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/mdsetup.h"
  60 #include "gromacs/domdec/partition.h"
  61 #include "gromacs/essentialdynamics/edsam.h"
  62 #include "gromacs/ewald/pme_load_balancing.h"
  63 #include "gromacs/ewald/pme_pp.h"
  64 #include "gromacs/fileio/trxio.h"
  65 #include "gromacs/gmxlib/network.h"
  66 #include "gromacs/gmxlib/nrnb.h"
  67 #include "gromacs/gpu_utils/gpu_utils.h"
  68 #include "gromacs/listed_forces/listed_forces.h"
  69 #include "gromacs/math/functions.h"
  70 #include "gromacs/math/utilities.h"
  71 #include "gromacs/math/vec.h"
  72 #include "gromacs/math/vectypes.h"
  73 #include "gromacs/mdlib/checkpointhandler.h"
  74 #include "gromacs/mdlib/compute_io.h"
  75 #include "gromacs/mdlib/constr.h"
  76 #include "gromacs/mdlib/ebin.h"
  77 #include "gromacs/mdlib/enerdata_utils.h"
  78 #include "gromacs/mdlib/energyoutput.h"
  79 #include "gromacs/mdlib/expanded.h"
  80 #include "gromacs/mdlib/force.h"
  81 #include "gromacs/mdlib/force_flags.h"
  82 #include "gromacs/mdlib/forcerec.h"
  83 #include "gromacs/mdlib/freeenergyparameters.h"
  84 #include "gromacs/mdlib/md_support.h"
  85 #include "gromacs/mdlib/mdatoms.h"
  86 #include "gromacs/mdlib/mdoutf.h"
  87 #include "gromacs/mdlib/membed.h"
  88 #include "gromacs/mdlib/resethandler.h"
  89 #include "gromacs/mdlib/sighandler.h"
  90 #include "gromacs/mdlib/simulationsignal.h"
  91 #include "gromacs/mdlib/stat.h"
  92 #include "gromacs/mdlib/stophandler.h"
  93 #include "gromacs/mdlib/tgroup.h"
  94 #include "gromacs/mdlib/trajectory_writing.h"
  95 #include "gromacs/mdlib/update.h"
  96 #include "gromacs/mdlib/vcm.h"
  97 #include "gromacs/mdlib/vsite.h"
  98 #include "gromacs/mdrunutility/handlerestart.h"
  99 #include "gromacs/mdrunutility/multisim.h"
 100 #include "gromacs/mdrunutility/printtime.h"
 101 #include "gromacs/mdtypes/awh_history.h"
 102 #include "gromacs/mdtypes/awh_params.h"
 103 #include "gromacs/mdtypes/commrec.h"
 104 #include "gromacs/mdtypes/df_history.h"
 105 #include "gromacs/mdtypes/energyhistory.h"
 106 #include "gromacs/mdtypes/forcebuffers.h"
 107 #include "gromacs/mdtypes/forcerec.h"
 108 #include "gromacs/mdtypes/group.h"
 109 #include "gromacs/mdtypes/inputrec.h"
 110 #include "gromacs/mdtypes/interaction_const.h"
 111 #include "gromacs/mdtypes/md_enums.h"
 112 #include "gromacs/mdtypes/mdatom.h"
 113 #include "gromacs/mdtypes/mdrunoptions.h"
 114 #include "gromacs/mdtypes/observableshistory.h"
 115 #include "gromacs/mdtypes/simulation_workload.h"
 116 #include "gromacs/mdtypes/state.h"
 117 #include "gromacs/mimic/utilities.h"
 118 #include "gromacs/pbcutil/pbc.h"
 119 #include "gromacs/pulling/pull.h"
 120 #include "gromacs/swap/swapcoords.h"
 121 #include "gromacs/timing/wallcycle.h"
 122 #include "gromacs/timing/walltime_accounting.h"
 123 #include "gromacs/topology/atoms.h"
 124 #include "gromacs/topology/idef.h"
 125 #include "gromacs/topology/mtop_util.h"
 126 #include "gromacs/topology/topology.h"
 127 #include "gromacs/trajectory/trajectoryframe.h"
 128 #include "gromacs/utility/basedefinitions.h"
 129 #include "gromacs/utility/cstringutil.h"
 130 #include "gromacs/utility/fatalerror.h"
 131 #include "gromacs/utility/logger.h"
 132 #include "gromacs/utility/real.h"
 133
 134 #include "legacysimulator.h"
 135 #include "replicaexchange.h"
 136 #include "shellfc.h"
 137
 138 using gmx::SimulationSignaller;
 139 using gmx::VirtualSitesHandler;
 140
 141 /*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
 142  *
 143  * \param[in]     rerunFrame      The trajectory frame to compute energy/forces for
 144  * \param[in,out] globalState     The global state container
 145  * \param[in]     constructVsites When true, vsite coordinates are constructed
 146  * \param[in]     vsite           Vsite setup, can be nullptr when \p constructVsites = false
 147  * \param[in]     timeStep        Time step, used for constructing vsites
 148  */
 149 static void prepareRerunState(const t_trxframe&          rerunFrame,
 150                               t_state*                   globalState,
 151                               bool                       constructVsites,
 152                               const VirtualSitesHandler* vsite,
 153                               double                     timeStep)
 154 {
 155     auto x      = makeArrayRef(globalState->x);
 156     auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec*>(rerunFrame.x), globalState->natoms);
 157     std::copy(rerunX.begin(), rerunX.end(), x.begin());
 158     copy_mat(rerunFrame.box, globalState->box);
 159
 160     if (constructVsites)
 161     {
 162         GMX_ASSERT(vsite, "Need valid vsite for constructing vsites");
 163
 164         vsite->construct(globalState->x, timeStep, globalState->v, globalState->box);
 165     }
 166 }
 167
 168 void gmx::LegacySimulator::do_rerun()
 169 {
 170     // TODO Historically, the EM and MD "integrators" used different
 171     // names for the t_inputrec *parameter, but these must have the
 172     // same name, now that it's a member of a struct. We use this ir
 173     // alias to avoid a large ripple of nearly useless changes.
 174     // t_inputrec is being replaced by IMdpOptionsProvider, so this
 175     // will go away eventually.
 176     const t_inputrec* ir = inputrec;
 177     int64_t           step, step_rel;
 178     double            t;
 179     bool              isLastStep               = false;
 180     bool              doFreeEnergyPerturbation = false;
 181     unsigned int      force_flags;
 182     tensor            force_vir, shake_vir, total_vir, pres;
 183     t_trxstatus*      status = nullptr;
 184     rvec              mu_tot;
 185     t_trxframe        rerun_fr;
 186     gmx_localtop_t    top(top_global->ffparams);
 187     ForceBuffers      f;
 188     gmx_global_stat_t gstat;
 189     gmx_shellfc_t*    shellfc;
 190
 191     double cycles;
 192
 193     /* Domain decomposition could incorrectly miss a bonded
 194        interaction, but checking for that requires a global
 195        communication stage, which does not otherwise happen in DD
 196        code. So we do that alongside the first global energy reduction
 197        after a new DD is made. These variables handle whether the
 198        check happens, and the result it returns. */
 199     bool shouldCheckNumberOfBondedInteractions = false;
 200     int  totalNumberOfBondedInteractions       = -1;
 201
 202     SimulationSignals signals;
 203     // Most global communnication stages don't propagate mdrun
 204     // signals, and will use this object to achieve that.
 205     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 206
 207     GMX_LOG(mdlog.info)
 208             .asParagraph()
 209             .appendText(
 210                     "Note that it is planned that the command gmx mdrun -rerun will "
 211                     "be available in a different form in a future version of GROMACS, "
 212                     "e.g. gmx rerun -f.");
 213
 214     if (ir->efep != efepNO
 215         && (mdAtoms->mdatoms()->nMassPerturbed > 0 || (constr && constr->havePerturbedConstraints())))
 216     {
 217         gmx_fatal(FARGS,
 218                   "Perturbed masses or constraints are not supported by rerun. "
 219                   "Either make a .tpr without mass and constraint perturbation, "
 220                   "or use GROMACS 2018.4, 2018.5 or later 2018 version.");
 221     }
 222     if (ir->bExpanded)
 223     {
 224         gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
 225     }
 226     if (ir->bSimTemp)
 227     {
 228         gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
 229     }
 230     if (ir->bDoAwh)
 231     {
 232         gmx_fatal(FARGS, "AWH not supported by rerun.");
 233     }
 234     if (replExParams.exchangeInterval > 0)
 235     {
 236         gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
 237     }
 238     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 239     {
 240         gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
 241     }
 242     if (ir->bIMD)
 243     {
 244         gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
 245     }
 246     if (isMultiSim(ms))
 247     {
 248         gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
 249     }
 250     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](int i) {
 251             return i != eannNO;
 252         }))
 253     {
 254         gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
 255     }
 256
 257     /* Rerun can't work if an output file name is the same as the input file name.
 258      * If this is the case, the user will get an error telling them what the issue is.
 259      */
 260     if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0
 261         || strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
 262     {
 263         gmx_fatal(FARGS,
 264                   "When using mdrun -rerun, the name of the input trajectory file "
 265                   "%s cannot be identical to the name of an output file (whether "
 266                   "given explicitly with -o or -x, or by default)",
 267                   opt2fn("-rerun", nfile, fnm));
 268     }
 269
 270     /* Settings for rerun */
 271     {
 272         // TODO: Avoid changing inputrec (#3854)
 273         auto* nonConstInputrec               = const_cast<t_inputrec*>(inputrec);
 274         nonConstInputrec->nstlist            = 1;
 275         nonConstInputrec->nstcalcenergy      = 1;
 276         nonConstInputrec->nstxout_compressed = 0;
 277     }
 278     int        nstglobalcomm = 1;
 279     const bool bNS           = true;
 280
 281     const SimulationGroups* groups = &top_global->groups;
 282     if (ir->eI == eiMimic)
 283     {
 284         auto nonConstGlobalTopology                          = const_cast<gmx_mtop_t*>(top_global);
 285         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 286     }
 287     int*                fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
 288     gmx::ArrayRef<real> lambda    = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
 289     initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
 290     const bool        simulationsShareState = false;
 291     gmx_mdoutf*       outf                  = init_mdoutf(fplog,
 292                                    nfile,
 293                                    fnm,
 294                                    mdrunOptions,
 295                                    cr,
 296                                    outputProvider,
 297                                    mdModulesNotifier,
 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                                    mdModulesNotifier);
 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     // Local state only becomes valid now.
 334     std::unique_ptr<t_state> stateInstance;
 335     t_state*                 state;
 336
 337     if (DOMAINDECOMP(cr))
 338     {
 339         stateInstance = std::make_unique<t_state>();
 340         state         = stateInstance.get();
 341         dd_init_local_state(cr->dd, state_global, state);
 342
 343         /* Distribute the charge groups over the nodes from the master node */
 344         dd_partition_system(fplog,
 345                             mdlog,
 346                             ir->init_step,
 347                             cr,
 348                             TRUE,
 349                             1,
 350                             state_global,
 351                             *top_global,
 352                             ir,
 353                             imdSession,
 354                             pull_work,
 355                             state,
 356                             &f,
 357                             mdAtoms,
 358                             &top,
 359                             fr,
 360                             vsite,
 361                             constr,
 362                             nrnb,
 363                             nullptr,
 364                             FALSE);
 365         shouldCheckNumberOfBondedInteractions = true;
 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[efptMASS]);
 384
 385     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 386     {
 387         doFreeEnergyPerturbation = true;
 388     }
 389
 390     {
 391         int cglo_flags =
 392                 (CGLO_GSTAT
 393                  | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 394         bool   bSumEkinhOld = false;
 395         t_vcm* vcm          = nullptr;
 396         compute_globals(gstat,
 397                         cr,
 398                         ir,
 399                         fr,
 400                         ekind,
 401                         makeConstArrayRef(state->x),
 402                         makeConstArrayRef(state->v),
 403                         state->box,
 404                         mdatoms,
 405                         nrnb,
 406                         vcm,
 407                         nullptr,
 408                         enerd,
 409                         force_vir,
 410                         shake_vir,
 411                         total_vir,
 412                         pres,
 413                         gmx::ArrayRef<real>{},
 414                         &nullSignaller,
 415                         state->box,
 416                         &totalNumberOfBondedInteractions,
 417                         &bSumEkinhOld,
 418                         cglo_flags);
 419     }
 420     checkNumberOfBondedInteractions(mdlog,
 421                                     cr,
 422                                     totalNumberOfBondedInteractions,
 423                                     top_global,
 424                                     &top,
 425                                     makeConstArrayRef(state->x),
 426                                     state->box,
 427                                     &shouldCheckNumberOfBondedInteractions);
 428
 429     if (MASTER(cr))
 430     {
 431         fprintf(stderr,
 432                 "starting md rerun '%s', reading coordinates from"
 433                 " input trajectory '%s'\n\n",
 434                 *(top_global->name),
 435                 opt2fn("-rerun", nfile, fnm));
 436         if (mdrunOptions.verbose)
 437         {
 438             fprintf(stderr,
 439                     "Calculated time to finish depends on nsteps from "
 440                     "run input file,\nwhich may not correspond to the time "
 441                     "needed to process input trajectory.\n\n");
 442         }
 443         fprintf(fplog, "\n");
 444     }
 445
 446     walltime_accounting_start_time(walltime_accounting);
 447     wallcycle_start(wcycle, ewcRUN);
 448     print_start(fplog, cr, walltime_accounting, "mdrun");
 449
 450     /***********************************************************
 451      *
 452      *             Loop over MD steps
 453      *
 454      ************************************************************/
 455
 456     if (constr)
 457     {
 458         GMX_LOG(mdlog.info)
 459                 .asParagraph()
 460                 .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
 461     }
 462
 463     rerun_fr.natoms = 0;
 464     if (MASTER(cr))
 465     {
 466         isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
 467         if (rerun_fr.natoms != top_global->natoms)
 468         {
 469             gmx_fatal(FARGS,
 470                       "Number of atoms in trajectory (%d) does not match the "
 471                       "run input file (%d)\n",
 472                       rerun_fr.natoms,
 473                       top_global->natoms);
 474         }
 475
 476         if (ir->pbcType != PbcType::No)
 477         {
 478             if (!rerun_fr.bBox)
 479             {
 480                 gmx_fatal(FARGS,
 481                           "Rerun trajectory frame step %" PRId64
 482                           " time %f "
 483                           "does not contain a box, while pbc is used",
 484                           rerun_fr.step,
 485                           rerun_fr.time);
 486             }
 487             if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
 488             {
 489                 gmx_fatal(FARGS,
 490                           "Rerun trajectory frame step %" PRId64
 491                           " time %f "
 492                           "has too small box dimensions",
 493                           rerun_fr.step,
 494                           rerun_fr.time);
 495             }
 496         }
 497     }
 498
 499     GMX_LOG(mdlog.info)
 500             .asParagraph()
 501             .appendText(
 502                     "Rerun does not report kinetic energy, total energy, temperature, virial and "
 503                     "pressure.");
 504
 505     if (PAR(cr))
 506     {
 507         rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 508     }
 509
 510     if (ir->pbcType != PbcType::No)
 511     {
 512         /* Set the shift vectors.
 513          * Necessary here when have a static box different from the tpr box.
 514          */
 515         calc_shifts(rerun_fr.box, fr->shift_vec);
 516     }
 517
 518     step     = ir->init_step;
 519     step_rel = 0;
 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, ewcSTEP);
 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 != efepNO && 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, ir->delta_t);
 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             shouldCheckNumberOfBondedInteractions = true;
 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 != efepNO)
 626         {
 627             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 628         }
 629
 630         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 631                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
 632                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 633
 634         if (shellfc)
 635         {
 636             /* Now is the time to relax the shells */
 637             relax_shell_flexcon(fplog,
 638                                 cr,
 639                                 ms,
 640                                 mdrunOptions.verbose,
 641                                 enforcedRotation,
 642                                 step,
 643                                 ir,
 644                                 imdSession,
 645                                 pull_work,
 646                                 bNS,
 647                                 force_flags,
 648                                 &top,
 649                                 constr,
 650                                 enerd,
 651                                 state->natoms,
 652                                 state->x.arrayRefWithPadding(),
 653                                 state->v.arrayRefWithPadding(),
 654                                 state->box,
 655                                 state->lambda,
 656                                 &state->hist,
 657                                 &f.view(),
 658                                 force_vir,
 659                                 mdatoms,
 660                                 nrnb,
 661                                 wcycle,
 662                                 shellfc,
 663                                 fr,
 664                                 runScheduleWork,
 665                                 t,
 666                                 mu_tot,
 667                                 vsite,
 668                                 ddBalanceRegionHandler);
 669         }
 670         else
 671         {
 672             /* The coordinates (x) are shifted (to get whole molecules)
 673              * in do_force.
 674              * This is parallellized as well, and does communication too.
 675              * Check comments in sim_util.c
 676              */
 677             Awh*       awh = nullptr;
 678             gmx_edsam* ed  = nullptr;
 679             do_force(fplog,
 680                      cr,
 681                      ms,
 682                      ir,
 683                      awh,
 684                      enforcedRotation,
 685                      imdSession,
 686                      pull_work,
 687                      step,
 688                      nrnb,
 689                      wcycle,
 690                      &top,
 691                      state->box,
 692                      state->x.arrayRefWithPadding(),
 693                      &state->hist,
 694                      &f.view(),
 695                      force_vir,
 696                      mdatoms,
 697                      enerd,
 698                      state->lambda,
 699                      fr,
 700                      runScheduleWork,
 701                      vsite,
 702                      mu_tot,
 703                      t,
 704                      ed,
 705                      GMX_FORCE_NS | force_flags,
 706                      ddBalanceRegionHandler);
 707         }
 708
 709         /* Now we have the energies and forces corresponding to the
 710          * coordinates at time t.
 711          */
 712         {
 713             const bool isCheckpointingStep = false;
 714             const bool doRerun             = true;
 715             const bool bSumEkinhOld        = false;
 716             do_md_trajectory_writing(fplog,
 717                                      cr,
 718                                      nfile,
 719                                      fnm,
 720                                      step,
 721                                      step_rel,
 722                                      t,
 723                                      ir,
 724                                      state,
 725                                      state_global,
 726                                      observablesHistory,
 727                                      top_global,
 728                                      fr,
 729                                      outf,
 730                                      energyOutput,
 731                                      ekind,
 732                                      f.view().force(),
 733                                      isCheckpointingStep,
 734                                      doRerun,
 735                                      isLastStep,
 736                                      mdrunOptions.writeConfout,
 737                                      bSumEkinhOld);
 738         }
 739
 740         stopHandler->setSignal();
 741
 742         {
 743             const bool          doInterSimSignal = false;
 744             const bool          doIntraSimSignal = true;
 745             bool                bSumEkinhOld     = false;
 746             t_vcm*              vcm              = nullptr;
 747             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 748
 749             compute_globals(gstat,
 750                             cr,
 751                             ir,
 752                             fr,
 753                             ekind,
 754                             makeConstArrayRef(state->x),
 755                             makeConstArrayRef(state->v),
 756                             state->box,
 757                             mdatoms,
 758                             nrnb,
 759                             vcm,
 760                             wcycle,
 761                             enerd,
 762                             force_vir,
 763                             shake_vir,
 764                             total_vir,
 765                             pres,
 766                             constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
 767                             &signaller,
 768                             state->box,
 769                             &totalNumberOfBondedInteractions,
 770                             &bSumEkinhOld,
 771                             CGLO_GSTAT | CGLO_ENERGY
 772                                     | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
 773                                                                              : 0));
 774             checkNumberOfBondedInteractions(mdlog,
 775                                             cr,
 776                                             totalNumberOfBondedInteractions,
 777                                             top_global,
 778                                             &top,
 779                                             makeConstArrayRef(state->x),
 780                                             state->box,
 781                                             &shouldCheckNumberOfBondedInteractions);
 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,
 799                                              ir->expandedvals,
 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                                              shake_vir,
 808                                              force_vir,
 809                                              total_vir,
 810                                              pres,
 811                                              ekind,
 812                                              mu_tot,
 813                                              constr);
 814
 815             const bool do_ene = true;
 816             const bool do_log = true;
 817             Awh*       awh    = nullptr;
 818             const bool do_dr  = ir->nstdisreout != 0;
 819             const bool do_or  = ir->nstorireout != 0;
 820
 821             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 822             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 823                                                do_ene,
 824                                                do_dr,
 825                                                do_or,
 826                                                do_log ? fplog : nullptr,
 827                                                step,
 828                                                t,
 829                                                fr->fcdata.get(),
 830                                                awh);
 831
 832             if (do_per_step(step, ir->nstlog))
 833             {
 834                 if (fflush(fplog) != 0)
 835                 {
 836                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 837                 }
 838             }
 839         }
 840
 841         /* Print the remaining wall clock time for the run */
 842         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 843         {
 844             if (shellfc)
 845             {
 846                 fprintf(stderr, "\n");
 847             }
 848             print_time(stderr, walltime_accounting, step, ir, cr);
 849         }
 850
 851         /* Ion/water position swapping.
 852          * Not done in last step since trajectory writing happens before this call
 853          * in the MD loop and exchanges would be lost anyway. */
 854         if ((ir->eSwapCoords != eswapNO) && (step > 0) && !isLastStep && do_per_step(step, ir->swap->nstswap))
 855         {
 856             const bool doRerun = true;
 857             do_swapcoords(cr,
 858                           step,
 859                           t,
 860                           ir,
 861                           swap,
 862                           wcycle,
 863                           rerun_fr.x,
 864                           rerun_fr.box,
 865                           MASTER(cr) && mdrunOptions.verbose,
 866                           doRerun);
 867         }
 868
 869         if (MASTER(cr))
 870         {
 871             /* read next frame from input trajectory */
 872             isLastStep = !read_next_frame(oenv, status, &rerun_fr);
 873         }
 874
 875         if (PAR(cr))
 876         {
 877             rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 878         }
 879
 880         cycles = wallcycle_stop(wcycle, ewcSTEP);
 881         if (DOMAINDECOMP(cr) && wcycle)
 882         {
 883             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 884         }
 885
 886         if (!rerun_fr.bStep)
 887         {
 888             /* increase the MD step number */
 889             step++;
 890             step_rel++;
 891         }
 892     }
 893     /* End of main MD loop */
 894
 895     /* Closing TNG files can include compressing data. Therefore it is good to do that
 896      * before stopping the time measurements. */
 897     mdoutf_tng_close(outf);
 898
 899     /* Stop measuring walltime */
 900     walltime_accounting_end_time(walltime_accounting);
 901
 902     if (MASTER(cr))
 903     {
 904         close_trx(status);
 905     }
 906
 907     if (!thisRankHasDuty(cr, DUTY_PME))
 908     {
 909         /* Tell the PME only node to finish */
 910         gmx_pme_send_finish(cr);
 911     }
 912
 913     done_mdoutf(outf);
 914
 915     done_shellfc(fplog, shellfc, step_rel);
 916
 917     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 918 }