist            = 1;
 204         nonConstInputrec->nstcalcenergy      = 1;
 205         nonConstInputrec->nstxout_compressed = 0;
 206     }
 207     int        nstglobalcomm = 1;
 208     const bool bNS           = true;
 209
 210     if (MASTER(cr))
 211     {
 212         MimicCommunicator::init();
 213         auto* nonConstGlobalTopology = const_cast<gmx_mtop_t*>(&top_global);
 214         MimicCommunicator::sendInitData(nonConstGlobalTopology, state_global->x);
 215         // TODO: Avoid changing inputrec (#3854)
 216         auto* nonConstInputrec   = const_cast<t_inputrec*>(inputrec);
 217         nonConstInputrec->nsteps = MimicCommunicator::getStepNumber();
 218     }
 219     if (DOMAINDECOMP(cr))
 220     {
 221         // TODO: Avoid changing inputrec (#3854)
 222         auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
 223         gmx_bcast(sizeof(ir->nsteps), &nonConstInputrec->nsteps, cr->mpi_comm_mygroup);
 224     }
 225
 226     const SimulationGroups* groups = &top_global.groups;
 227     {
 228         auto* nonConstGlobalTopology                         = const_cast<gmx_mtop_t*>(&top_global);
 229         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
 230     }
 231
 232     initialize_lambdas(fplog,
 233                        ir->efep,
 234                        ir->bSimTemp,
 235                        *ir->fepvals,
 236                        ir->simtempvals->temperatures,
 237                        gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
 238                        MASTER(cr),
 239                        &state_global->fep_state,
 240                        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                                    mdModulesNotifiers,
 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                                    mdModulesNotifiers);
 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     }
 320     else
 321     {
 322         state_change_natoms(state_global, state_global->natoms);
 323         /* Copy the pointer to the global state */
 324         state = state_global;
 325
 326         mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 327     }
 328
 329     auto* mdatoms = mdAtoms->mdatoms();
 330
 331     // NOTE: The global state is no longer used at this point.
 332     // But state_global is still used as temporary storage space for writing
 333     // the global state to file and potentially for replica exchange.
 334     // (Global topology should persist.)
 335
 336     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 337
 338     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 339     {
 340         doFreeEnergyPerturbation = true;
 341     }
 342
 343     {
 344         int cglo_flags = CGLO_GSTAT;
 345         if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
 346         {
 347             cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 348         }
 349         bool   bSumEkinhOld = false;
 350         t_vcm* vcm          = nullptr;
 351         compute_globals(gstat,
 352                         cr,
 353                         ir,
 354                         fr,
 355                         ekind,
 356                         makeConstArrayRef(state->x),
 357                         makeConstArrayRef(state->v),
 358                         state->box,
 359                         mdatoms,
 360                         nrnb,
 361                         vcm,
 362                         nullptr,
 363                         enerd,
 364                         force_vir,
 365                         shake_vir,
 366                         total_vir,
 367                         pres,
 368                         gmx::ArrayRef<real>{},
 369                         &nullSignaller,
 370                         state->box,
 371                         &bSumEkinhOld,
 372                         cglo_flags);
 373         if (DOMAINDECOMP(cr))
 374         {
 375             checkNumberOfBondedInteractions(
 376                     mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
 377         }
 378     }
 379
 380     if (MASTER(cr))
 381     {
 382         fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global.name));
 383         if (mdrunOptions.verbose)
 384         {
 385             fprintf(stderr,
 386                     "Calculated time to finish depends on nsteps from "
 387                     "run input file,\nwhich may not correspond to the time "
 388                     "needed to process input trajectory.\n\n");
 389         }
 390         fprintf(fplog, "\n");
 391     }
 392
 393     walltime_accounting_start_time(walltime_accounting);
 394     wallcycle_start(wcycle, WallCycleCounter::Run);
 395     print_start(fplog, cr, walltime_accounting, "mdrun");
 396
 397     /***********************************************************
 398      *
 399      *             Loop over MD steps
 400      *
 401      ************************************************************/
 402
 403     if (constr)
 404     {
 405         GMX_LOG(mdlog.info)
 406                 .asParagraph()
 407                 .appendText(
 408                         "Simulations has constraints. Constraints will "
 409                         "be handled by CPMD.");
 410     }
 411
 412     GMX_LOG(mdlog.info)
 413             .asParagraph()
 414             .appendText(
 415                     "MiMiC does not report kinetic energy, total energy, temperature, virial and "
 416                     "pressure.");
 417
 418     step     = ir->init_step;
 419     step_rel = 0;
 420
 421     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 422             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 423             false,
 424             MASTER(cr),
 425             ir->nstlist,
 426             mdrunOptions.reproducible,
 427             nstglobalcomm,
 428             mdrunOptions.maximumHoursToRun,
 429             ir->nstlist == 0,
 430             fplog,
 431             step,
 432             bNS,
 433             walltime_accounting);
 434
 435     // we don't do counter resetting in rerun - finish will always be valid
 436     walltime_accounting_set_valid_finish(walltime_accounting);
 437
 438     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 439
 440     /* and stop now if we should */
 441     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 442     while (!isLastStep)
 443     {
 444         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 445         wallcycle_start(wcycle, WallCycleCounter::Step);
 446
 447         t = step;
 448
 449         if (MASTER(cr))
 450         {
 451             MimicCommunicator::getCoords(&state_global->x, state_global->natoms);
 452         }
 453
 454         if (ir->efep != FreeEnergyPerturbationType::No)
 455         {
 456             state->lambda = currentLambdas(step, *(ir->fepvals), state_global->fep_state);
 457         }
 458
 459         if (MASTER(cr))
 460         {
 461             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 462             if (constructVsites && DOMAINDECOMP(cr))
 463             {
 464                 gmx_fatal(FARGS,
 465                           "Vsite recalculation with -rerun is not implemented with domain "
 466                           "decomposition, "
 467                           "use a single rank");
 468             }
 469             if (constructVsites)
 470             {
 471                 wallcycle_start(wcycle, WallCycleCounter::VsiteConstr);
 472                 vsite->construct(state->x, state->v, state->box, VSiteOperation::PositionsAndVelocities);
 473                 wallcycle_stop(wcycle, WallCycleCounter::VsiteConstr);
 474             }
 475         }
 476
 477         if (DOMAINDECOMP(cr))
 478         {
 479             /* Repartition the domain decomposition */
 480             const bool bMasterState = true;
 481             dd_partition_system(fplog,
 482                                 mdlog,
 483                                 step,
 484                                 cr,
 485                                 bMasterState,
 486                                 nstglobalcomm,
 487                                 state_global,
 488                                 top_global,
 489                                 *ir,
 490                                 imdSession,
 491                                 pull_work,
 492                                 state,
 493                                 &f,
 494                                 mdAtoms,
 495                                 &top,
 496                                 fr,
 497                                 vsite,
 498                                 constr,
 499                                 nrnb,
 500                                 wcycle,
 501                                 mdrunOptions.verbose);
 502         }
 503
 504         if (MASTER(cr))
 505         {
 506             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 507         }
 508
 509         if (ir->efep != FreeEnergyPerturbationType::No)
 510         {
 511             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 512         }
 513
 514         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 515                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
 516                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 517
 518         if (shellfc)
 519         {
 520             /* Now is the time to relax the shells */
 521             relax_shell_flexcon(fplog,
 522                                 cr,
 523                                 ms,
 524                                 mdrunOptions.verbose,
 525                                 enforcedRotation,
 526                                 step,
 527                                 ir,
 528                                 imdSession,
 529                                 pull_work,
 530                                 bNS,
 531                                 force_flags,
 532                                 &top,
 533                                 constr,
 534                                 enerd,
 535                                 state->natoms,
 536                                 state->x.arrayRefWithPadding(),
 537                                 state->v.arrayRefWithPadding(),
 538                                 state->box,
 539                                 state->lambda,
 540                                 &state->hist,
 541                                 &f.view(),
 542                                 force_vir,
 543                                 *mdatoms,
 544                                 nrnb,
 545                                 wcycle,
 546                                 shellfc,
 547                                 fr,
 548                                 runScheduleWork,
 549                                 t,
 550                                 mu_tot,
 551                                 vsite,
 552                                 ddBalanceRegionHandler);
 553         }
 554         else
 555         {
 556             /* The coordinates (x) are shifted (to get whole molecules)
 557              * in do_force.
 558              * This is parallellized as well, and does communication too.
 559              * Check comments in sim_util.c
 560              */
 561             Awh*       awh = nullptr;
 562             gmx_edsam* ed  = nullptr;
 563             do_force(fplog,
 564                      cr,
 565                      ms,
 566                      *ir,
 567                      awh,
 568                      enforcedRotation,
 569                      imdSession,
 570                      pull_work,
 571                      step,
 572                      nrnb,
 573                      wcycle,
 574                      &top,
 575                      state->box,
 576                      state->x.arrayRefWithPadding(),
 577                      &state->hist,
 578                      &f.view(),
 579                      force_vir,
 580                      mdatoms,
 581                      enerd,
 582                      state->lambda,
 583                      fr,
 584                      runScheduleWork,
 585                      vsite,
 586                      mu_tot,
 587                      t,
 588                      ed,
 589                      GMX_FORCE_NS | force_flags,
 590                      ddBalanceRegionHandler);
 591         }
 592
 593         /* Now we have the energies and forces corresponding to the
 594          * coordinates at time t.
 595          */
 596         {
 597             const bool isCheckpointingStep = false;
 598             const bool doRerun             = false;
 599             const bool bSumEkinhOld        = false;
 600             do_md_trajectory_writing(fplog,
 601                                      cr,
 602                                      nfile,
 603                                      fnm,
 604                                      step,
 605                                      step_rel,
 606                                      t,
 607                                      ir,
 608                                      state,
 609                                      state_global,
 610                                      observablesHistory,
 611                                      top_global,
 612                                      fr,
 613                                      outf,
 614                                      energyOutput,
 615                                      ekind,
 616                                      f.view().force(),
 617                                      isCheckpointingStep,
 618                                      doRerun,
 619                                      isLastStep,
 620                                      mdrunOptions.writeConfout,
 621                                      bSumEkinhOld);
 622         }
 623
 624         stopHandler->setSignal();
 625
 626         {
 627             const bool          doInterSimSignal = false;
 628             const bool          doIntraSimSignal = true;
 629             bool                bSumEkinhOld     = false;
 630             t_vcm*              vcm              = nullptr;
 631             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 632
 633             int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
 634             if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
 635             {
 636                 cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 637             }
 638             compute_globals(gstat,
 639                             cr,
 640                             ir,
 641                             fr,
 642                             ekind,
 643                             makeConstArrayRef(state->x),
 644                             makeConstArrayRef(state->v),
 645                             state->box,
 646                             mdatoms,
 647                             nrnb,
 648                             vcm,
 649                             wcycle,
 650                             enerd,
 651                             nullptr,
 652                             nullptr,
 653                             nullptr,
 654                             nullptr,
 655                             constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
 656                             &signaller,
 657                             state->box,
 658                             &bSumEkinhOld,
 659                             cglo_flags);
 660             if (DOMAINDECOMP(cr))
 661             {
 662                 checkNumberOfBondedInteractions(
 663                         mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
 664             }
 665         }
 666
 667         {
 668             gmx::HostVector<gmx::RVec>     fglobal(top_global.natoms);
 669             gmx::ArrayRef<gmx::RVec>       ftemp;
 670             gmx::ArrayRef<const gmx::RVec> flocal = f.view().force();
 671             if (DOMAINDECOMP(cr))
 672             {
 673                 ftemp = gmx::makeArrayRef(fglobal);
 674                 dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl, flocal, ftemp);
 675             }
 676             else
 677             {
 678                 ftemp = f.view().force();
 679             }
 680
 681             if (MASTER(cr))
 682             {
 683                 MimicCommunicator::sendEnergies(enerd->term[F_EPOT]);
 684                 MimicCommunicator::sendForces(ftemp, state_global->natoms);
 685             }
 686         }
 687
 688
 689         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 690            the virial that should probably be addressed eventually. state->veta has better properies,
 691            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 692            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 693
 694         if (ir->efep != FreeEnergyPerturbationType::No)
 695         {
 696             /* Sum up the foreign energy and dhdl terms for md and sd.
 697                Currently done every step so that dhdl is correct in the .edr */
 698             accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
 699         }
 700
 701         /* Output stuff */
 702         if (MASTER(cr))
 703         {
 704             const bool bCalcEnerStep = true;
 705             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 706                                              bCalcEnerStep,
 707                                              t,
 708                                              mdatoms->tmass,
 709                                              enerd,
 710                                              ir->fepvals.get(),
 711                                              ir->expandedvals.get(),
 712                                              state->box,
 713                                              PTCouplingArrays({ state->boxv,
 714                                                                 state->nosehoover_xi,
 715                                                                 state->nosehoover_vxi,
 716                                                                 state->nhpres_xi,
 717                                                                 state->nhpres_vxi }),
 718                                              state->fep_state,
 719                                              total_vir,
 720                                              pres,
 721                                              ekind,
 722                                              mu_tot,
 723                                              constr);
 724
 725             const bool do_ene = true;
 726             const bool do_log = true;
 727             Awh*       awh    = nullptr;
 728             const bool do_dr  = ir->nstdisreout != 0;
 729             const bool do_or  = ir->nstorireout != 0;
 730
 731             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 732             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 733                                                do_ene,
 734                                                do_dr,
 735                                                do_or,
 736                                                do_log ? fplog : nullptr,
 737                                                step,
 738                                                t,
 739                                                fr->fcdata.get(),
 740                                                awh);
 741
 742             if (do_per_step(step, ir->nstlog))
 743             {
 744                 if (fflush(fplog) != 0)
 745                 {
 746                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 747                 }
 748             }
 749         }
 750
 751         /* Print the remaining wall clock time for the run */
 752         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 753         {
 754             if (shellfc)
 755             {
 756                 fprintf(stderr, "\n");
 757             }
 758             print_time(stderr, walltime_accounting, step, ir, cr);
 759         }
 760
 761         cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
 762         if (DOMAINDECOMP(cr) && wcycle)
 763         {
 764             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 765         }
 766
 767         /* increase the MD step number */
 768         step++;
 769         step_rel++;
 770     }
 771     /* End of main MD loop */
 772
 773     /* Closing TNG files can include compressing data. Therefore it is good to do that
 774      * before stopping the time measurements. */
 775     mdoutf_tng_close(outf);
 776
 777     /* Stop measuring walltime */
 778     walltime_accounting_end_time(walltime_accounting);
 779
 780     if (MASTER(cr))
 781     {
 782         MimicCommunicator::finalize();
 783     }
 784
 785     if (!thisRankHasDuty(cr, DUTY_PME))
 786     {
 787         /* Tell the PME only node to finish */
 788         gmx_pme_send_finish(cr);
 789     }
 790
 791     done_mdoutf(outf);
 792
 793     done_shellfc(fplog, shellfc, step_rel);
 794
 795     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 796 }