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     ForceBuffers      f;
 187     gmx_global_stat_t gstat;
 188     gmx_shellfc_t*    shellfc;
 189
 190     double cycles;
 191
 192     SimulationSignals signals;
 193     // Most global communnication stages don't propagate mdrun
 194     // signals, and will use this object to achieve that.
 195     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 196
 197     GMX_LOG(mdlog.info)
 198             .asParagraph()
 199             .appendText(
 200                     "Note that it is planned that the command gmx mdrun -rerun will "
 201                     "be available in a different form in a future version of GROMACS, "
 202                     "e.g. gmx rerun -f.");
 203
 204     if (ir->efep != FreeEnergyPerturbationType::No
 205         && (mdAtoms->mdatoms()->nMassPerturbed > 0 || (constr && constr->havePerturbedConstraints())))
 206     {
 207         gmx_fatal(FARGS,
 208                   "Perturbed masses or constraints are not supported by rerun. "
 209                   "Either make a .tpr without mass and constraint perturbation, "
 210                   "or use GROMACS 2018.4, 2018.5 or later 2018 version.");
 211     }
 212     if (ir->bExpanded)
 213     {
 214         gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
 215     }
 216     if (ir->bSimTemp)
 217     {
 218         gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
 219     }
 220     if (ir->bDoAwh)
 221     {
 222         gmx_fatal(FARGS, "AWH not supported by rerun.");
 223     }
 224     if (replExParams.exchangeInterval > 0)
 225     {
 226         gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
 227     }
 228     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 229     {
 230         gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
 231     }
 232     if (ir->bIMD)
 233     {
 234         gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
 235     }
 236     if (isMultiSim(ms))
 237     {
 238         gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
 239     }
 240     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](SimulatedAnnealing i) {
 241             return i != SimulatedAnnealing::No;
 242         }))
 243     {
 244         gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
 245     }
 246
 247     /* Rerun can't work if an output file name is the same as the input file name.
 248      * If this is the case, the user will get an error telling them what the issue is.
 249      */
 250     if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0
 251         || strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
 252     {
 253         gmx_fatal(FARGS,
 254                   "When using mdrun -rerun, the name of the input trajectory file "
 255                   "%s cannot be identical to the name of an output file (whether "
 256                   "given explicitly with -o or -x, or by default)",
 257                   opt2fn("-rerun", nfile, fnm));
 258     }
 259
 260     /* Settings for rerun */
 261     {
 262         // TODO: Avoid changing inputrec (#3854)
 263         auto* nonConstInputrec               = const_cast<t_inputrec*>(inputrec);
 264         nonConstInputrec->nstlist            = 1;
 265         nonConstInputrec->nstcalcenergy      = 1;
 266         nonConstInputrec->nstxout_compressed = 0;
 267     }
 268     int        nstglobalcomm = 1;
 269     const bool bNS           = true;
 270
 271     ObservablesReducer observablesReducer = observablesReducerBuilder->build();
 272
 273     const SimulationGroups* groups = &top_global.groups;
 274     if (ir->eI == IntegrationAlgorithm::Mimic)
 275     {
 276         auto* nonConstGlobalTopology                         = const_cast<gmx_mtop_t*>(&top_global);
 277         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
 278     }
 279     int*                fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
 280     gmx::ArrayRef<real> lambda    = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
 281     initialize_lambdas(fplog,
 282                        ir->efep,
 283                        ir->bSimTemp,
 284                        *ir->fepvals,
 285                        ir->simtempvals->temperatures,
 286                        gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
 287                        MASTER(cr),
 288                        fep_state,
 289                        lambda);
 290     const bool        simulationsShareState = false;
 291     gmx_mdoutf*       outf                  = init_mdoutf(fplog,
 292                                    nfile,
 293                                    fnm,
 294                                    mdrunOptions,
 295                                    cr,
 296                                    outputProvider,
 297                                    mdModulesNotifiers,
 298                                    ir,
 299                                    top_global,
 300                                    oenv,
 301                                    wcycle,
 302                                    StartingBehavior::NewSimulation,
 303                                    simulationsShareState,
 304                                    ms);
 305     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
 306                                    top_global,
 307                                    *ir,
 308                                    pull_work,
 309                                    mdoutf_get_fp_dhdl(outf),
 310                                    true,
 311                                    StartingBehavior::NewSimulation,
 312                                    simulationsShareState,
 313                                    mdModulesNotifiers);
 314
 315     gstat = global_stat_init(ir);
 316
 317     /* Check for polarizable models and flexible constraints */
 318     shellfc = init_shell_flexcon(fplog,
 319                                  top_global,
 320                                  constr ? constr->numFlexibleConstraints() : 0,
 321                                  ir->nstcalcenergy,
 322                                  DOMAINDECOMP(cr),
 323                                  runScheduleWork->simulationWork.useGpuPme);
 324
 325     {
 326         double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
 327         if ((io > 2000) && MASTER(cr))
 328         {
 329             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 330         }
 331     }
 332
 333     if (DOMAINDECOMP(cr))
 334     {
 335         // Local state only becomes valid now.
 336         dd_init_local_state(*cr->dd, state_global, state);
 337
 338         /* Distribute the charge groups over the nodes from the master node */
 339         dd_partition_system(fplog,
 340                             mdlog,
 341                             ir->init_step,
 342                             cr,
 343                             TRUE,
 344                             1,
 345                             state_global,
 346                             top_global,
 347                             *ir,
 348                             imdSession,
 349                             pull_work,
 350                             state,
 351                             &f,
 352                             mdAtoms,
 353                             top,
 354                             fr,
 355                             vsite,
 356                             constr,
 357                             nrnb,
 358                             nullptr,
 359                             FALSE);
 360     }
 361     else
 362     {
 363         state_change_natoms(state_global, state_global->natoms);
 364         /* Copy the pointer to the global state */
 365         state = state_global;
 366
 367         mdAlgorithmsSetupAtomData(cr, *ir, top_global, top, fr, &f, mdAtoms, constr, vsite, shellfc);
 368     }
 369
 370     auto* mdatoms = mdAtoms->mdatoms();
 371     fr->longRangeNonbondeds->updateAfterPartition(*mdatoms);
 372
 373     // NOTE: The global state is no longer used at this point.
 374     // But state_global is still used as temporary storage space for writing
 375     // the global state to file and potentially for replica exchange.
 376     // (Global topology should persist.)
 377
 378     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 379
 380     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 381     {
 382         doFreeEnergyPerturbation = true;
 383     }
 384
 385     int64_t step     = ir->init_step;
 386     int64_t step_rel = 0;
 387
 388     {
 389         int    cglo_flags   = CGLO_GSTAT;
 390         bool   bSumEkinhOld = false;
 391         t_vcm* vcm          = nullptr;
 392         compute_globals(gstat,
 393                         cr,
 394                         ir,
 395                         fr,
 396                         ekind,
 397                         makeConstArrayRef(state->x),
 398                         makeConstArrayRef(state->v),
 399                         state->box,
 400                         mdatoms,
 401                         nrnb,
 402                         vcm,
 403                         nullptr,
 404                         enerd,
 405                         force_vir,
 406                         shake_vir,
 407                         total_vir,
 408                         pres,
 409                         gmx::ArrayRef<real>{},
 410                         &nullSignaller,
 411                         state->box,
 412                         &bSumEkinhOld,
 413                         cglo_flags,
 414                         step,
 415                         &observablesReducer);
 416         // Clean up after pre-step use of compute_globals()
 417         observablesReducer.markAsReadyToReduce();
 418     }
 419
 420     if (MASTER(cr))
 421     {
 422         fprintf(stderr,
 423                 "starting md rerun '%s', reading coordinates from"
 424                 " input trajectory '%s'\n\n",
 425                 *(top_global.name),
 426                 opt2fn("-rerun", nfile, fnm));
 427         if (mdrunOptions.verbose)
 428         {
 429             fprintf(stderr,
 430                     "Calculated time to finish depends on nsteps from "
 431                     "run input file,\nwhich may not correspond to the time "
 432                     "needed to process input trajectory.\n\n");
 433         }
 434         fprintf(fplog, "\n");
 435     }
 436
 437     walltime_accounting_start_time(walltime_accounting);
 438     wallcycle_start(wcycle, WallCycleCounter::Run);
 439     print_start(fplog, cr, walltime_accounting, "mdrun");
 440
 441     /***********************************************************
 442      *
 443      *             Loop over MD steps
 444      *
 445      ************************************************************/
 446
 447     if (constr)
 448     {
 449         GMX_LOG(mdlog.info)
 450                 .asParagraph()
 451                 .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
 452     }
 453
 454     rerun_fr.natoms = 0;
 455     if (MASTER(cr))
 456     {
 457         isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
 458         if (rerun_fr.natoms != top_global.natoms)
 459         {
 460             gmx_fatal(FARGS,
 461                       "Number of atoms in trajectory (%d) does not match the "
 462                       "run input file (%d)\n",
 463                       rerun_fr.natoms,
 464                       top_global.natoms);
 465         }
 466
 467         if (ir->pbcType != PbcType::No)
 468         {
 469             if (!rerun_fr.bBox)
 470             {
 471                 gmx_fatal(FARGS,
 472                           "Rerun trajectory frame step %" PRId64
 473                           " time %f "
 474                           "does not contain a box, while pbc is used",
 475                           rerun_fr.step,
 476                           rerun_fr.time);
 477             }
 478             if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
 479             {
 480                 gmx_fatal(FARGS,
 481                           "Rerun trajectory frame step %" PRId64
 482                           " time %f "
 483                           "has too small box dimensions",
 484                           rerun_fr.step,
 485                           rerun_fr.time);
 486             }
 487         }
 488     }
 489
 490     GMX_LOG(mdlog.info)
 491             .asParagraph()
 492             .appendText(
 493                     "Rerun does not report kinetic energy, total energy, temperature, virial and "
 494                     "pressure.");
 495
 496     if (PAR(cr))
 497     {
 498         rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 499     }
 500
 501     if (ir->pbcType != PbcType::No)
 502     {
 503         /* Set the shift vectors.
 504          * Necessary here when have a static box different from the tpr box.
 505          */
 506         calc_shifts(rerun_fr.box, fr->shift_vec);
 507     }
 508
 509     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 510             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 511             false,
 512             MASTER(cr),
 513             ir->nstlist,
 514             mdrunOptions.reproducible,
 515             nstglobalcomm,
 516             mdrunOptions.maximumHoursToRun,
 517             ir->nstlist == 0,
 518             fplog,
 519             step,
 520             bNS,
 521             walltime_accounting);
 522
 523     // we don't do counter resetting in rerun - finish will always be valid
 524     walltime_accounting_set_valid_finish(walltime_accounting);
 525
 526     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 527
 528     /* and stop now if we should */
 529     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 530     while (!isLastStep)
 531     {
 532         wallcycle_start(wcycle, WallCycleCounter::Step);
 533
 534         if (rerun_fr.bStep)
 535         {
 536             step     = rerun_fr.step;
 537             step_rel = step - ir->init_step;
 538         }
 539         if (rerun_fr.bTime)
 540         {
 541             t = rerun_fr.time;
 542         }
 543         else
 544         {
 545             t = step;
 546         }
 547
 548         if (ir->efep != FreeEnergyPerturbationType::No && MASTER(cr))
 549         {
 550             if (rerun_fr.bLambda)
 551             {
 552                 ir->fepvals->init_lambda = rerun_fr.lambda;
 553             }
 554             else
 555             {
 556                 if (rerun_fr.bFepState)
 557                 {
 558                     state->fep_state = rerun_fr.fep_state;
 559                 }
 560             }
 561
 562             state_global->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
 563         }
 564
 565         if (MASTER(cr))
 566         {
 567             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 568             if (constructVsites && DOMAINDECOMP(cr))
 569             {
 570                 gmx_fatal(FARGS,
 571                           "Vsite recalculation with -rerun is not implemented with domain "
 572                           "decomposition, "
 573                           "use a single rank");
 574             }
 575             prepareRerunState(rerun_fr, state_global, constructVsites, vsite);
 576         }
 577
 578         isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
 579
 580         if (DOMAINDECOMP(cr))
 581         {
 582             /* Repartition the domain decomposition */
 583             const bool bMasterState = true;
 584             dd_partition_system(fplog,
 585                                 mdlog,
 586                                 step,
 587                                 cr,
 588                                 bMasterState,
 589                                 nstglobalcomm,
 590                                 state_global,
 591                                 top_global,
 592                                 *ir,
 593                                 imdSession,
 594                                 pull_work,
 595                                 state,
 596                                 &f,
 597                                 mdAtoms,
 598                                 top,
 599                                 fr,
 600                                 vsite,
 601                                 constr,
 602                                 nrnb,
 603                                 wcycle,
 604                                 mdrunOptions.verbose);
 605         }
 606
 607         if (MASTER(cr))
 608         {
 609             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 610         }
 611
 612         if (ir->efep != FreeEnergyPerturbationType::No)
 613         {
 614             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 615         }
 616
 617         fr->longRangeNonbondeds->updateAfterPartition(*mdatoms);
 618
 619         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 620                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
 621                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 622
 623         if (shellfc)
 624         {
 625             /* Now is the time to relax the shells */
 626             relax_shell_flexcon(fplog,
 627                                 cr,
 628                                 ms,
 629                                 mdrunOptions.verbose,
 630                                 enforcedRotation,
 631                                 step,
 632                                 ir,
 633                                 imdSession,
 634                                 pull_work,
 635                                 bNS,
 636                                 force_flags,
 637                                 top,
 638                                 constr,
 639                                 enerd,
 640                                 state->natoms,
 641                                 state->x.arrayRefWithPadding(),
 642                                 state->v.arrayRefWithPadding(),
 643                                 state->box,
 644                                 state->lambda,
 645                                 &state->hist,
 646                                 &f.view(),
 647                                 force_vir,
 648                                 *mdatoms,
 649                                 fr->longRangeNonbondeds.get(),
 650                                 nrnb,
 651                                 wcycle,
 652                                 shellfc,
 653                                 fr,
 654                                 runScheduleWork,
 655                                 t,
 656                                 mu_tot,
 657                                 vsite,
 658                                 ddBalanceRegionHandler);
 659         }
 660         else
 661         {
 662             /* The coordinates (x) are shifted (to get whole molecules)
 663              * in do_force.
 664              * This is parallellized as well, and does communication too.
 665              * Check comments in sim_util.c
 666              */
 667             Awh*       awh = nullptr;
 668             gmx_edsam* ed  = nullptr;
 669             do_force(fplog,
 670                      cr,
 671                      ms,
 672                      *ir,
 673                      awh,
 674                      enforcedRotation,
 675                      imdSession,
 676                      pull_work,
 677                      step,
 678                      nrnb,
 679                      wcycle,
 680                      top,
 681                      state->box,
 682                      state->x.arrayRefWithPadding(),
 683                      &state->hist,
 684                      &f.view(),
 685                      force_vir,
 686                      mdatoms,
 687                      enerd,
 688                      state->lambda,
 689                      fr,
 690                      runScheduleWork,
 691                      vsite,
 692                      mu_tot,
 693                      t,
 694                      ed,
 695                      fr->longRangeNonbondeds.get(),
 696                      GMX_FORCE_NS | force_flags,
 697                      ddBalanceRegionHandler);
 698         }
 699
 700         /* Now we have the energies and forces corresponding to the
 701          * coordinates at time t.
 702          */
 703         {
 704             const bool isCheckpointingStep = false;
 705             const bool doRerun             = true;
 706             const bool bSumEkinhOld        = false;
 707             do_md_trajectory_writing(fplog,
 708                                      cr,
 709                                      nfile,
 710                                      fnm,
 711                                      step,
 712                                      step_rel,
 713                                      t,
 714                                      ir,
 715                                      state,
 716                                      state_global,
 717                                      observablesHistory,
 718                                      top_global,
 719                                      fr,
 720                                      outf,
 721                                      energyOutput,
 722                                      ekind,
 723                                      f.view().force(),
 724                                      isCheckpointingStep,
 725                                      doRerun,
 726                                      isLastStep,
 727                                      mdrunOptions.writeConfout,
 728                                      bSumEkinhOld);
 729         }
 730
 731         stopHandler->setSignal();
 732
 733         {
 734             const bool          doInterSimSignal = false;
 735             const bool          doIntraSimSignal = true;
 736             bool                bSumEkinhOld     = false;
 737             t_vcm*              vcm              = nullptr;
 738             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 739
 740             int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
 741             compute_globals(gstat,
 742                             cr,
 743                             ir,
 744                             fr,
 745                             ekind,
 746                             makeConstArrayRef(state->x),
 747                             makeConstArrayRef(state->v),
 748                             state->box,
 749                             mdatoms,
 750                             nrnb,
 751                             vcm,
 752                             wcycle,
 753                             enerd,
 754                             force_vir,
 755                             shake_vir,
 756                             total_vir,
 757                             pres,
 758                             constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
 759                             &signaller,
 760                             state->box,
 761                             &bSumEkinhOld,
 762                             cglo_flags,
 763                             step,
 764                             &observablesReducer);
 765             // Clean up after pre-step use of compute_globals()
 766             observablesReducer.markAsReadyToReduce();
 767         }
 768
 769         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 770            the virial that should probably be addressed eventually. state->veta has better properies,
 771            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 772            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 773
 774         /* Output stuff */
 775         if (MASTER(cr))
 776         {
 777             const bool bCalcEnerStep = true;
 778             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 779                                              bCalcEnerStep,
 780                                              t,
 781                                              mdatoms->tmass,
 782                                              enerd,
 783                                              ir->fepvals.get(),
 784                                              ir->expandedvals.get(),
 785                                              state->box,
 786                                              PTCouplingArrays({ state->boxv,
 787                                                                 state->nosehoover_xi,
 788                                                                 state->nosehoover_vxi,
 789                                                                 state->nhpres_xi,
 790                                                                 state->nhpres_vxi }),
 791                                              state->fep_state,
 792                                              total_vir,
 793                                              pres,
 794                                              ekind,
 795                                              mu_tot,
 796                                              constr);
 797
 798             const bool do_ene = true;
 799             const bool do_log = true;
 800             Awh*       awh    = nullptr;
 801             const bool do_dr  = ir->nstdisreout != 0;
 802             const bool do_or  = ir->nstorireout != 0;
 803
 804             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 805             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 806                                                do_ene,
 807                                                do_dr,
 808                                                do_or,
 809                                                do_log ? fplog : nullptr,
 810                                                step,
 811                                                t,
 812                                                fr->fcdata.get(),
 813                                                awh);
 814
 815             if (ir->bPull)
 816             {
 817                 pull_print_output(pull_work, step, t);
 818             }
 819
 820             if (do_per_step(step, ir->nstlog))
 821             {
 822                 if (fflush(fplog) != 0)
 823                 {
 824                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 825                 }
 826             }
 827         }
 828
 829         /* Print the remaining wall clock time for the run */
 830         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 831         {
 832             if (shellfc)
 833             {
 834                 fprintf(stderr, "\n");
 835             }
 836             print_time(stderr, walltime_accounting, step, ir, cr);
 837         }
 838
 839         /* Ion/water position swapping.
 840          * Not done in last step since trajectory writing happens before this call
 841          * in the MD loop and exchanges would be lost anyway. */
 842         if ((ir->eSwapCoords != SwapType::No) && (step > 0) && !isLastStep
 843             && do_per_step(step, ir->swap->nstswap))
 844         {
 845             const bool doRerun = true;
 846             do_swapcoords(cr,
 847                           step,
 848                           t,
 849                           ir,
 850                           swap,
 851                           wcycle,
 852                           rerun_fr.x,
 853                           rerun_fr.box,
 854                           MASTER(cr) && mdrunOptions.verbose,
 855                           doRerun);
 856         }
 857
 858         if (MASTER(cr))
 859         {
 860             /* read next frame from input trajectory */
 861             isLastStep = !read_next_frame(oenv, status, &rerun_fr);
 862         }
 863
 864         if (PAR(cr))
 865         {
 866             rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 867         }
 868
 869         cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
 870         if (DOMAINDECOMP(cr) && wcycle)
 871         {
 872             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 873         }
 874
 875         if (!rerun_fr.bStep)
 876         {
 877             /* increase the MD step number */
 878             step++;
 879             step_rel++;
 880         }
 881         observablesReducer.markAsReadyToReduce();
 882     }
 883     /* End of main MD loop */
 884
 885     /* Closing TNG files can include compressing data. Therefore it is good to do that
 886      * before stopping the time measurements. */
 887     mdoutf_tng_close(outf);
 888
 889     /* Stop measuring walltime */
 890     walltime_accounting_end_time(walltime_accounting);
 891
 892     if (MASTER(cr))
 893     {
 894         close_trx(status);
 895     }
 896
 897     if (!thisRankHasDuty(cr, DUTY_PME))
 898     {
 899         /* Tell the PME only node to finish */
 900         gmx_pme_send_finish(cr);
 901     }
 902
 903     done_mdoutf(outf);
 904
 905     done_shellfc(fplog, shellfc, step_rel);
 906
 907     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 908 }