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/observablesreducer.h"
 117 #include "gromacs/mdtypes/simulation_workload.h"
 118 #include "gromacs/mdtypes/state.h"
 119 #include "gromacs/mimic/utilities.h"
 120 #include "gromacs/pbcutil/pbc.h"
 121 #include "gromacs/pulling/output.h"
 122 #include "gromacs/pulling/pull.h"
 123 #include "gromacs/swap/swapcoords.h"
 124 #include "gromacs/timing/wallcycle.h"
 125 #include "gromacs/timing/walltime_accounting.h"
 126 #include "gromacs/topology/atoms.h"
 127 #include "gromacs/topology/idef.h"
 128 #include "gromacs/topology/mtop_util.h"
 129 #include "gromacs/topology/topology.h"
 130 #include "gromacs/trajectory/trajectoryframe.h"
 131 #include "gromacs/utility/basedefinitions.h"
 132 #include "gromacs/utility/cstringutil.h"
 133 #include "gromacs/utility/fatalerror.h"
 134 #include "gromacs/utility/logger.h"
 135 #include "gromacs/utility/real.h"
 136
 137 #include "legacysimulator.h"
 138 #include "replicaexchange.h"
 139 #include "shellfc.h"
 140
 141 using gmx::SimulationSignaller;
 142 using gmx::VirtualSitesHandler;
 143
 144 /*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
 145  *
 146  * \param[in]     rerunFrame      The trajectory frame to compute energy/forces for
 147  * \param[in,out] globalState     The global state container
 148  * \param[in]     constructVsites When true, vsite coordinates are constructed
 149  * \param[in]     vsite           Vsite setup, can be nullptr when \p constructVsites = false
 150  */
 151 static void prepareRerunState(const t_trxframe&          rerunFrame,
 152                               t_state*                   globalState,
 153                               bool                       constructVsites,
 154                               const VirtualSitesHandler* vsite)
 155 {
 156     auto x      = makeArrayRef(globalState->x);
 157     auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec*>(rerunFrame.x), globalState->natoms);
 158     std::copy(rerunX.begin(), rerunX.end(), x.begin());
 159     copy_mat(rerunFrame.box, globalState->box);
 160
 161     if (constructVsites)
 162     {
 163         GMX_ASSERT(vsite, "Need valid vsite for constructing vsites");
 164
 165         vsite->construct(globalState->x, globalState->v, globalState->box, gmx::VSiteOperation::PositionsAndVelocities);
 166     }
 167 }
 168
 169 void gmx::LegacySimulator::do_rerun()
 170 {
 171     // TODO Historically, the EM and MD "integrators" used different
 172     // names for the t_inputrec *parameter, but these must have the
 173     // same name, now that it's a member of a struct. We use this ir
 174     // alias to avoid a large ripple of nearly useless changes.
 175     // t_inputrec is being replaced by IMdpOptionsProvider, so this
 176     // will go away eventually.
 177     const t_inputrec* ir = inputrec;
 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     ObservablesReducer observablesReducer = observablesReducerBuilder->build();
 273
 274     const SimulationGroups* groups = &top_global.groups;
 275     if (ir->eI == IntegrationAlgorithm::Mimic)
 276     {
 277         auto* nonConstGlobalTopology                         = const_cast<gmx_mtop_t*>(&top_global);
 278         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
 279     }
 280     int*                fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
 281     gmx::ArrayRef<real> lambda    = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
 282     initialize_lambdas(fplog,
 283                        ir->efep,
 284                        ir->bSimTemp,
 285                        *ir->fepvals,
 286                        ir->simtempvals->temperatures,
 287                        gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
 288                        MASTER(cr),
 289                        fep_state,
 290                        lambda);
 291     const bool        simulationsShareState = false;
 292     gmx_mdoutf*       outf                  = init_mdoutf(fplog,
 293                                    nfile,
 294                                    fnm,
 295                                    mdrunOptions,
 296                                    cr,
 297                                    outputProvider,
 298                                    mdModulesNotifiers,
 299                                    ir,
 300                                    top_global,
 301                                    oenv,
 302                                    wcycle,
 303                                    StartingBehavior::NewSimulation,
 304                                    simulationsShareState,
 305                                    ms);
 306     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
 307                                    top_global,
 308                                    *ir,
 309                                    pull_work,
 310                                    mdoutf_get_fp_dhdl(outf),
 311                                    true,
 312                                    StartingBehavior::NewSimulation,
 313                                    simulationsShareState,
 314                                    mdModulesNotifiers);
 315
 316     gstat = global_stat_init(ir);
 317
 318     /* Check for polarizable models and flexible constraints */
 319     shellfc = init_shell_flexcon(fplog,
 320                                  top_global,
 321                                  constr ? constr->numFlexibleConstraints() : 0,
 322                                  ir->nstcalcenergy,
 323                                  DOMAINDECOMP(cr),
 324                                  runScheduleWork->simulationWork.useGpuPme);
 325
 326     {
 327         double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
 328         if ((io > 2000) && MASTER(cr))
 329         {
 330             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 331         }
 332     }
 333
 334     // Local state only becomes valid now.
 335     std::unique_ptr<t_state> stateInstance;
 336     t_state*                 state;
 337
 338     if (DOMAINDECOMP(cr))
 339     {
 340         stateInstance = std::make_unique<t_state>();
 341         state         = stateInstance.get();
 342         dd_init_local_state(*cr->dd, state_global, state);
 343
 344         /* Distribute the charge groups over the nodes from the master node */
 345         dd_partition_system(fplog,
 346                             mdlog,
 347                             ir->init_step,
 348                             cr,
 349                             TRUE,
 350                             1,
 351                             state_global,
 352                             top_global,
 353                             *ir,
 354                             imdSession,
 355                             pull_work,
 356                             state,
 357                             &f,
 358                             mdAtoms,
 359                             &top,
 360                             fr,
 361                             vsite,
 362                             constr,
 363                             nrnb,
 364                             nullptr,
 365                             FALSE);
 366     }
 367     else
 368     {
 369         state_change_natoms(state_global, state_global->natoms);
 370         /* Copy the pointer to the global state */
 371         state = state_global;
 372
 373         mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 374     }
 375
 376     auto* mdatoms = mdAtoms->mdatoms();
 377
 378     // NOTE: The global state is no longer used at this point.
 379     // But state_global is still used as temporary storage space for writing
 380     // the global state to file and potentially for replica exchange.
 381     // (Global topology should persist.)
 382
 383     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 384
 385     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 386     {
 387         doFreeEnergyPerturbation = true;
 388     }
 389
 390     int64_t step     = ir->init_step;
 391     int64_t step_rel = 0;
 392
 393     {
 394         int cglo_flags = CGLO_GSTAT;
 395         if (DOMAINDECOMP(cr) && dd_localTopologyChecker(*cr->dd).shouldCheckNumberOfBondedInteractions())
 396         {
 397             cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 398         }
 399         bool   bSumEkinhOld = false;
 400         t_vcm* vcm          = nullptr;
 401         compute_globals(gstat,
 402                         cr,
 403                         ir,
 404                         fr,
 405                         ekind,
 406                         makeConstArrayRef(state->x),
 407                         makeConstArrayRef(state->v),
 408                         state->box,
 409                         mdatoms,
 410                         nrnb,
 411                         vcm,
 412                         nullptr,
 413                         enerd,
 414                         force_vir,
 415                         shake_vir,
 416                         total_vir,
 417                         pres,
 418                         gmx::ArrayRef<real>{},
 419                         &nullSignaller,
 420                         state->box,
 421                         &bSumEkinhOld,
 422                         cglo_flags,
 423                         step,
 424                         &observablesReducer);
 425         if (DOMAINDECOMP(cr))
 426         {
 427             dd_localTopologyChecker(cr->dd)->checkNumberOfBondedInteractions(
 428                     &top, makeConstArrayRef(state->x), state->box);
 429         }
 430     }
 431
 432     if (MASTER(cr))
 433     {
 434         fprintf(stderr,
 435                 "starting md rerun '%s', reading coordinates from"
 436                 " input trajectory '%s'\n\n",
 437                 *(top_global.name),
 438                 opt2fn("-rerun", nfile, fnm));
 439         if (mdrunOptions.verbose)
 440         {
 441             fprintf(stderr,
 442                     "Calculated time to finish depends on nsteps from "
 443                     "run input file,\nwhich may not correspond to the time "
 444                     "needed to process input trajectory.\n\n");
 445         }
 446         fprintf(fplog, "\n");
 447     }
 448
 449     walltime_accounting_start_time(walltime_accounting);
 450     wallcycle_start(wcycle, WallCycleCounter::Run);
 451     print_start(fplog, cr, walltime_accounting, "mdrun");
 452
 453     /***********************************************************
 454      *
 455      *             Loop over MD steps
 456      *
 457      ************************************************************/
 458
 459     if (constr)
 460     {
 461         GMX_LOG(mdlog.info)
 462                 .asParagraph()
 463                 .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
 464     }
 465
 466     rerun_fr.natoms = 0;
 467     if (MASTER(cr))
 468     {
 469         isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
 470         if (rerun_fr.natoms != top_global.natoms)
 471         {
 472             gmx_fatal(FARGS,
 473                       "Number of atoms in trajectory (%d) does not match the "
 474                       "run input file (%d)\n",
 475                       rerun_fr.natoms,
 476                       top_global.natoms);
 477         }
 478
 479         if (ir->pbcType != PbcType::No)
 480         {
 481             if (!rerun_fr.bBox)
 482             {
 483                 gmx_fatal(FARGS,
 484                           "Rerun trajectory frame step %" PRId64
 485                           " time %f "
 486                           "does not contain a box, while pbc is used",
 487                           rerun_fr.step,
 488                           rerun_fr.time);
 489             }
 490             if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
 491             {
 492                 gmx_fatal(FARGS,
 493                           "Rerun trajectory frame step %" PRId64
 494                           " time %f "
 495                           "has too small box dimensions",
 496                           rerun_fr.step,
 497                           rerun_fr.time);
 498             }
 499         }
 500     }
 501
 502     GMX_LOG(mdlog.info)
 503             .asParagraph()
 504             .appendText(
 505                     "Rerun does not report kinetic energy, total energy, temperature, virial and "
 506                     "pressure.");
 507
 508     if (PAR(cr))
 509     {
 510         rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 511     }
 512
 513     if (ir->pbcType != PbcType::No)
 514     {
 515         /* Set the shift vectors.
 516          * Necessary here when have a static box different from the tpr box.
 517          */
 518         calc_shifts(rerun_fr.box, fr->shift_vec);
 519     }
 520
 521     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 522             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 523             false,
 524             MASTER(cr),
 525             ir->nstlist,
 526             mdrunOptions.reproducible,
 527             nstglobalcomm,
 528             mdrunOptions.maximumHoursToRun,
 529             ir->nstlist == 0,
 530             fplog,
 531             step,
 532             bNS,
 533             walltime_accounting);
 534
 535     // we don't do counter resetting in rerun - finish will always be valid
 536     walltime_accounting_set_valid_finish(walltime_accounting);
 537
 538     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 539
 540     /* and stop now if we should */
 541     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 542     while (!isLastStep)
 543     {
 544         wallcycle_start(wcycle, WallCycleCounter::Step);
 545
 546         if (rerun_fr.bStep)
 547         {
 548             step     = rerun_fr.step;
 549             step_rel = step - ir->init_step;
 550         }
 551         if (rerun_fr.bTime)
 552         {
 553             t = rerun_fr.time;
 554         }
 555         else
 556         {
 557             t = step;
 558         }
 559
 560         if (ir->efep != FreeEnergyPerturbationType::No && MASTER(cr))
 561         {
 562             if (rerun_fr.bLambda)
 563             {
 564                 ir->fepvals->init_lambda = rerun_fr.lambda;
 565             }
 566             else
 567             {
 568                 if (rerun_fr.bFepState)
 569                 {
 570                     state->fep_state = rerun_fr.fep_state;
 571                 }
 572             }
 573
 574             state_global->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
 575         }
 576
 577         if (MASTER(cr))
 578         {
 579             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 580             if (constructVsites && DOMAINDECOMP(cr))
 581             {
 582                 gmx_fatal(FARGS,
 583                           "Vsite recalculation with -rerun is not implemented with domain "
 584                           "decomposition, "
 585                           "use a single rank");
 586             }
 587             prepareRerunState(rerun_fr, state_global, constructVsites, vsite);
 588         }
 589
 590         isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
 591
 592         if (DOMAINDECOMP(cr))
 593         {
 594             /* Repartition the domain decomposition */
 595             const bool bMasterState = true;
 596             dd_partition_system(fplog,
 597                                 mdlog,
 598                                 step,
 599                                 cr,
 600                                 bMasterState,
 601                                 nstglobalcomm,
 602                                 state_global,
 603                                 top_global,
 604                                 *ir,
 605                                 imdSession,
 606                                 pull_work,
 607                                 state,
 608                                 &f,
 609                                 mdAtoms,
 610                                 &top,
 611                                 fr,
 612                                 vsite,
 613                                 constr,
 614                                 nrnb,
 615                                 wcycle,
 616                                 mdrunOptions.verbose);
 617         }
 618
 619         if (MASTER(cr))
 620         {
 621             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 622         }
 623
 624         if (ir->efep != FreeEnergyPerturbationType::No)
 625         {
 626             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 627         }
 628
 629         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 630                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
 631                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 632
 633         if (shellfc)
 634         {
 635             /* Now is the time to relax the shells */
 636             relax_shell_flexcon(fplog,
 637                                 cr,
 638                                 ms,
 639                                 mdrunOptions.verbose,
 640                                 enforcedRotation,
 641                                 step,
 642                                 ir,
 643                                 imdSession,
 644                                 pull_work,
 645                                 bNS,
 646                                 force_flags,
 647                                 &top,
 648                                 constr,
 649                                 enerd,
 650                                 state->natoms,
 651                                 state->x.arrayRefWithPadding(),
 652                                 state->v.arrayRefWithPadding(),
 653                                 state->box,
 654                                 state->lambda,
 655                                 &state->hist,
 656                                 &f.view(),
 657                                 force_vir,
 658                                 *mdatoms,
 659                                 nrnb,
 660                                 wcycle,
 661                                 shellfc,
 662                                 fr,
 663                                 runScheduleWork,
 664                                 t,
 665                                 mu_tot,
 666                                 vsite,
 667                                 ddBalanceRegionHandler);
 668         }
 669         else
 670         {
 671             /* The coordinates (x) are shifted (to get whole molecules)
 672              * in do_force.
 673              * This is parallellized as well, and does communication too.
 674              * Check comments in sim_util.c
 675              */
 676             Awh*       awh = nullptr;
 677             gmx_edsam* ed  = nullptr;
 678             do_force(fplog,
 679                      cr,
 680                      ms,
 681                      *ir,
 682                      awh,
 683                      enforcedRotation,
 684                      imdSession,
 685                      pull_work,
 686                      step,
 687                      nrnb,
 688                      wcycle,
 689                      &top,
 690                      state->box,
 691                      state->x.arrayRefWithPadding(),
 692                      &state->hist,
 693                      &f.view(),
 694                      force_vir,
 695                      mdatoms,
 696                      enerd,
 697                      state->lambda,
 698                      fr,
 699                      runScheduleWork,
 700                      vsite,
 701                      mu_tot,
 702                      t,
 703                      ed,
 704                      GMX_FORCE_NS | force_flags,
 705                      ddBalanceRegionHandler);
 706         }
 707
 708         /* Now we have the energies and forces corresponding to the
 709          * coordinates at time t.
 710          */
 711         {
 712             const bool isCheckpointingStep = false;
 713             const bool doRerun             = true;
 714             const bool bSumEkinhOld        = false;
 715             do_md_trajectory_writing(fplog,
 716                                      cr,
 717                                      nfile,
 718                                      fnm,
 719                                      step,
 720                                      step_rel,
 721                                      t,
 722                                      ir,
 723                                      state,
 724                                      state_global,
 725                                      observablesHistory,
 726                                      top_global,
 727                                      fr,
 728                                      outf,
 729                                      energyOutput,
 730                                      ekind,
 731                                      f.view().force(),
 732                                      isCheckpointingStep,
 733                                      doRerun,
 734                                      isLastStep,
 735                                      mdrunOptions.writeConfout,
 736                                      bSumEkinhOld);
 737         }
 738
 739         stopHandler->setSignal();
 740
 741         {
 742             const bool          doInterSimSignal = false;
 743             const bool          doIntraSimSignal = true;
 744             bool                bSumEkinhOld     = false;
 745             t_vcm*              vcm              = nullptr;
 746             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 747
 748             int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
 749             if (DOMAINDECOMP(cr) && dd_localTopologyChecker(*cr->dd).shouldCheckNumberOfBondedInteractions())
 750             {
 751                 cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 752             }
 753             compute_globals(gstat,
 754                             cr,
 755                             ir,
 756                             fr,
 757                             ekind,
 758                             makeConstArrayRef(state->x),
 759                             makeConstArrayRef(state->v),
 760                             state->box,
 761                             mdatoms,
 762                             nrnb,
 763                             vcm,
 764                             wcycle,
 765                             enerd,
 766                             force_vir,
 767                             shake_vir,
 768                             total_vir,
 769                             pres,
 770                             constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
 771                             &signaller,
 772                             state->box,
 773                             &bSumEkinhOld,
 774                             cglo_flags,
 775                             step,
 776                             &observablesReducer);
 777             if (DOMAINDECOMP(cr))
 778             {
 779                 dd_localTopologyChecker(cr->dd)->checkNumberOfBondedInteractions(
 780                         &top, makeConstArrayRef(state->x), state->box);
 781             }
 782         }
 783
 784         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 785            the virial that should probably be addressed eventually. state->veta has better properies,
 786            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 787            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 788
 789         /* Output stuff */
 790         if (MASTER(cr))
 791         {
 792             const bool bCalcEnerStep = true;
 793             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 794                                              bCalcEnerStep,
 795                                              t,
 796                                              mdatoms->tmass,
 797                                              enerd,
 798                                              ir->fepvals.get(),
 799                                              ir->expandedvals.get(),
 800                                              state->box,
 801                                              PTCouplingArrays({ state->boxv,
 802                                                                 state->nosehoover_xi,
 803                                                                 state->nosehoover_vxi,
 804                                                                 state->nhpres_xi,
 805                                                                 state->nhpres_vxi }),
 806                                              state->fep_state,
 807                                              total_vir,
 808                                              pres,
 809                                              ekind,
 810                                              mu_tot,
 811                                              constr);
 812
 813             const bool do_ene = true;
 814             const bool do_log = true;
 815             Awh*       awh    = nullptr;
 816             const bool do_dr  = ir->nstdisreout != 0;
 817             const bool do_or  = ir->nstorireout != 0;
 818
 819             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 820             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 821                                                do_ene,
 822                                                do_dr,
 823                                                do_or,
 824                                                do_log ? fplog : nullptr,
 825                                                step,
 826                                                t,
 827                                                fr->fcdata.get(),
 828                                                awh);
 829
 830             if (ir->bPull)
 831             {
 832                 pull_print_output(pull_work, step, t);
 833             }
 834
 835             if (do_per_step(step, ir->nstlog))
 836             {
 837                 if (fflush(fplog) != 0)
 838                 {
 839                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 840                 }
 841             }
 842         }
 843
 844         /* Print the remaining wall clock time for the run */
 845         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 846         {
 847             if (shellfc)
 848             {
 849                 fprintf(stderr, "\n");
 850             }
 851             print_time(stderr, walltime_accounting, step, ir, cr);
 852         }
 853
 854         /* Ion/water position swapping.
 855          * Not done in last step since trajectory writing happens before this call
 856          * in the MD loop and exchanges would be lost anyway. */
 857         if ((ir->eSwapCoords != SwapType::No) && (step > 0) && !isLastStep
 858             && do_per_step(step, ir->swap->nstswap))
 859         {
 860             const bool doRerun = true;
 861             do_swapcoords(cr,
 862                           step,
 863                           t,
 864                           ir,
 865                           swap,
 866                           wcycle,
 867                           rerun_fr.x,
 868                           rerun_fr.box,
 869                           MASTER(cr) && mdrunOptions.verbose,
 870                           doRerun);
 871         }
 872
 873         if (MASTER(cr))
 874         {
 875             /* read next frame from input trajectory */
 876             isLastStep = !read_next_frame(oenv, status, &rerun_fr);
 877         }
 878
 879         if (PAR(cr))
 880         {
 881             rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 882         }
 883
 884         cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
 885         if (DOMAINDECOMP(cr) && wcycle)
 886         {
 887             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 888         }
 889
 890         if (!rerun_fr.bStep)
 891         {
 892             /* increase the MD step number */
 893             step++;
 894             step_rel++;
 895         }
 896     }
 897     /* End of main MD loop */
 898
 899     /* Closing TNG files can include compressing data. Therefore it is good to do that
 900      * before stopping the time measurements. */
 901     mdoutf_tng_close(outf);
 902
 903     /* Stop measuring walltime */
 904     walltime_accounting_end_time(walltime_accounting);
 905
 906     if (MASTER(cr))
 907     {
 908         close_trx(status);
 909     }
 910
 911     if (!thisRankHasDuty(cr, DUTY_PME))
 912     {
 913         /* Tell the PME only node to finish */
 914         gmx_pme_send_finish(cr);
 915     }
 916
 917     done_mdoutf(outf);
 918
 919     done_shellfc(fplog, shellfc, step_rel);
 920
 921     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 922 }