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  *
  14  * GROMACS is distributed in the hope that it will be useful,
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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     SimulationSignals signals;
 192     // Most global communnication stages don't propagate mdrun
 193     // signals, and will use this object to achieve that.
 194     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 195
 196     GMX_LOG(mdlog.info)
 197             .asParagraph()
 198             .appendText(
 199                     "Note that it is planned that the command gmx mdrun -rerun will "
 200                     "be available in a different form in a future version of GROMACS, "
 201                     "e.g. gmx rerun -f.");
 202
 203     if (ir->efep != FreeEnergyPerturbationType::No
 204         && (mdAtoms->mdatoms()->nMassPerturbed > 0 || (constr && constr->havePerturbedConstraints())))
 205     {
 206         gmx_fatal(FARGS,
 207                   "Perturbed masses or constraints are not supported by rerun. "
 208                   "Either make a .tpr without mass and constraint perturbation, "
 209                   "or use GROMACS 2018.4, 2018.5 or later 2018 version.");
 210     }
 211     if (ir->bExpanded)
 212     {
 213         gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
 214     }
 215     if (ir->bSimTemp)
 216     {
 217         gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
 218     }
 219     if (ir->bDoAwh)
 220     {
 221         gmx_fatal(FARGS, "AWH not supported by rerun.");
 222     }
 223     if (replExParams.exchangeInterval > 0)
 224     {
 225         gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
 226     }
 227     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 228     {
 229         gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
 230     }
 231     if (ir->bIMD)
 232     {
 233         gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
 234     }
 235     if (isMultiSim(ms))
 236     {
 237         gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
 238     }
 239     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](SimulatedAnnealing i) {
 240             return i != SimulatedAnnealing::No;
 241         }))
 242     {
 243         gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
 244     }
 245
 246     /* Rerun can't work if an output file name is the same as the input file name.
 247      * If this is the case, the user will get an error telling them what the issue is.
 248      */
 249     if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0
 250         || strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
 251     {
 252         gmx_fatal(FARGS,
 253                   "When using mdrun -rerun, the name of the input trajectory file "
 254                   "%s cannot be identical to the name of an output file (whether "
 255                   "given explicitly with -o or -x, or by default)",
 256                   opt2fn("-rerun", nfile, fnm));
 257     }
 258
 259     /* Settings for rerun */
 260     {
 261         // TODO: Avoid changing inputrec (#3854)
 262         auto* nonConstInputrec               = const_cast<t_inputrec*>(inputrec);
 263         nonConstInputrec->nstlist            = 1;
 264         nonConstInputrec->nstcalcenergy      = 1;
 265         nonConstInputrec->nstxout_compressed = 0;
 266     }
 267     int        nstglobalcomm = 1;
 268     const bool bNS           = true;
 269
 270     const SimulationGroups* groups = &top_global.groups;
 271     if (ir->eI == IntegrationAlgorithm::Mimic)
 272     {
 273         auto* nonConstGlobalTopology                         = const_cast<gmx_mtop_t*>(&top_global);
 274         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
 275     }
 276     int*                fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
 277     gmx::ArrayRef<real> lambda    = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
 278     initialize_lambdas(fplog,
 279                        ir->efep,
 280                        ir->bSimTemp,
 281                        *ir->fepvals,
 282                        ir->simtempvals->temperatures,
 283                        gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
 284                        MASTER(cr),
 285                        fep_state,
 286                        lambda);
 287     const bool        simulationsShareState = false;
 288     gmx_mdoutf*       outf                  = init_mdoutf(fplog,
 289                                    nfile,
 290                                    fnm,
 291                                    mdrunOptions,
 292                                    cr,
 293                                    outputProvider,
 294                                    mdModulesNotifiers,
 295                                    ir,
 296                                    top_global,
 297                                    oenv,
 298                                    wcycle,
 299                                    StartingBehavior::NewSimulation,
 300                                    simulationsShareState,
 301                                    ms);
 302     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
 303                                    top_global,
 304                                    *ir,
 305                                    pull_work,
 306                                    mdoutf_get_fp_dhdl(outf),
 307                                    true,
 308                                    StartingBehavior::NewSimulation,
 309                                    simulationsShareState,
 310                                    mdModulesNotifiers);
 311
 312     gstat = global_stat_init(ir);
 313
 314     /* Check for polarizable models and flexible constraints */
 315     shellfc = init_shell_flexcon(fplog,
 316                                  top_global,
 317                                  constr ? constr->numFlexibleConstraints() : 0,
 318                                  ir->nstcalcenergy,
 319                                  DOMAINDECOMP(cr),
 320                                  runScheduleWork->simulationWork.useGpuPme);
 321
 322     {
 323         double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
 324         if ((io > 2000) && MASTER(cr))
 325         {
 326             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 327         }
 328     }
 329
 330     // Local state only becomes valid now.
 331     std::unique_ptr<t_state> stateInstance;
 332     t_state*                 state;
 333
 334     if (DOMAINDECOMP(cr))
 335     {
 336         stateInstance = std::make_unique<t_state>();
 337         state         = stateInstance.get();
 338         dd_init_local_state(*cr->dd, state_global, state);
 339
 340         /* Distribute the charge groups over the nodes from the master node */
 341         dd_partition_system(fplog,
 342                             mdlog,
 343                             ir->init_step,
 344                             cr,
 345                             TRUE,
 346                             1,
 347                             state_global,
 348                             top_global,
 349                             *ir,
 350                             imdSession,
 351                             pull_work,
 352                             state,
 353                             &f,
 354                             mdAtoms,
 355                             &top,
 356                             fr,
 357                             vsite,
 358                             constr,
 359                             nrnb,
 360                             nullptr,
 361                             FALSE);
 362     }
 363     else
 364     {
 365         state_change_natoms(state_global, state_global->natoms);
 366         /* Copy the pointer to the global state */
 367         state = state_global;
 368
 369         mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 370     }
 371
 372     auto* mdatoms = mdAtoms->mdatoms();
 373
 374     // NOTE: The global state is no longer used at this point.
 375     // But state_global is still used as temporary storage space for writing
 376     // the global state to file and potentially for replica exchange.
 377     // (Global topology should persist.)
 378
 379     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 380
 381     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 382     {
 383         doFreeEnergyPerturbation = true;
 384     }
 385
 386     {
 387         int cglo_flags = CGLO_GSTAT;
 388         if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
 389         {
 390             cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 391         }
 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                         &bSumEkinhOld,
 415                         cglo_flags);
 416         if (DOMAINDECOMP(cr))
 417         {
 418             checkNumberOfBondedInteractions(
 419                     mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
 420         }
 421     }
 422
 423     if (MASTER(cr))
 424     {
 425         fprintf(stderr,
 426                 "starting md rerun '%s', reading coordinates from"
 427                 " input trajectory '%s'\n\n",
 428                 *(top_global.name),
 429                 opt2fn("-rerun", nfile, fnm));
 430         if (mdrunOptions.verbose)
 431         {
 432             fprintf(stderr,
 433                     "Calculated time to finish depends on nsteps from "
 434                     "run input file,\nwhich may not correspond to the time "
 435                     "needed to process input trajectory.\n\n");
 436         }
 437         fprintf(fplog, "\n");
 438     }
 439
 440     walltime_accounting_start_time(walltime_accounting);
 441     wallcycle_start(wcycle, WallCycleCounter::Run);
 442     print_start(fplog, cr, walltime_accounting, "mdrun");
 443
 444     /***********************************************************
 445      *
 446      *             Loop over MD steps
 447      *
 448      ************************************************************/
 449
 450     if (constr)
 451     {
 452         GMX_LOG(mdlog.info)
 453                 .asParagraph()
 454                 .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
 455     }
 456
 457     rerun_fr.natoms = 0;
 458     if (MASTER(cr))
 459     {
 460         isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
 461         if (rerun_fr.natoms != top_global.natoms)
 462         {
 463             gmx_fatal(FARGS,
 464                       "Number of atoms in trajectory (%d) does not match the "
 465                       "run input file (%d)\n",
 466                       rerun_fr.natoms,
 467                       top_global.natoms);
 468         }
 469
 470         if (ir->pbcType != PbcType::No)
 471         {
 472             if (!rerun_fr.bBox)
 473             {
 474                 gmx_fatal(FARGS,
 475                           "Rerun trajectory frame step %" PRId64
 476                           " time %f "
 477                           "does not contain a box, while pbc is used",
 478                           rerun_fr.step,
 479                           rerun_fr.time);
 480             }
 481             if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
 482             {
 483                 gmx_fatal(FARGS,
 484                           "Rerun trajectory frame step %" PRId64
 485                           " time %f "
 486                           "has too small box dimensions",
 487                           rerun_fr.step,
 488                           rerun_fr.time);
 489             }
 490         }
 491     }
 492
 493     GMX_LOG(mdlog.info)
 494             .asParagraph()
 495             .appendText(
 496                     "Rerun does not report kinetic energy, total energy, temperature, virial and "
 497                     "pressure.");
 498
 499     if (PAR(cr))
 500     {
 501         rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 502     }
 503
 504     if (ir->pbcType != PbcType::No)
 505     {
 506         /* Set the shift vectors.
 507          * Necessary here when have a static box different from the tpr box.
 508          */
 509         calc_shifts(rerun_fr.box, fr->shift_vec);
 510     }
 511
 512     step     = ir->init_step;
 513     step_rel = 0;
 514
 515     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 516             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 517             false,
 518             MASTER(cr),
 519             ir->nstlist,
 520             mdrunOptions.reproducible,
 521             nstglobalcomm,
 522             mdrunOptions.maximumHoursToRun,
 523             ir->nstlist == 0,
 524             fplog,
 525             step,
 526             bNS,
 527             walltime_accounting);
 528
 529     // we don't do counter resetting in rerun - finish will always be valid
 530     walltime_accounting_set_valid_finish(walltime_accounting);
 531
 532     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 533
 534     /* and stop now if we should */
 535     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 536     while (!isLastStep)
 537     {
 538         wallcycle_start(wcycle, WallCycleCounter::Step);
 539
 540         if (rerun_fr.bStep)
 541         {
 542             step     = rerun_fr.step;
 543             step_rel = step - ir->init_step;
 544         }
 545         if (rerun_fr.bTime)
 546         {
 547             t = rerun_fr.time;
 548         }
 549         else
 550         {
 551             t = step;
 552         }
 553
 554         if (ir->efep != FreeEnergyPerturbationType::No && MASTER(cr))
 555         {
 556             if (rerun_fr.bLambda)
 557             {
 558                 ir->fepvals->init_lambda = rerun_fr.lambda;
 559             }
 560             else
 561             {
 562                 if (rerun_fr.bFepState)
 563                 {
 564                     state->fep_state = rerun_fr.fep_state;
 565                 }
 566             }
 567
 568             state_global->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
 569         }
 570
 571         if (MASTER(cr))
 572         {
 573             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 574             if (constructVsites && DOMAINDECOMP(cr))
 575             {
 576                 gmx_fatal(FARGS,
 577                           "Vsite recalculation with -rerun is not implemented with domain "
 578                           "decomposition, "
 579                           "use a single rank");
 580             }
 581             prepareRerunState(rerun_fr, state_global, constructVsites, vsite);
 582         }
 583
 584         isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
 585
 586         if (DOMAINDECOMP(cr))
 587         {
 588             /* Repartition the domain decomposition */
 589             const bool bMasterState = true;
 590             dd_partition_system(fplog,
 591                                 mdlog,
 592                                 step,
 593                                 cr,
 594                                 bMasterState,
 595                                 nstglobalcomm,
 596                                 state_global,
 597                                 top_global,
 598                                 *ir,
 599                                 imdSession,
 600                                 pull_work,
 601                                 state,
 602                                 &f,
 603                                 mdAtoms,
 604                                 &top,
 605                                 fr,
 606                                 vsite,
 607                                 constr,
 608                                 nrnb,
 609                                 wcycle,
 610                                 mdrunOptions.verbose);
 611         }
 612
 613         if (MASTER(cr))
 614         {
 615             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 616         }
 617
 618         if (ir->efep != FreeEnergyPerturbationType::No)
 619         {
 620             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 621         }
 622
 623         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 624                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
 625                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 626
 627         if (shellfc)
 628         {
 629             /* Now is the time to relax the shells */
 630             relax_shell_flexcon(fplog,
 631                                 cr,
 632                                 ms,
 633                                 mdrunOptions.verbose,
 634                                 enforcedRotation,
 635                                 step,
 636                                 ir,
 637                                 imdSession,
 638                                 pull_work,
 639                                 bNS,
 640                                 force_flags,
 641                                 &top,
 642                                 constr,
 643                                 enerd,
 644                                 state->natoms,
 645                                 state->x.arrayRefWithPadding(),
 646                                 state->v.arrayRefWithPadding(),
 647                                 state->box,
 648                                 state->lambda,
 649                                 &state->hist,
 650                                 &f.view(),
 651                                 force_vir,
 652                                 *mdatoms,
 653                                 nrnb,
 654                                 wcycle,
 655                                 shellfc,
 656                                 fr,
 657                                 runScheduleWork,
 658                                 t,
 659                                 mu_tot,
 660                                 vsite,
 661                                 ddBalanceRegionHandler);
 662         }
 663         else
 664         {
 665             /* The coordinates (x) are shifted (to get whole molecules)
 666              * in do_force.
 667              * This is parallellized as well, and does communication too.
 668              * Check comments in sim_util.c
 669              */
 670             Awh*       awh = nullptr;
 671             gmx_edsam* ed  = nullptr;
 672             do_force(fplog,
 673                      cr,
 674                      ms,
 675                      *ir,
 676                      awh,
 677                      enforcedRotation,
 678                      imdSession,
 679                      pull_work,
 680                      step,
 681                      nrnb,
 682                      wcycle,
 683                      &top,
 684                      state->box,
 685                      state->x.arrayRefWithPadding(),
 686                      &state->hist,
 687                      &f.view(),
 688                      force_vir,
 689                      mdatoms,
 690                      enerd,
 691                      state->lambda,
 692                      fr,
 693                      runScheduleWork,
 694                      vsite,
 695                      mu_tot,
 696                      t,
 697                      ed,
 698                      GMX_FORCE_NS | force_flags,
 699                      ddBalanceRegionHandler);
 700         }
 701
 702         /* Now we have the energies and forces corresponding to the
 703          * coordinates at time t.
 704          */
 705         {
 706             const bool isCheckpointingStep = false;
 707             const bool doRerun             = true;
 708             const bool bSumEkinhOld        = false;
 709             do_md_trajectory_writing(fplog,
 710                                      cr,
 711                                      nfile,
 712                                      fnm,
 713                                      step,
 714                                      step_rel,
 715                                      t,
 716                                      ir,
 717                                      state,
 718                                      state_global,
 719                                      observablesHistory,
 720                                      top_global,
 721                                      fr,
 722                                      outf,
 723                                      energyOutput,
 724                                      ekind,
 725                                      f.view().force(),
 726                                      isCheckpointingStep,
 727                                      doRerun,
 728                                      isLastStep,
 729                                      mdrunOptions.writeConfout,
 730                                      bSumEkinhOld);
 731         }
 732
 733         stopHandler->setSignal();
 734
 735         {
 736             const bool          doInterSimSignal = false;
 737             const bool          doIntraSimSignal = true;
 738             bool                bSumEkinhOld     = false;
 739             t_vcm*              vcm              = nullptr;
 740             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 741
 742             int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
 743             if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
 744             {
 745                 cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 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                             &bSumEkinhOld,
 768                             cglo_flags);
 769             if (DOMAINDECOMP(cr))
 770             {
 771                 checkNumberOfBondedInteractions(
 772                         mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
 773             }
 774         }
 775
 776         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 777            the virial that should probably be addressed eventually. state->veta has better properies,
 778            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 779            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 780
 781         /* Output stuff */
 782         if (MASTER(cr))
 783         {
 784             const bool bCalcEnerStep = true;
 785             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 786                                              bCalcEnerStep,
 787                                              t,
 788                                              mdatoms->tmass,
 789                                              enerd,
 790                                              ir->fepvals.get(),
 791                                              ir->expandedvals.get(),
 792                                              state->box,
 793                                              PTCouplingArrays({ state->boxv,
 794                                                                 state->nosehoover_xi,
 795                                                                 state->nosehoover_vxi,
 796                                                                 state->nhpres_xi,
 797                                                                 state->nhpres_vxi }),
 798                                              state->fep_state,
 799                                              shake_vir,
 800                                              force_vir,
 801                                              total_vir,
 802                                              pres,
 803                                              ekind,
 804                                              mu_tot,
 805                                              constr);
 806
 807             const bool do_ene = true;
 808             const bool do_log = true;
 809             Awh*       awh    = nullptr;
 810             const bool do_dr  = ir->nstdisreout != 0;
 811             const bool do_or  = ir->nstorireout != 0;
 812
 813             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 814             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 815                                                do_ene,
 816                                                do_dr,
 817                                                do_or,
 818                                                do_log ? fplog : nullptr,
 819                                                step,
 820                                                t,
 821                                                fr->fcdata.get(),
 822                                                awh);
 823
 824             if (do_per_step(step, ir->nstlog))
 825             {
 826                 if (fflush(fplog) != 0)
 827                 {
 828                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 829                 }
 830             }
 831         }
 832
 833         /* Print the remaining wall clock time for the run */
 834         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 835         {
 836             if (shellfc)
 837             {
 838                 fprintf(stderr, "\n");
 839             }
 840             print_time(stderr, walltime_accounting, step, ir, cr);
 841         }
 842
 843         /* Ion/water position swapping.
 844          * Not done in last step since trajectory writing happens before this call
 845          * in the MD loop and exchanges would be lost anyway. */
 846         if ((ir->eSwapCoords != SwapType::No) && (step > 0) && !isLastStep
 847             && do_per_step(step, ir->swap->nstswap))
 848         {
 849             const bool doRerun = true;
 850             do_swapcoords(cr,
 851                           step,
 852                           t,
 853                           ir,
 854                           swap,
 855                           wcycle,
 856                           rerun_fr.x,
 857                           rerun_fr.box,
 858                           MASTER(cr) && mdrunOptions.verbose,
 859                           doRerun);
 860         }
 861
 862         if (MASTER(cr))
 863         {
 864             /* read next frame from input trajectory */
 865             isLastStep = !read_next_frame(oenv, status, &rerun_fr);
 866         }
 867
 868         if (PAR(cr))
 869         {
 870             rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 871         }
 872
 873         cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
 874         if (DOMAINDECOMP(cr) && wcycle)
 875         {
 876             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 877         }
 878
 879         if (!rerun_fr.bStep)
 880         {
 881             /* increase the MD step number */
 882             step++;
 883             step_rel++;
 884         }
 885     }
 886     /* End of main MD loop */
 887
 888     /* Closing TNG files can include compressing data. Therefore it is good to do that
 889      * before stopping the time measurements. */
 890     mdoutf_tng_close(outf);
 891
 892     /* Stop measuring walltime */
 893     walltime_accounting_end_time(walltime_accounting);
 894
 895     if (MASTER(cr))
 896     {
 897         close_trx(status);
 898     }
 899
 900     if (!thisRankHasDuty(cr, DUTY_PME))
 901     {
 902         /* Tell the PME only node to finish */
 903         gmx_pme_send_finish(cr);
 904     }
 905
 906     done_mdoutf(outf);
 907
 908     done_shellfc(fplog, shellfc, step_rel);
 909
 910     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 911 }