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/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     fr->longRangeNonbondeds->updateAfterPartition(*mdatoms);
 378
 379     // NOTE: The global state is no longer used at this point.
 380     // But state_global is still used as temporary storage space for writing
 381     // the global state to file and potentially for replica exchange.
 382     // (Global topology should persist.)
 383
 384     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 385
 386     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 387     {
 388         doFreeEnergyPerturbation = true;
 389     }
 390
 391     int64_t step     = ir->init_step;
 392     int64_t step_rel = 0;
 393
 394     {
 395         int cglo_flags = CGLO_GSTAT;
 396         if (DOMAINDECOMP(cr) && dd_localTopologyChecker(*cr->dd).shouldCheckNumberOfBondedInteractions())
 397         {
 398             cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 399         }
 400         bool   bSumEkinhOld = false;
 401         t_vcm* vcm          = nullptr;
 402         compute_globals(gstat,
 403                         cr,
 404                         ir,
 405                         fr,
 406                         ekind,
 407                         makeConstArrayRef(state->x),
 408                         makeConstArrayRef(state->v),
 409                         state->box,
 410                         mdatoms,
 411                         nrnb,
 412                         vcm,
 413                         nullptr,
 414                         enerd,
 415                         force_vir,
 416                         shake_vir,
 417                         total_vir,
 418                         pres,
 419                         gmx::ArrayRef<real>{},
 420                         &nullSignaller,
 421                         state->box,
 422                         &bSumEkinhOld,
 423                         cglo_flags,
 424                         step,
 425                         &observablesReducer);
 426         if (DOMAINDECOMP(cr))
 427         {
 428             dd_localTopologyChecker(cr->dd)->checkNumberOfBondedInteractions(
 429                     &top, makeConstArrayRef(state->x), state->box);
 430         }
 431     }
 432
 433     if (MASTER(cr))
 434     {
 435         fprintf(stderr,
 436                 "starting md rerun '%s', reading coordinates from"
 437                 " input trajectory '%s'\n\n",
 438                 *(top_global.name),
 439                 opt2fn("-rerun", nfile, fnm));
 440         if (mdrunOptions.verbose)
 441         {
 442             fprintf(stderr,
 443                     "Calculated time to finish depends on nsteps from "
 444                     "run input file,\nwhich may not correspond to the time "
 445                     "needed to process input trajectory.\n\n");
 446         }
 447         fprintf(fplog, "\n");
 448     }
 449
 450     walltime_accounting_start_time(walltime_accounting);
 451     wallcycle_start(wcycle, WallCycleCounter::Run);
 452     print_start(fplog, cr, walltime_accounting, "mdrun");
 453
 454     /***********************************************************
 455      *
 456      *             Loop over MD steps
 457      *
 458      ************************************************************/
 459
 460     if (constr)
 461     {
 462         GMX_LOG(mdlog.info)
 463                 .asParagraph()
 464                 .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
 465     }
 466
 467     rerun_fr.natoms = 0;
 468     if (MASTER(cr))
 469     {
 470         isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
 471         if (rerun_fr.natoms != top_global.natoms)
 472         {
 473             gmx_fatal(FARGS,
 474                       "Number of atoms in trajectory (%d) does not match the "
 475                       "run input file (%d)\n",
 476                       rerun_fr.natoms,
 477                       top_global.natoms);
 478         }
 479
 480         if (ir->pbcType != PbcType::No)
 481         {
 482             if (!rerun_fr.bBox)
 483             {
 484                 gmx_fatal(FARGS,
 485                           "Rerun trajectory frame step %" PRId64
 486                           " time %f "
 487                           "does not contain a box, while pbc is used",
 488                           rerun_fr.step,
 489                           rerun_fr.time);
 490             }
 491             if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
 492             {
 493                 gmx_fatal(FARGS,
 494                           "Rerun trajectory frame step %" PRId64
 495                           " time %f "
 496                           "has too small box dimensions",
 497                           rerun_fr.step,
 498                           rerun_fr.time);
 499             }
 500         }
 501     }
 502
 503     GMX_LOG(mdlog.info)
 504             .asParagraph()
 505             .appendText(
 506                     "Rerun does not report kinetic energy, total energy, temperature, virial and "
 507                     "pressure.");
 508
 509     if (PAR(cr))
 510     {
 511         rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 512     }
 513
 514     if (ir->pbcType != PbcType::No)
 515     {
 516         /* Set the shift vectors.
 517          * Necessary here when have a static box different from the tpr box.
 518          */
 519         calc_shifts(rerun_fr.box, fr->shift_vec);
 520     }
 521
 522     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 523             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 524             false,
 525             MASTER(cr),
 526             ir->nstlist,
 527             mdrunOptions.reproducible,
 528             nstglobalcomm,
 529             mdrunOptions.maximumHoursToRun,
 530             ir->nstlist == 0,
 531             fplog,
 532             step,
 533             bNS,
 534             walltime_accounting);
 535
 536     // we don't do counter resetting in rerun - finish will always be valid
 537     walltime_accounting_set_valid_finish(walltime_accounting);
 538
 539     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 540
 541     /* and stop now if we should */
 542     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 543     while (!isLastStep)
 544     {
 545         wallcycle_start(wcycle, WallCycleCounter::Step);
 546
 547         if (rerun_fr.bStep)
 548         {
 549             step     = rerun_fr.step;
 550             step_rel = step - ir->init_step;
 551         }
 552         if (rerun_fr.bTime)
 553         {
 554             t = rerun_fr.time;
 555         }
 556         else
 557         {
 558             t = step;
 559         }
 560
 561         if (ir->efep != FreeEnergyPerturbationType::No && MASTER(cr))
 562         {
 563             if (rerun_fr.bLambda)
 564             {
 565                 ir->fepvals->init_lambda = rerun_fr.lambda;
 566             }
 567             else
 568             {
 569                 if (rerun_fr.bFepState)
 570                 {
 571                     state->fep_state = rerun_fr.fep_state;
 572                 }
 573             }
 574
 575             state_global->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
 576         }
 577
 578         if (MASTER(cr))
 579         {
 580             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 581             if (constructVsites && DOMAINDECOMP(cr))
 582             {
 583                 gmx_fatal(FARGS,
 584                           "Vsite recalculation with -rerun is not implemented with domain "
 585                           "decomposition, "
 586                           "use a single rank");
 587             }
 588             prepareRerunState(rerun_fr, state_global, constructVsites, vsite);
 589         }
 590
 591         isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
 592
 593         if (DOMAINDECOMP(cr))
 594         {
 595             /* Repartition the domain decomposition */
 596             const bool bMasterState = true;
 597             dd_partition_system(fplog,
 598                                 mdlog,
 599                                 step,
 600                                 cr,
 601                                 bMasterState,
 602                                 nstglobalcomm,
 603                                 state_global,
 604                                 top_global,
 605                                 *ir,
 606                                 imdSession,
 607                                 pull_work,
 608                                 state,
 609                                 &f,
 610                                 mdAtoms,
 611                                 &top,
 612                                 fr,
 613                                 vsite,
 614                                 constr,
 615                                 nrnb,
 616                                 wcycle,
 617                                 mdrunOptions.verbose);
 618         }
 619
 620         if (MASTER(cr))
 621         {
 622             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 623         }
 624
 625         if (ir->efep != FreeEnergyPerturbationType::No)
 626         {
 627             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 628         }
 629
 630         fr->longRangeNonbondeds->updateAfterPartition(*mdatoms);
 631
 632         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 633                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
 634                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 635
 636         if (shellfc)
 637         {
 638             /* Now is the time to relax the shells */
 639             relax_shell_flexcon(fplog,
 640                                 cr,
 641                                 ms,
 642                                 mdrunOptions.verbose,
 643                                 enforcedRotation,
 644                                 step,
 645                                 ir,
 646                                 imdSession,
 647                                 pull_work,
 648                                 bNS,
 649                                 force_flags,
 650                                 &top,
 651                                 constr,
 652                                 enerd,
 653                                 state->natoms,
 654                                 state->x.arrayRefWithPadding(),
 655                                 state->v.arrayRefWithPadding(),
 656                                 state->box,
 657                                 state->lambda,
 658                                 &state->hist,
 659                                 &f.view(),
 660                                 force_vir,
 661                                 *mdatoms,
 662                                 fr->longRangeNonbondeds.get(),
 663                                 nrnb,
 664                                 wcycle,
 665                                 shellfc,
 666                                 fr,
 667                                 runScheduleWork,
 668                                 t,
 669                                 mu_tot,
 670                                 vsite,
 671                                 ddBalanceRegionHandler);
 672         }
 673         else
 674         {
 675             /* The coordinates (x) are shifted (to get whole molecules)
 676              * in do_force.
 677              * This is parallellized as well, and does communication too.
 678              * Check comments in sim_util.c
 679              */
 680             Awh*       awh = nullptr;
 681             gmx_edsam* ed  = nullptr;
 682             do_force(fplog,
 683                      cr,
 684                      ms,
 685                      *ir,
 686                      awh,
 687                      enforcedRotation,
 688                      imdSession,
 689                      pull_work,
 690                      step,
 691                      nrnb,
 692                      wcycle,
 693                      &top,
 694                      state->box,
 695                      state->x.arrayRefWithPadding(),
 696                      &state->hist,
 697                      &f.view(),
 698                      force_vir,
 699                      mdatoms,
 700                      enerd,
 701                      state->lambda,
 702                      fr,
 703                      runScheduleWork,
 704                      vsite,
 705                      mu_tot,
 706                      t,
 707                      ed,
 708                      fr->longRangeNonbondeds.get(),
 709                      GMX_FORCE_NS | force_flags,
 710                      ddBalanceRegionHandler);
 711         }
 712
 713         /* Now we have the energies and forces corresponding to the
 714          * coordinates at time t.
 715          */
 716         {
 717             const bool isCheckpointingStep = false;
 718             const bool doRerun             = true;
 719             const bool bSumEkinhOld        = false;
 720             do_md_trajectory_writing(fplog,
 721                                      cr,
 722                                      nfile,
 723                                      fnm,
 724                                      step,
 725                                      step_rel,
 726                                      t,
 727                                      ir,
 728                                      state,
 729                                      state_global,
 730                                      observablesHistory,
 731                                      top_global,
 732                                      fr,
 733                                      outf,
 734                                      energyOutput,
 735                                      ekind,
 736                                      f.view().force(),
 737                                      isCheckpointingStep,
 738                                      doRerun,
 739                                      isLastStep,
 740                                      mdrunOptions.writeConfout,
 741                                      bSumEkinhOld);
 742         }
 743
 744         stopHandler->setSignal();
 745
 746         {
 747             const bool          doInterSimSignal = false;
 748             const bool          doIntraSimSignal = true;
 749             bool                bSumEkinhOld     = false;
 750             t_vcm*              vcm              = nullptr;
 751             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 752
 753             int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
 754             if (DOMAINDECOMP(cr) && dd_localTopologyChecker(*cr->dd).shouldCheckNumberOfBondedInteractions())
 755             {
 756                 cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 757             }
 758             compute_globals(gstat,
 759                             cr,
 760                             ir,
 761                             fr,
 762                             ekind,
 763                             makeConstArrayRef(state->x),
 764                             makeConstArrayRef(state->v),
 765                             state->box,
 766                             mdatoms,
 767                             nrnb,
 768                             vcm,
 769                             wcycle,
 770                             enerd,
 771                             force_vir,
 772                             shake_vir,
 773                             total_vir,
 774                             pres,
 775                             constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
 776                             &signaller,
 777                             state->box,
 778                             &bSumEkinhOld,
 779                             cglo_flags,
 780                             step,
 781                             &observablesReducer);
 782             if (DOMAINDECOMP(cr))
 783             {
 784                 dd_localTopologyChecker(cr->dd)->checkNumberOfBondedInteractions(
 785                         &top, makeConstArrayRef(state->x), state->box);
 786             }
 787         }
 788
 789         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 790            the virial that should probably be addressed eventually. state->veta has better properies,
 791            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 792            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 793
 794         /* Output stuff */
 795         if (MASTER(cr))
 796         {
 797             const bool bCalcEnerStep = true;
 798             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 799                                              bCalcEnerStep,
 800                                              t,
 801                                              mdatoms->tmass,
 802                                              enerd,
 803                                              ir->fepvals.get(),
 804                                              ir->expandedvals.get(),
 805                                              state->box,
 806                                              PTCouplingArrays({ state->boxv,
 807                                                                 state->nosehoover_xi,
 808                                                                 state->nosehoover_vxi,
 809                                                                 state->nhpres_xi,
 810                                                                 state->nhpres_vxi }),
 811                                              state->fep_state,
 812                                              total_vir,
 813                                              pres,
 814                                              ekind,
 815                                              mu_tot,
 816                                              constr);
 817
 818             const bool do_ene = true;
 819             const bool do_log = true;
 820             Awh*       awh    = nullptr;
 821             const bool do_dr  = ir->nstdisreout != 0;
 822             const bool do_or  = ir->nstorireout != 0;
 823
 824             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 825             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 826                                                do_ene,
 827                                                do_dr,
 828                                                do_or,
 829                                                do_log ? fplog : nullptr,
 830                                                step,
 831                                                t,
 832                                                fr->fcdata.get(),
 833                                                awh);
 834
 835             if (ir->bPull)
 836             {
 837                 pull_print_output(pull_work, step, t);
 838             }
 839
 840             if (do_per_step(step, ir->nstlog))
 841             {
 842                 if (fflush(fplog) != 0)
 843                 {
 844                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 845                 }
 846             }
 847         }
 848
 849         /* Print the remaining wall clock time for the run */
 850         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 851         {
 852             if (shellfc)
 853             {
 854                 fprintf(stderr, "\n");
 855             }
 856             print_time(stderr, walltime_accounting, step, ir, cr);
 857         }
 858
 859         /* Ion/water position swapping.
 860          * Not done in last step since trajectory writing happens before this call
 861          * in the MD loop and exchanges would be lost anyway. */
 862         if ((ir->eSwapCoords != SwapType::No) && (step > 0) && !isLastStep
 863             && do_per_step(step, ir->swap->nstswap))
 864         {
 865             const bool doRerun = true;
 866             do_swapcoords(cr,
 867                           step,
 868                           t,
 869                           ir,
 870                           swap,
 871                           wcycle,
 872                           rerun_fr.x,
 873                           rerun_fr.box,
 874                           MASTER(cr) && mdrunOptions.verbose,
 875                           doRerun);
 876         }
 877
 878         if (MASTER(cr))
 879         {
 880             /* read next frame from input trajectory */
 881             isLastStep = !read_next_frame(oenv, status, &rerun_fr);
 882         }
 883
 884         if (PAR(cr))
 885         {
 886             rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 887         }
 888
 889         cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
 890         if (DOMAINDECOMP(cr) && wcycle)
 891         {
 892             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 893         }
 894
 895         if (!rerun_fr.bStep)
 896         {
 897             /* increase the MD step number */
 898             step++;
 899             step_rel++;
 900         }
 901     }
 902     /* End of main MD loop */
 903
 904     /* Closing TNG files can include compressing data. Therefore it is good to do that
 905      * before stopping the time measurements. */
 906     mdoutf_tng_close(outf);
 907
 908     /* Stop measuring walltime */
 909     walltime_accounting_end_time(walltime_accounting);
 910
 911     if (MASTER(cr))
 912     {
 913         close_trx(status);
 914     }
 915
 916     if (!thisRankHasDuty(cr, DUTY_PME))
 917     {
 918         /* Tell the PME only node to finish */
 919         gmx_pme_send_finish(cr);
 920     }
 921
 922     done_mdoutf(outf);
 923
 924     done_shellfc(fplog, shellfc, step_rel);
 925
 926     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 927 }