src/gromacs/mdrun/rerun.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
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  17  * Lesser General Public License for more details.
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  34  */
  35 /*! \internal \file
  36  *
  37  * \brief Implements the loop for simulation reruns
  38  *
  39  * \author Pascal Merz <pascal.merz@colorado.edu>
  40  * \ingroup module_mdrun
  41  */
  42 #include "gmxpre.h"
  43
  44 #include <cinttypes>
  45 #include <cmath>
  46 #include <cstdio>
  47 #include <cstdlib>
  48
  49 #include <algorithm>
  50 #include <memory>
  51
  52 #include "gromacs/applied_forces/awh/awh.h"
  53 #include "gromacs/commandline/filenm.h"
  54 #include "gromacs/domdec/collect.h"
  55 #include "gromacs/domdec/dlbtiming.h"
  56 #include "gromacs/domdec/domdec.h"
  57 #include "gromacs/domdec/domdec_network.h"
  58 #include "gromacs/domdec/domdec_struct.h"
  59 #include "gromacs/domdec/mdsetup.h"
  60 #include "gromacs/domdec/partition.h"
  61 #include "gromacs/essentialdynamics/edsam.h"
  62 #include "gromacs/ewald/pme_load_balancing.h"
  63 #include "gromacs/ewald/pme_pp.h"
  64 #include "gromacs/fileio/trxio.h"
  65 #include "gromacs/gmxlib/network.h"
  66 #include "gromacs/gmxlib/nrnb.h"
  67 #include "gromacs/gpu_utils/gpu_utils.h"
  68 #include "gromacs/listed_forces/listed_forces.h"
  69 #include "gromacs/math/functions.h"
  70 #include "gromacs/math/utilities.h"
  71 #include "gromacs/math/vec.h"
  72 #include "gromacs/math/vectypes.h"
  73 #include "gromacs/mdlib/checkpointhandler.h"
  74 #include "gromacs/mdlib/compute_io.h"
  75 #include "gromacs/mdlib/constr.h"
  76 #include "gromacs/mdlib/ebin.h"
  77 #include "gromacs/mdlib/enerdata_utils.h"
  78 #include "gromacs/mdlib/energyoutput.h"
  79 #include "gromacs/mdlib/expanded.h"
  80 #include "gromacs/mdlib/force.h"
  81 #include "gromacs/mdlib/force_flags.h"
  82 #include "gromacs/mdlib/forcerec.h"
  83 #include "gromacs/mdlib/freeenergyparameters.h"
  84 #include "gromacs/mdlib/md_support.h"
  85 #include "gromacs/mdlib/mdatoms.h"
  86 #include "gromacs/mdlib/mdoutf.h"
  87 #include "gromacs/mdlib/membed.h"
  88 #include "gromacs/mdlib/resethandler.h"
  89 #include "gromacs/mdlib/sighandler.h"
  90 #include "gromacs/mdlib/simulationsignal.h"
  91 #include "gromacs/mdlib/stat.h"
  92 #include "gromacs/mdlib/stophandler.h"
  93 #include "gromacs/mdlib/tgroup.h"
  94 #include "gromacs/mdlib/trajectory_writing.h"
  95 #include "gromacs/mdlib/update.h"
  96 #include "gromacs/mdlib/vcm.h"
  97 #include "gromacs/mdlib/vsite.h"
  98 #include "gromacs/mdrunutility/handlerestart.h"
  99 #include "gromacs/mdrunutility/multisim.h"
 100 #include "gromacs/mdrunutility/printtime.h"
 101 #include "gromacs/mdtypes/awh_history.h"
 102 #include "gromacs/mdtypes/awh_params.h"
 103 #include "gromacs/mdtypes/commrec.h"
 104 #include "gromacs/mdtypes/df_history.h"
 105 #include "gromacs/mdtypes/energyhistory.h"
 106 #include "gromacs/mdtypes/forcebuffers.h"
 107 #include "gromacs/mdtypes/forcerec.h"
 108 #include "gromacs/mdtypes/group.h"
 109 #include "gromacs/mdtypes/inputrec.h"
 110 #include "gromacs/mdtypes/interaction_const.h"
 111 #include "gromacs/mdtypes/md_enums.h"
 112 #include "gromacs/mdtypes/mdatom.h"
 113 #include "gromacs/mdtypes/mdrunoptions.h"
 114 #include "gromacs/mdtypes/observableshistory.h"
 115 #include "gromacs/mdtypes/simulation_workload.h"
 116 #include "gromacs/mdtypes/state.h"
 117 #include "gromacs/mimic/utilities.h"
 118 #include "gromacs/pbcutil/pbc.h"
 119 #include "gromacs/pulling/pull.h"
 120 #include "gromacs/swap/swapcoords.h"
 121 #include "gromacs/timing/wallcycle.h"
 122 #include "gromacs/timing/walltime_accounting.h"
 123 #include "gromacs/topology/atoms.h"
 124 #include "gromacs/topology/idef.h"
 125 #include "gromacs/topology/mtop_util.h"
 126 #include "gromacs/topology/topology.h"
 127 #include "gromacs/trajectory/trajectoryframe.h"
 128 #include "gromacs/utility/basedefinitions.h"
 129 #include "gromacs/utility/cstringutil.h"
 130 #include "gromacs/utility/fatalerror.h"
 131 #include "gromacs/utility/logger.h"
 132 #include "gromacs/utility/real.h"
 133
 134 #include "legacysimulator.h"
 135 #include "replicaexchange.h"
 136 #include "shellfc.h"
 137
 138 using gmx::SimulationSignaller;
 139 using gmx::VirtualSitesHandler;
 140
 141 /*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
 142  *
 143  * \param[in]     rerunFrame      The trajectory frame to compute energy/forces for
 144  * \param[in,out] globalState     The global state container
 145  * \param[in]     constructVsites When true, vsite coordinates are constructed
 146  * \param[in]     vsite           Vsite setup, can be nullptr when \p constructVsites = false
 147  */
 148 static void prepareRerunState(const t_trxframe&          rerunFrame,
 149                               t_state*                   globalState,
 150                               bool                       constructVsites,
 151                               const VirtualSitesHandler* vsite)
 152 {
 153     auto x      = makeArrayRef(globalState->x);
 154     auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec*>(rerunFrame.x), globalState->natoms);
 155     std::copy(rerunX.begin(), rerunX.end(), x.begin());
 156     copy_mat(rerunFrame.box, globalState->box);
 157
 158     if (constructVsites)
 159     {
 160         GMX_ASSERT(vsite, "Need valid vsite for constructing vsites");
 161
 162         vsite->construct(globalState->x, globalState->v, globalState->box, gmx::VSiteOperation::PositionsAndVelocities);
 163     }
 164 }
 165
 166 void gmx::LegacySimulator::do_rerun()
 167 {
 168     // TODO Historically, the EM and MD "integrators" used different
 169     // names for the t_inputrec *parameter, but these must have the
 170     // same name, now that it's a member of a struct. We use this ir
 171     // alias to avoid a large ripple of nearly useless changes.
 172     // t_inputrec is being replaced by IMdpOptionsProvider, so this
 173     // will go away eventually.
 174     const t_inputrec* ir = inputrec;
 175     int64_t           step, step_rel;
 176     double            t;
 177     bool              isLastStep               = false;
 178     bool              doFreeEnergyPerturbation = false;
 179     unsigned int      force_flags;
 180     tensor            force_vir, shake_vir, total_vir, pres;
 181     t_trxstatus*      status = nullptr;
 182     rvec              mu_tot;
 183     t_trxframe        rerun_fr;
 184     gmx_localtop_t    top(top_global.ffparams);
 185     ForceBuffers      f;
 186     gmx_global_stat_t gstat;
 187     gmx_shellfc_t*    shellfc;
 188
 189     double cycles;
 190
 191     /* Domain decomposition could incorrectly miss a bonded
 192        interaction, but checking for that requires a global
 193        communication stage, which does not otherwise happen in DD
 194        code. So we do that alongside the first global energy reduction
 195        after a new DD is made. These variables handle whether the
 196        check happens, and the result it returns. */
 197     bool shouldCheckNumberOfBondedInteractions = false;
 198     int  totalNumberOfBondedInteractions       = -1;
 199
 200     SimulationSignals signals;
 201     // Most global communnication stages don't propagate mdrun
 202     // signals, and will use this object to achieve that.
 203     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 204
 205     GMX_LOG(mdlog.info)
 206             .asParagraph()
 207             .appendText(
 208                     "Note that it is planned that the command gmx mdrun -rerun will "
 209                     "be available in a different form in a future version of GROMACS, "
 210                     "e.g. gmx rerun -f.");
 211
 212     if (ir->efep != FreeEnergyPerturbationType::No
 213         && (mdAtoms->mdatoms()->nMassPerturbed > 0 || (constr && constr->havePerturbedConstraints())))
 214     {
 215         gmx_fatal(FARGS,
 216                   "Perturbed masses or constraints are not supported by rerun. "
 217                   "Either make a .tpr without mass and constraint perturbation, "
 218                   "or use GROMACS 2018.4, 2018.5 or later 2018 version.");
 219     }
 220     if (ir->bExpanded)
 221     {
 222         gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
 223     }
 224     if (ir->bSimTemp)
 225     {
 226         gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
 227     }
 228     if (ir->bDoAwh)
 229     {
 230         gmx_fatal(FARGS, "AWH not supported by rerun.");
 231     }
 232     if (replExParams.exchangeInterval > 0)
 233     {
 234         gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
 235     }
 236     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 237     {
 238         gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
 239     }
 240     if (ir->bIMD)
 241     {
 242         gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
 243     }
 244     if (isMultiSim(ms))
 245     {
 246         gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
 247     }
 248     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](SimulatedAnnealing i) {
 249             return i != SimulatedAnnealing::No;
 250         }))
 251     {
 252         gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
 253     }
 254
 255     /* Rerun can't work if an output file name is the same as the input file name.
 256      * If this is the case, the user will get an error telling them what the issue is.
 257      */
 258     if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0
 259         || strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
 260     {
 261         gmx_fatal(FARGS,
 262                   "When using mdrun -rerun, the name of the input trajectory file "
 263                   "%s cannot be identical to the name of an output file (whether "
 264                   "given explicitly with -o or -x, or by default)",
 265                   opt2fn("-rerun", nfile, fnm));
 266     }
 267
 268     /* Settings for rerun */
 269     {
 270         // TODO: Avoid changing inputrec (#3854)
 271         auto* nonConstInputrec               = const_cast<t_inputrec*>(inputrec);
 272         nonConstInputrec->nstlist            = 1;
 273         nonConstInputrec->nstcalcenergy      = 1;
 274         nonConstInputrec->nstxout_compressed = 0;
 275     }
 276     int        nstglobalcomm = 1;
 277     const bool bNS           = true;
 278
 279     const SimulationGroups* groups = &top_global.groups;
 280     if (ir->eI == IntegrationAlgorithm::Mimic)
 281     {
 282         auto nonConstGlobalTopology                          = const_cast<gmx_mtop_t*>(&top_global);
 283         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
 284     }
 285     int*                fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
 286     gmx::ArrayRef<real> lambda    = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
 287     initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
 288     const bool        simulationsShareState = false;
 289     gmx_mdoutf*       outf                  = init_mdoutf(fplog,
 290                                    nfile,
 291                                    fnm,
 292                                    mdrunOptions,
 293                                    cr,
 294                                    outputProvider,
 295                                    mdModulesNotifier,
 296                                    ir,
 297                                    top_global,
 298                                    oenv,
 299                                    wcycle,
 300                                    StartingBehavior::NewSimulation,
 301                                    simulationsShareState,
 302                                    ms);
 303     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
 304                                    top_global,
 305                                    *ir,
 306                                    pull_work,
 307                                    mdoutf_get_fp_dhdl(outf),
 308                                    true,
 309                                    StartingBehavior::NewSimulation,
 310                                    simulationsShareState,
 311                                    mdModulesNotifier);
 312
 313     gstat = global_stat_init(ir);
 314
 315     /* Check for polarizable models and flexible constraints */
 316     shellfc = init_shell_flexcon(fplog,
 317                                  top_global,
 318                                  constr ? constr->numFlexibleConstraints() : 0,
 319                                  ir->nstcalcenergy,
 320                                  DOMAINDECOMP(cr),
 321                                  runScheduleWork->simulationWork.useGpuPme);
 322
 323     {
 324         double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
 325         if ((io > 2000) && MASTER(cr))
 326         {
 327             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 328         }
 329     }
 330
 331     // Local state only becomes valid now.
 332     std::unique_ptr<t_state> stateInstance;
 333     t_state*                 state;
 334
 335     if (DOMAINDECOMP(cr))
 336     {
 337         stateInstance = std::make_unique<t_state>();
 338         state         = stateInstance.get();
 339         dd_init_local_state(*cr->dd, state_global, state);
 340
 341         /* Distribute the charge groups over the nodes from the master node */
 342         dd_partition_system(fplog,
 343                             mdlog,
 344                             ir->init_step,
 345                             cr,
 346                             TRUE,
 347                             1,
 348                             state_global,
 349                             top_global,
 350                             *ir,
 351                             imdSession,
 352                             pull_work,
 353                             state,
 354                             &f,
 355                             mdAtoms,
 356                             &top,
 357                             fr,
 358                             vsite,
 359                             constr,
 360                             nrnb,
 361                             nullptr,
 362                             FALSE);
 363         shouldCheckNumberOfBondedInteractions = true;
 364     }
 365     else
 366     {
 367         state_change_natoms(state_global, state_global->natoms);
 368         /* Copy the pointer to the global state */
 369         state = state_global;
 370
 371         mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 372     }
 373
 374     auto mdatoms = mdAtoms->mdatoms();
 375
 376     // NOTE: The global state is no longer used at this point.
 377     // But state_global is still used as temporary storage space for writing
 378     // the global state to file and potentially for replica exchange.
 379     // (Global topology should persist.)
 380
 381     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 382
 383     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 384     {
 385         doFreeEnergyPerturbation = true;
 386     }
 387
 388     {
 389         int cglo_flags =
 390                 (CGLO_GSTAT
 391                  | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 392         bool   bSumEkinhOld = false;
 393         t_vcm* vcm          = nullptr;
 394         compute_globals(gstat,
 395                         cr,
 396                         ir,
 397                         fr,
 398                         ekind,
 399                         makeConstArrayRef(state->x),
 400                         makeConstArrayRef(state->v),
 401                         state->box,
 402                         mdatoms,
 403                         nrnb,
 404                         vcm,
 405                         nullptr,
 406                         enerd,
 407                         force_vir,
 408                         shake_vir,
 409                         total_vir,
 410                         pres,
 411                         gmx::ArrayRef<real>{},
 412                         &nullSignaller,
 413                         state->box,
 414                         &totalNumberOfBondedInteractions,
 415                         &bSumEkinhOld,
 416                         cglo_flags);
 417     }
 418     checkNumberOfBondedInteractions(mdlog,
 419                                     cr,
 420                                     totalNumberOfBondedInteractions,
 421                                     top_global,
 422                                     &top,
 423                                     makeConstArrayRef(state->x),
 424                                     state->box,
 425                                     &shouldCheckNumberOfBondedInteractions);
 426
 427     if (MASTER(cr))
 428     {
 429         fprintf(stderr,
 430                 "starting md rerun '%s', reading coordinates from"
 431                 " input trajectory '%s'\n\n",
 432                 *(top_global.name),
 433                 opt2fn("-rerun", nfile, fnm));
 434         if (mdrunOptions.verbose)
 435         {
 436             fprintf(stderr,
 437                     "Calculated time to finish depends on nsteps from "
 438                     "run input file,\nwhich may not correspond to the time "
 439                     "needed to process input trajectory.\n\n");
 440         }
 441         fprintf(fplog, "\n");
 442     }
 443
 444     walltime_accounting_start_time(walltime_accounting);
 445     wallcycle_start(wcycle, ewcRUN);
 446     print_start(fplog, cr, walltime_accounting, "mdrun");
 447
 448     /***********************************************************
 449      *
 450      *             Loop over MD steps
 451      *
 452      ************************************************************/
 453
 454     if (constr)
 455     {
 456         GMX_LOG(mdlog.info)
 457                 .asParagraph()
 458                 .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
 459     }
 460
 461     rerun_fr.natoms = 0;
 462     if (MASTER(cr))
 463     {
 464         isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
 465         if (rerun_fr.natoms != top_global.natoms)
 466         {
 467             gmx_fatal(FARGS,
 468                       "Number of atoms in trajectory (%d) does not match the "
 469                       "run input file (%d)\n",
 470                       rerun_fr.natoms,
 471                       top_global.natoms);
 472         }
 473
 474         if (ir->pbcType != PbcType::No)
 475         {
 476             if (!rerun_fr.bBox)
 477             {
 478                 gmx_fatal(FARGS,
 479                           "Rerun trajectory frame step %" PRId64
 480                           " time %f "
 481                           "does not contain a box, while pbc is used",
 482                           rerun_fr.step,
 483                           rerun_fr.time);
 484             }
 485             if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
 486             {
 487                 gmx_fatal(FARGS,
 488                           "Rerun trajectory frame step %" PRId64
 489                           " time %f "
 490                           "has too small box dimensions",
 491                           rerun_fr.step,
 492                           rerun_fr.time);
 493             }
 494         }
 495     }
 496
 497     GMX_LOG(mdlog.info)
 498             .asParagraph()
 499             .appendText(
 500                     "Rerun does not report kinetic energy, total energy, temperature, virial and "
 501                     "pressure.");
 502
 503     if (PAR(cr))
 504     {
 505         rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 506     }
 507
 508     if (ir->pbcType != PbcType::No)
 509     {
 510         /* Set the shift vectors.
 511          * Necessary here when have a static box different from the tpr box.
 512          */
 513         calc_shifts(rerun_fr.box, fr->shift_vec);
 514     }
 515
 516     step     = ir->init_step;
 517     step_rel = 0;
 518
 519     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 520             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 521             false,
 522             MASTER(cr),
 523             ir->nstlist,
 524             mdrunOptions.reproducible,
 525             nstglobalcomm,
 526             mdrunOptions.maximumHoursToRun,
 527             ir->nstlist == 0,
 528             fplog,
 529             step,
 530             bNS,
 531             walltime_accounting);
 532
 533     // we don't do counter resetting in rerun - finish will always be valid
 534     walltime_accounting_set_valid_finish(walltime_accounting);
 535
 536     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 537
 538     /* and stop now if we should */
 539     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 540     while (!isLastStep)
 541     {
 542         wallcycle_start(wcycle, ewcSTEP);
 543
 544         if (rerun_fr.bStep)
 545         {
 546             step     = rerun_fr.step;
 547             step_rel = step - ir->init_step;
 548         }
 549         if (rerun_fr.bTime)
 550         {
 551             t = rerun_fr.time;
 552         }
 553         else
 554         {
 555             t = step;
 556         }
 557
 558         if (ir->efep != FreeEnergyPerturbationType::No && MASTER(cr))
 559         {
 560             if (rerun_fr.bLambda)
 561             {
 562                 ir->fepvals->init_lambda = rerun_fr.lambda;
 563             }
 564             else
 565             {
 566                 if (rerun_fr.bFepState)
 567                 {
 568                     state->fep_state = rerun_fr.fep_state;
 569                 }
 570             }
 571
 572             state_global->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
 573         }
 574
 575         if (MASTER(cr))
 576         {
 577             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 578             if (constructVsites && DOMAINDECOMP(cr))
 579             {
 580                 gmx_fatal(FARGS,
 581                           "Vsite recalculation with -rerun is not implemented with domain "
 582                           "decomposition, "
 583                           "use a single rank");
 584             }
 585             prepareRerunState(rerun_fr, state_global, constructVsites, vsite);
 586         }
 587
 588         isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
 589
 590         if (DOMAINDECOMP(cr))
 591         {
 592             /* Repartition the domain decomposition */
 593             const bool bMasterState = true;
 594             dd_partition_system(fplog,
 595                                 mdlog,
 596                                 step,
 597                                 cr,
 598                                 bMasterState,
 599                                 nstglobalcomm,
 600                                 state_global,
 601                                 top_global,
 602                                 *ir,
 603                                 imdSession,
 604                                 pull_work,
 605                                 state,
 606                                 &f,
 607                                 mdAtoms,
 608                                 &top,
 609                                 fr,
 610                                 vsite,
 611                                 constr,
 612                                 nrnb,
 613                                 wcycle,
 614                                 mdrunOptions.verbose);
 615             shouldCheckNumberOfBondedInteractions = true;
 616         }
 617
 618         if (MASTER(cr))
 619         {
 620             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 621         }
 622
 623         if (ir->efep != FreeEnergyPerturbationType::No)
 624         {
 625             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 626         }
 627
 628         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 629                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
 630                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 631
 632         if (shellfc)
 633         {
 634             /* Now is the time to relax the shells */
 635             relax_shell_flexcon(fplog,
 636                                 cr,
 637                                 ms,
 638                                 mdrunOptions.verbose,
 639                                 enforcedRotation,
 640                                 step,
 641                                 ir,
 642                                 imdSession,
 643                                 pull_work,
 644                                 bNS,
 645                                 force_flags,
 646                                 &top,
 647                                 constr,
 648                                 enerd,
 649                                 state->natoms,
 650                                 state->x.arrayRefWithPadding(),
 651                                 state->v.arrayRefWithPadding(),
 652                                 state->box,
 653                                 state->lambda,
 654                                 &state->hist,
 655                                 &f.view(),
 656                                 force_vir,
 657                                 mdatoms,
 658                                 nrnb,
 659                                 wcycle,
 660                                 shellfc,
 661                                 fr,
 662                                 runScheduleWork,
 663                                 t,
 664                                 mu_tot,
 665                                 vsite,
 666                                 ddBalanceRegionHandler);
 667         }
 668         else
 669         {
 670             /* The coordinates (x) are shifted (to get whole molecules)
 671              * in do_force.
 672              * This is parallellized as well, and does communication too.
 673              * Check comments in sim_util.c
 674              */
 675             Awh*       awh = nullptr;
 676             gmx_edsam* ed  = nullptr;
 677             do_force(fplog,
 678                      cr,
 679                      ms,
 680                      *ir,
 681                      awh,
 682                      enforcedRotation,
 683                      imdSession,
 684                      pull_work,
 685                      step,
 686                      nrnb,
 687                      wcycle,
 688                      &top,
 689                      state->box,
 690                      state->x.arrayRefWithPadding(),
 691                      &state->hist,
 692                      &f.view(),
 693                      force_vir,
 694                      mdatoms,
 695                      enerd,
 696                      state->lambda,
 697                      fr,
 698                      runScheduleWork,
 699                      vsite,
 700                      mu_tot,
 701                      t,
 702                      ed,
 703                      GMX_FORCE_NS | force_flags,
 704                      ddBalanceRegionHandler);
 705         }
 706
 707         /* Now we have the energies and forces corresponding to the
 708          * coordinates at time t.
 709          */
 710         {
 711             const bool isCheckpointingStep = false;
 712             const bool doRerun             = true;
 713             const bool bSumEkinhOld        = false;
 714             do_md_trajectory_writing(fplog,
 715                                      cr,
 716                                      nfile,
 717                                      fnm,
 718                                      step,
 719                                      step_rel,
 720                                      t,
 721                                      ir,
 722                                      state,
 723                                      state_global,
 724                                      observablesHistory,
 725                                      top_global,
 726                                      fr,
 727                                      outf,
 728                                      energyOutput,
 729                                      ekind,
 730                                      f.view().force(),
 731                                      isCheckpointingStep,
 732                                      doRerun,
 733                                      isLastStep,
 734                                      mdrunOptions.writeConfout,
 735                                      bSumEkinhOld);
 736         }
 737
 738         stopHandler->setSignal();
 739
 740         {
 741             const bool          doInterSimSignal = false;
 742             const bool          doIntraSimSignal = true;
 743             bool                bSumEkinhOld     = false;
 744             t_vcm*              vcm              = nullptr;
 745             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 746
 747             compute_globals(gstat,
 748                             cr,
 749                             ir,
 750                             fr,
 751                             ekind,
 752                             makeConstArrayRef(state->x),
 753                             makeConstArrayRef(state->v),
 754                             state->box,
 755                             mdatoms,
 756                             nrnb,
 757                             vcm,
 758                             wcycle,
 759                             enerd,
 760                             force_vir,
 761                             shake_vir,
 762                             total_vir,
 763                             pres,
 764                             constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
 765                             &signaller,
 766                             state->box,
 767                             &totalNumberOfBondedInteractions,
 768                             &bSumEkinhOld,
 769                             CGLO_GSTAT | CGLO_ENERGY
 770                                     | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
 771                                                                              : 0));
 772             checkNumberOfBondedInteractions(mdlog,
 773                                             cr,
 774                                             totalNumberOfBondedInteractions,
 775                                             top_global,
 776                                             &top,
 777                                             makeConstArrayRef(state->x),
 778                                             state->box,
 779                                             &shouldCheckNumberOfBondedInteractions);
 780         }
 781
 782         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 783            the virial that should probably be addressed eventually. state->veta has better properies,
 784            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 785            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 786
 787         /* Output stuff */
 788         if (MASTER(cr))
 789         {
 790             const bool bCalcEnerStep = true;
 791             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 792                                              bCalcEnerStep,
 793                                              t,
 794                                              mdatoms->tmass,
 795                                              enerd,
 796                                              ir->fepvals.get(),
 797                                              ir->expandedvals.get(),
 798                                              state->box,
 799                                              PTCouplingArrays({ state->boxv,
 800                                                                 state->nosehoover_xi,
 801                                                                 state->nosehoover_vxi,
 802                                                                 state->nhpres_xi,
 803                                                                 state->nhpres_vxi }),
 804                                              state->fep_state,
 805                                              shake_vir,
 806                                              force_vir,
 807                                              total_vir,
 808                                              pres,
 809                                              ekind,
 810                                              mu_tot,
 811                                              constr);
 812
 813             const bool do_ene = true;
 814             const bool do_log = true;
 815             Awh*       awh    = nullptr;
 816             const bool do_dr  = ir->nstdisreout != 0;
 817             const bool do_or  = ir->nstorireout != 0;
 818
 819             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 820             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 821                                                do_ene,
 822                                                do_dr,
 823                                                do_or,
 824                                                do_log ? fplog : nullptr,
 825                                                step,
 826                                                t,
 827                                                fr->fcdata.get(),
 828                                                awh);
 829
 830             if (do_per_step(step, ir->nstlog))
 831             {
 832                 if (fflush(fplog) != 0)
 833                 {
 834                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 835                 }
 836             }
 837         }
 838
 839         /* Print the remaining wall clock time for the run */
 840         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 841         {
 842             if (shellfc)
 843             {
 844                 fprintf(stderr, "\n");
 845             }
 846             print_time(stderr, walltime_accounting, step, ir, cr);
 847         }
 848
 849         /* Ion/water position swapping.
 850          * Not done in last step since trajectory writing happens before this call
 851          * in the MD loop and exchanges would be lost anyway. */
 852         if ((ir->eSwapCoords != SwapType::No) && (step > 0) && !isLastStep
 853             && do_per_step(step, ir->swap->nstswap))
 854         {
 855             const bool doRerun = true;
 856             do_swapcoords(cr,
 857                           step,
 858                           t,
 859                           ir,
 860                           swap,
 861                           wcycle,
 862                           rerun_fr.x,
 863                           rerun_fr.box,
 864                           MASTER(cr) && mdrunOptions.verbose,
 865                           doRerun);
 866         }
 867
 868         if (MASTER(cr))
 869         {
 870             /* read next frame from input trajectory */
 871             isLastStep = !read_next_frame(oenv, status, &rerun_fr);
 872         }
 873
 874         if (PAR(cr))
 875         {
 876             rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 877         }
 878
 879         cycles = wallcycle_stop(wcycle, ewcSTEP);
 880         if (DOMAINDECOMP(cr) && wcycle)
 881         {
 882             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 883         }
 884
 885         if (!rerun_fr.bStep)
 886         {
 887             /* increase the MD step number */
 888             step++;
 889             step_rel++;
 890         }
 891     }
 892     /* End of main MD loop */
 893
 894     /* Closing TNG files can include compressing data. Therefore it is good to do that
 895      * before stopping the time measurements. */
 896     mdoutf_tng_close(outf);
 897
 898     /* Stop measuring walltime */
 899     walltime_accounting_end_time(walltime_accounting);
 900
 901     if (MASTER(cr))
 902     {
 903         close_trx(status);
 904     }
 905
 906     if (!thisRankHasDuty(cr, DUTY_PME))
 907     {
 908         /* Tell the PME only node to finish */
 909         gmx_pme_send_finish(cr);
 910     }
 911
 912     done_mdoutf(outf);
 913
 914     done_shellfc(fplog, shellfc, step_rel);
 915
 916     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 917 }