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