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     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, *ir, MASTER(cr), fep_state, lambda);
 279     const bool        simulationsShareState = false;
 280     gmx_mdoutf*       outf                  = init_mdoutf(fplog,
 281                                    nfile,
 282                                    fnm,
 283                                    mdrunOptions,
 284                                    cr,
 285                                    outputProvider,
 286                                    mdModulesNotifier,
 287                                    ir,
 288                                    top_global,
 289                                    oenv,
 290                                    wcycle,
 291                                    StartingBehavior::NewSimulation,
 292                                    simulationsShareState,
 293                                    ms);
 294     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
 295                                    top_global,
 296                                    *ir,
 297                                    pull_work,
 298                                    mdoutf_get_fp_dhdl(outf),
 299                                    true,
 300                                    StartingBehavior::NewSimulation,
 301                                    simulationsShareState,
 302                                    mdModulesNotifier);
 303
 304     gstat = global_stat_init(ir);
 305
 306     /* Check for polarizable models and flexible constraints */
 307     shellfc = init_shell_flexcon(fplog,
 308                                  top_global,
 309                                  constr ? constr->numFlexibleConstraints() : 0,
 310                                  ir->nstcalcenergy,
 311                                  DOMAINDECOMP(cr),
 312                                  runScheduleWork->simulationWork.useGpuPme);
 313
 314     {
 315         double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
 316         if ((io > 2000) && MASTER(cr))
 317         {
 318             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 319         }
 320     }
 321
 322     // Local state only becomes valid now.
 323     std::unique_ptr<t_state> stateInstance;
 324     t_state*                 state;
 325
 326     if (DOMAINDECOMP(cr))
 327     {
 328         stateInstance = std::make_unique<t_state>();
 329         state         = stateInstance.get();
 330         dd_init_local_state(*cr->dd, state_global, state);
 331
 332         /* Distribute the charge groups over the nodes from the master node */
 333         dd_partition_system(fplog,
 334                             mdlog,
 335                             ir->init_step,
 336                             cr,
 337                             TRUE,
 338                             1,
 339                             state_global,
 340                             top_global,
 341                             *ir,
 342                             imdSession,
 343                             pull_work,
 344                             state,
 345                             &f,
 346                             mdAtoms,
 347                             &top,
 348                             fr,
 349                             vsite,
 350                             constr,
 351                             nrnb,
 352                             nullptr,
 353                             FALSE);
 354     }
 355     else
 356     {
 357         state_change_natoms(state_global, state_global->natoms);
 358         /* Copy the pointer to the global state */
 359         state = state_global;
 360
 361         mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 362     }
 363
 364     auto mdatoms = mdAtoms->mdatoms();
 365
 366     // NOTE: The global state is no longer used at this point.
 367     // But state_global is still used as temporary storage space for writing
 368     // the global state to file and potentially for replica exchange.
 369     // (Global topology should persist.)
 370
 371     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 372
 373     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 374     {
 375         doFreeEnergyPerturbation = true;
 376     }
 377
 378     {
 379         int cglo_flags = CGLO_GSTAT;
 380         if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
 381         {
 382             cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 383         }
 384         bool   bSumEkinhOld = false;
 385         t_vcm* vcm          = nullptr;
 386         compute_globals(gstat,
 387                         cr,
 388                         ir,
 389                         fr,
 390                         ekind,
 391                         makeConstArrayRef(state->x),
 392                         makeConstArrayRef(state->v),
 393                         state->box,
 394                         mdatoms,
 395                         nrnb,
 396                         vcm,
 397                         nullptr,
 398                         enerd,
 399                         force_vir,
 400                         shake_vir,
 401                         total_vir,
 402                         pres,
 403                         gmx::ArrayRef<real>{},
 404                         &nullSignaller,
 405                         state->box,
 406                         &bSumEkinhOld,
 407                         cglo_flags);
 408         if (DOMAINDECOMP(cr))
 409         {
 410             checkNumberOfBondedInteractions(
 411                     mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
 412         }
 413     }
 414
 415     if (MASTER(cr))
 416     {
 417         fprintf(stderr,
 418                 "starting md rerun '%s', reading coordinates from"
 419                 " input trajectory '%s'\n\n",
 420                 *(top_global.name),
 421                 opt2fn("-rerun", nfile, fnm));
 422         if (mdrunOptions.verbose)
 423         {
 424             fprintf(stderr,
 425                     "Calculated time to finish depends on nsteps from "
 426                     "run input file,\nwhich may not correspond to the time "
 427                     "needed to process input trajectory.\n\n");
 428         }
 429         fprintf(fplog, "\n");
 430     }
 431
 432     walltime_accounting_start_time(walltime_accounting);
 433     wallcycle_start(wcycle, ewcRUN);
 434     print_start(fplog, cr, walltime_accounting, "mdrun");
 435
 436     /***********************************************************
 437      *
 438      *             Loop over MD steps
 439      *
 440      ************************************************************/
 441
 442     if (constr)
 443     {
 444         GMX_LOG(mdlog.info)
 445                 .asParagraph()
 446                 .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
 447     }
 448
 449     rerun_fr.natoms = 0;
 450     if (MASTER(cr))
 451     {
 452         isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
 453         if (rerun_fr.natoms != top_global.natoms)
 454         {
 455             gmx_fatal(FARGS,
 456                       "Number of atoms in trajectory (%d) does not match the "
 457                       "run input file (%d)\n",
 458                       rerun_fr.natoms,
 459                       top_global.natoms);
 460         }
 461
 462         if (ir->pbcType != PbcType::No)
 463         {
 464             if (!rerun_fr.bBox)
 465             {
 466                 gmx_fatal(FARGS,
 467                           "Rerun trajectory frame step %" PRId64
 468                           " time %f "
 469                           "does not contain a box, while pbc is used",
 470                           rerun_fr.step,
 471                           rerun_fr.time);
 472             }
 473             if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
 474             {
 475                 gmx_fatal(FARGS,
 476                           "Rerun trajectory frame step %" PRId64
 477                           " time %f "
 478                           "has too small box dimensions",
 479                           rerun_fr.step,
 480                           rerun_fr.time);
 481             }
 482         }
 483     }
 484
 485     GMX_LOG(mdlog.info)
 486             .asParagraph()
 487             .appendText(
 488                     "Rerun does not report kinetic energy, total energy, temperature, virial and "
 489                     "pressure.");
 490
 491     if (PAR(cr))
 492     {
 493         rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 494     }
 495
 496     if (ir->pbcType != PbcType::No)
 497     {
 498         /* Set the shift vectors.
 499          * Necessary here when have a static box different from the tpr box.
 500          */
 501         calc_shifts(rerun_fr.box, fr->shift_vec);
 502     }
 503
 504     step     = ir->init_step;
 505     step_rel = 0;
 506
 507     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 508             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 509             false,
 510             MASTER(cr),
 511             ir->nstlist,
 512             mdrunOptions.reproducible,
 513             nstglobalcomm,
 514             mdrunOptions.maximumHoursToRun,
 515             ir->nstlist == 0,
 516             fplog,
 517             step,
 518             bNS,
 519             walltime_accounting);
 520
 521     // we don't do counter resetting in rerun - finish will always be valid
 522     walltime_accounting_set_valid_finish(walltime_accounting);
 523
 524     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 525
 526     /* and stop now if we should */
 527     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 528     while (!isLastStep)
 529     {
 530         wallcycle_start(wcycle, ewcSTEP);
 531
 532         if (rerun_fr.bStep)
 533         {
 534             step     = rerun_fr.step;
 535             step_rel = step - ir->init_step;
 536         }
 537         if (rerun_fr.bTime)
 538         {
 539             t = rerun_fr.time;
 540         }
 541         else
 542         {
 543             t = step;
 544         }
 545
 546         if (ir->efep != FreeEnergyPerturbationType::No && MASTER(cr))
 547         {
 548             if (rerun_fr.bLambda)
 549             {
 550                 ir->fepvals->init_lambda = rerun_fr.lambda;
 551             }
 552             else
 553             {
 554                 if (rerun_fr.bFepState)
 555                 {
 556                     state->fep_state = rerun_fr.fep_state;
 557                 }
 558             }
 559
 560             state_global->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
 561         }
 562
 563         if (MASTER(cr))
 564         {
 565             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 566             if (constructVsites && DOMAINDECOMP(cr))
 567             {
 568                 gmx_fatal(FARGS,
 569                           "Vsite recalculation with -rerun is not implemented with domain "
 570                           "decomposition, "
 571                           "use a single rank");
 572             }
 573             prepareRerunState(rerun_fr, state_global, constructVsites, vsite);
 574         }
 575
 576         isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
 577
 578         if (DOMAINDECOMP(cr))
 579         {
 580             /* Repartition the domain decomposition */
 581             const bool bMasterState = true;
 582             dd_partition_system(fplog,
 583                                 mdlog,
 584                                 step,
 585                                 cr,
 586                                 bMasterState,
 587                                 nstglobalcomm,
 588                                 state_global,
 589                                 top_global,
 590                                 *ir,
 591                                 imdSession,
 592                                 pull_work,
 593                                 state,
 594                                 &f,
 595                                 mdAtoms,
 596                                 &top,
 597                                 fr,
 598                                 vsite,
 599                                 constr,
 600                                 nrnb,
 601                                 wcycle,
 602                                 mdrunOptions.verbose);
 603         }
 604
 605         if (MASTER(cr))
 606         {
 607             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 608         }
 609
 610         if (ir->efep != FreeEnergyPerturbationType::No)
 611         {
 612             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 613         }
 614
 615         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 616                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
 617                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 618
 619         if (shellfc)
 620         {
 621             /* Now is the time to relax the shells */
 622             relax_shell_flexcon(fplog,
 623                                 cr,
 624                                 ms,
 625                                 mdrunOptions.verbose,
 626                                 enforcedRotation,
 627                                 step,
 628                                 ir,
 629                                 imdSession,
 630                                 pull_work,
 631                                 bNS,
 632                                 force_flags,
 633                                 &top,
 634                                 constr,
 635                                 enerd,
 636                                 state->natoms,
 637                                 state->x.arrayRefWithPadding(),
 638                                 state->v.arrayRefWithPadding(),
 639                                 state->box,
 640                                 state->lambda,
 641                                 &state->hist,
 642                                 &f.view(),
 643                                 force_vir,
 644                                 *mdatoms,
 645                                 nrnb,
 646                                 wcycle,
 647                                 shellfc,
 648                                 fr,
 649                                 runScheduleWork,
 650                                 t,
 651                                 mu_tot,
 652                                 vsite,
 653                                 ddBalanceRegionHandler);
 654         }
 655         else
 656         {
 657             /* The coordinates (x) are shifted (to get whole molecules)
 658              * in do_force.
 659              * This is parallellized as well, and does communication too.
 660              * Check comments in sim_util.c
 661              */
 662             Awh*       awh = nullptr;
 663             gmx_edsam* ed  = nullptr;
 664             do_force(fplog,
 665                      cr,
 666                      ms,
 667                      *ir,
 668                      awh,
 669                      enforcedRotation,
 670                      imdSession,
 671                      pull_work,
 672                      step,
 673                      nrnb,
 674                      wcycle,
 675                      &top,
 676                      state->box,
 677                      state->x.arrayRefWithPadding(),
 678                      &state->hist,
 679                      &f.view(),
 680                      force_vir,
 681                      mdatoms,
 682                      enerd,
 683                      state->lambda,
 684                      fr,
 685                      runScheduleWork,
 686                      vsite,
 687                      mu_tot,
 688                      t,
 689                      ed,
 690                      GMX_FORCE_NS | force_flags,
 691                      ddBalanceRegionHandler);
 692         }
 693
 694         /* Now we have the energies and forces corresponding to the
 695          * coordinates at time t.
 696          */
 697         {
 698             const bool isCheckpointingStep = false;
 699             const bool doRerun             = true;
 700             const bool bSumEkinhOld        = false;
 701             do_md_trajectory_writing(fplog,
 702                                      cr,
 703                                      nfile,
 704                                      fnm,
 705                                      step,
 706                                      step_rel,
 707                                      t,
 708                                      ir,
 709                                      state,
 710                                      state_global,
 711                                      observablesHistory,
 712                                      top_global,
 713                                      fr,
 714                                      outf,
 715                                      energyOutput,
 716                                      ekind,
 717                                      f.view().force(),
 718                                      isCheckpointingStep,
 719                                      doRerun,
 720                                      isLastStep,
 721                                      mdrunOptions.writeConfout,
 722                                      bSumEkinhOld);
 723         }
 724
 725         stopHandler->setSignal();
 726
 727         {
 728             const bool          doInterSimSignal = false;
 729             const bool          doIntraSimSignal = true;
 730             bool                bSumEkinhOld     = false;
 731             t_vcm*              vcm              = nullptr;
 732             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 733
 734             int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
 735             if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
 736             {
 737                 cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 738             }
 739             compute_globals(gstat,
 740                             cr,
 741                             ir,
 742                             fr,
 743                             ekind,
 744                             makeConstArrayRef(state->x),
 745                             makeConstArrayRef(state->v),
 746                             state->box,
 747                             mdatoms,
 748                             nrnb,
 749                             vcm,
 750                             wcycle,
 751                             enerd,
 752                             force_vir,
 753                             shake_vir,
 754                             total_vir,
 755                             pres,
 756                             constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
 757                             &signaller,
 758                             state->box,
 759                             &bSumEkinhOld,
 760                             cglo_flags);
 761             if (DOMAINDECOMP(cr))
 762             {
 763                 checkNumberOfBondedInteractions(
 764                         mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
 765             }
 766         }
 767
 768         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 769            the virial that should probably be addressed eventually. state->veta has better properies,
 770            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 771            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 772
 773         /* Output stuff */
 774         if (MASTER(cr))
 775         {
 776             const bool bCalcEnerStep = true;
 777             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 778                                              bCalcEnerStep,
 779                                              t,
 780                                              mdatoms->tmass,
 781                                              enerd,
 782                                              ir->fepvals.get(),
 783                                              ir->expandedvals.get(),
 784                                              state->box,
 785                                              PTCouplingArrays({ state->boxv,
 786                                                                 state->nosehoover_xi,
 787                                                                 state->nosehoover_vxi,
 788                                                                 state->nhpres_xi,
 789                                                                 state->nhpres_vxi }),
 790                                              state->fep_state,
 791                                              shake_vir,
 792                                              force_vir,
 793                                              total_vir,
 794                                              pres,
 795                                              ekind,
 796                                              mu_tot,
 797                                              constr);
 798
 799             const bool do_ene = true;
 800             const bool do_log = true;
 801             Awh*       awh    = nullptr;
 802             const bool do_dr  = ir->nstdisreout != 0;
 803             const bool do_or  = ir->nstorireout != 0;
 804
 805             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 806             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 807                                                do_ene,
 808                                                do_dr,
 809                                                do_or,
 810                                                do_log ? fplog : nullptr,
 811                                                step,
 812                                                t,
 813                                                fr->fcdata.get(),
 814                                                awh);
 815
 816             if (do_per_step(step, ir->nstlog))
 817             {
 818                 if (fflush(fplog) != 0)
 819                 {
 820                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 821                 }
 822             }
 823         }
 824
 825         /* Print the remaining wall clock time for the run */
 826         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 827         {
 828             if (shellfc)
 829             {
 830                 fprintf(stderr, "\n");
 831             }
 832             print_time(stderr, walltime_accounting, step, ir, cr);
 833         }
 834
 835         /* Ion/water position swapping.
 836          * Not done in last step since trajectory writing happens before this call
 837          * in the MD loop and exchanges would be lost anyway. */
 838         if ((ir->eSwapCoords != SwapType::No) && (step > 0) && !isLastStep
 839             && do_per_step(step, ir->swap->nstswap))
 840         {
 841             const bool doRerun = true;
 842             do_swapcoords(cr,
 843                           step,
 844                           t,
 845                           ir,
 846                           swap,
 847                           wcycle,
 848                           rerun_fr.x,
 849                           rerun_fr.box,
 850                           MASTER(cr) && mdrunOptions.verbose,
 851                           doRerun);
 852         }
 853
 854         if (MASTER(cr))
 855         {
 856             /* read next frame from input trajectory */
 857             isLastStep = !read_next_frame(oenv, status, &rerun_fr);
 858         }
 859
 860         if (PAR(cr))
 861         {
 862             rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 863         }
 864
 865         cycles = wallcycle_stop(wcycle, ewcSTEP);
 866         if (DOMAINDECOMP(cr) && wcycle)
 867         {
 868             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 869         }
 870
 871         if (!rerun_fr.bStep)
 872         {
 873             /* increase the MD step number */
 874             step++;
 875             step_rel++;
 876         }
 877     }
 878     /* End of main MD loop */
 879
 880     /* Closing TNG files can include compressing data. Therefore it is good to do that
 881      * before stopping the time measurements. */
 882     mdoutf_tng_close(outf);
 883
 884     /* Stop measuring walltime */
 885     walltime_accounting_end_time(walltime_accounting);
 886
 887     if (MASTER(cr))
 888     {
 889         close_trx(status);
 890     }
 891
 892     if (!thisRankHasDuty(cr, DUTY_PME))
 893     {
 894         /* Tell the PME only node to finish */
 895         gmx_pme_send_finish(cr);
 896     }
 897
 898     done_mdoutf(outf);
 899
 900     done_shellfc(fplog, shellfc, step_rel);
 901
 902     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 903 }