src/gromacs/mdrun/rerun.cpp

   1 /*
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  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     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,
 251                     [](int i) { return i != eannNO; }))
 252     {
 253         gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
 254     }
 255
 256     /* Rerun can't work if an output file name is the same as the input file name.
 257      * If this is the case, the user will get an error telling them what the issue is.
 258      */
 259     if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0
 260         || strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
 261     {
 262         gmx_fatal(FARGS,
 263                   "When using mdrun -rerun, the name of the input trajectory file "
 264                   "%s cannot be identical to the name of an output file (whether "
 265                   "given explicitly with -o or -x, or by default)",
 266                   opt2fn("-rerun", nfile, fnm));
 267     }
 268
 269     /* Settings for rerun */
 270     ir->nstlist              = 1;
 271     ir->nstcalcenergy        = 1;
 272     int        nstglobalcomm = 1;
 273     const bool bNS           = true;
 274
 275     ir->nstxout_compressed         = 0;
 276     const SimulationGroups* groups = &top_global->groups;
 277     if (ir->eI == eiMimic)
 278     {
 279         auto nonConstGlobalTopology                          = const_cast<gmx_mtop_t*>(top_global);
 280         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 281     }
 282     int*                fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
 283     gmx::ArrayRef<real> lambda    = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
 284     initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
 285     const bool        simulationsShareState = false;
 286     gmx_mdoutf*       outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
 287                                    mdModulesNotifier, ir, top_global, oenv, wcycle,
 288                                    StartingBehavior::NewSimulation, simulationsShareState, ms);
 289     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
 290                                    mdoutf_get_fp_dhdl(outf), true, StartingBehavior::NewSimulation,
 291                                    simulationsShareState, mdModulesNotifier);
 292
 293     gstat = global_stat_init(ir);
 294
 295     /* Check for polarizable models and flexible constraints */
 296     shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
 297                                  ir->nstcalcenergy, DOMAINDECOMP(cr),
 298                                  runScheduleWork->simulationWork.useGpuPme);
 299
 300     {
 301         double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
 302         if ((io > 2000) && MASTER(cr))
 303         {
 304             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 305         }
 306     }
 307
 308     // Local state only becomes valid now.
 309     std::unique_ptr<t_state> stateInstance;
 310     t_state*                 state;
 311
 312     if (DOMAINDECOMP(cr))
 313     {
 314         stateInstance = std::make_unique<t_state>();
 315         state         = stateInstance.get();
 316         dd_init_local_state(cr->dd, state_global, state);
 317
 318         /* Distribute the charge groups over the nodes from the master node */
 319         dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
 320                             imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
 321                             nrnb, nullptr, FALSE);
 322         shouldCheckNumberOfBondedInteractions = true;
 323     }
 324     else
 325     {
 326         state_change_natoms(state_global, state_global->natoms);
 327         /* Copy the pointer to the global state */
 328         state = state_global;
 329
 330         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 331     }
 332
 333     auto mdatoms = mdAtoms->mdatoms();
 334
 335     // NOTE: The global state is no longer used at this point.
 336     // But state_global is still used as temporary storage space for writing
 337     // the global state to file and potentially for replica exchange.
 338     // (Global topology should persist.)
 339
 340     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 341
 342     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 343     {
 344         doFreeEnergyPerturbation = true;
 345     }
 346
 347     {
 348         int cglo_flags =
 349                 (CGLO_GSTAT
 350                  | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 351         bool   bSumEkinhOld = false;
 352         t_vcm* vcm          = nullptr;
 353         compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
 354                         makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
 355                         force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
 356                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 357     }
 358     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
 359                                     makeConstArrayRef(state->x), state->box,
 360                                     &shouldCheckNumberOfBondedInteractions);
 361
 362     if (MASTER(cr))
 363     {
 364         fprintf(stderr,
 365                 "starting md rerun '%s', reading coordinates from"
 366                 " input trajectory '%s'\n\n",
 367                 *(top_global->name), opt2fn("-rerun", nfile, fnm));
 368         if (mdrunOptions.verbose)
 369         {
 370             fprintf(stderr,
 371                     "Calculated time to finish depends on nsteps from "
 372                     "run input file,\nwhich may not correspond to the time "
 373                     "needed to process input trajectory.\n\n");
 374         }
 375         fprintf(fplog, "\n");
 376     }
 377
 378     walltime_accounting_start_time(walltime_accounting);
 379     wallcycle_start(wcycle, ewcRUN);
 380     print_start(fplog, cr, walltime_accounting, "mdrun");
 381
 382     /***********************************************************
 383      *
 384      *             Loop over MD steps
 385      *
 386      ************************************************************/
 387
 388     if (constr)
 389     {
 390         GMX_LOG(mdlog.info)
 391                 .asParagraph()
 392                 .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
 393     }
 394
 395     rerun_fr.natoms = 0;
 396     if (MASTER(cr))
 397     {
 398         isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
 399         if (rerun_fr.natoms != top_global->natoms)
 400         {
 401             gmx_fatal(FARGS,
 402                       "Number of atoms in trajectory (%d) does not match the "
 403                       "run input file (%d)\n",
 404                       rerun_fr.natoms, top_global->natoms);
 405         }
 406
 407         if (ir->pbcType != PbcType::No)
 408         {
 409             if (!rerun_fr.bBox)
 410             {
 411                 gmx_fatal(FARGS,
 412                           "Rerun trajectory frame step %" PRId64
 413                           " time %f "
 414                           "does not contain a box, while pbc is used",
 415                           rerun_fr.step, rerun_fr.time);
 416             }
 417             if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
 418             {
 419                 gmx_fatal(FARGS,
 420                           "Rerun trajectory frame step %" PRId64
 421                           " time %f "
 422                           "has too small box dimensions",
 423                           rerun_fr.step, rerun_fr.time);
 424             }
 425         }
 426     }
 427
 428     GMX_LOG(mdlog.info)
 429             .asParagraph()
 430             .appendText(
 431                     "Rerun does not report kinetic energy, total energy, temperature, virial and "
 432                     "pressure.");
 433
 434     if (PAR(cr))
 435     {
 436         rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 437     }
 438
 439     if (ir->pbcType != PbcType::No)
 440     {
 441         /* Set the shift vectors.
 442          * Necessary here when have a static box different from the tpr box.
 443          */
 444         calc_shifts(rerun_fr.box, fr->shift_vec);
 445     }
 446
 447     step     = ir->init_step;
 448     step_rel = 0;
 449
 450     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 451             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false, MASTER(cr),
 452             ir->nstlist, mdrunOptions.reproducible, nstglobalcomm, mdrunOptions.maximumHoursToRun,
 453             ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 454
 455     // we don't do counter resetting in rerun - finish will always be valid
 456     walltime_accounting_set_valid_finish(walltime_accounting);
 457
 458     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 459
 460     /* and stop now if we should */
 461     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 462     while (!isLastStep)
 463     {
 464         wallcycle_start(wcycle, ewcSTEP);
 465
 466         if (rerun_fr.bStep)
 467         {
 468             step     = rerun_fr.step;
 469             step_rel = step - ir->init_step;
 470         }
 471         if (rerun_fr.bTime)
 472         {
 473             t = rerun_fr.time;
 474         }
 475         else
 476         {
 477             t = step;
 478         }
 479
 480         if (ir->efep != efepNO && MASTER(cr))
 481         {
 482             if (rerun_fr.bLambda)
 483             {
 484                 ir->fepvals->init_lambda = rerun_fr.lambda;
 485             }
 486             else
 487             {
 488                 if (rerun_fr.bFepState)
 489                 {
 490                     state->fep_state = rerun_fr.fep_state;
 491                 }
 492             }
 493
 494             state_global->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
 495         }
 496
 497         if (MASTER(cr))
 498         {
 499             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 500             if (constructVsites && DOMAINDECOMP(cr))
 501             {
 502                 gmx_fatal(FARGS,
 503                           "Vsite recalculation with -rerun is not implemented with domain "
 504                           "decomposition, "
 505                           "use a single rank");
 506             }
 507             prepareRerunState(rerun_fr, state_global, constructVsites, vsite, ir->delta_t);
 508         }
 509
 510         isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
 511
 512         if (DOMAINDECOMP(cr))
 513         {
 514             /* Repartition the domain decomposition */
 515             const bool bMasterState = true;
 516             dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
 517                                 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
 518                                 fr, vsite, constr, nrnb, wcycle, mdrunOptions.verbose);
 519             shouldCheckNumberOfBondedInteractions = true;
 520         }
 521
 522         if (MASTER(cr))
 523         {
 524             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 525         }
 526
 527         if (ir->efep != efepNO)
 528         {
 529             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 530         }
 531
 532         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 533                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
 534                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 535
 536         if (shellfc)
 537         {
 538             /* Now is the time to relax the shells */
 539             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
 540                                 imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
 541                                 state->natoms, state->x.arrayRefWithPadding(),
 542                                 state->v.arrayRefWithPadding(), state->box, state->lambda,
 543                                 &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
 544                                 fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
 545         }
 546         else
 547         {
 548             /* The coordinates (x) are shifted (to get whole molecules)
 549              * in do_force.
 550              * This is parallellized as well, and does communication too.
 551              * Check comments in sim_util.c
 552              */
 553             Awh*       awh = nullptr;
 554             gmx_edsam* ed  = nullptr;
 555             do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
 556                      wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
 557                      &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
 558                      vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
 559         }
 560
 561         /* Now we have the energies and forces corresponding to the
 562          * coordinates at time t.
 563          */
 564         {
 565             const bool isCheckpointingStep = false;
 566             const bool doRerun             = true;
 567             const bool bSumEkinhOld        = false;
 568             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
 569                                      state_global, observablesHistory, top_global, fr, outf,
 570                                      energyOutput, ekind, f.view().force(), isCheckpointingStep,
 571                                      doRerun, isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
 572         }
 573
 574         stopHandler->setSignal();
 575
 576         if (vsite != nullptr)
 577         {
 578             wallcycle_start(wcycle, ewcVSITECONSTR);
 579             vsite->construct(state->x, ir->delta_t, state->v, state->box);
 580             wallcycle_stop(wcycle, ewcVSITECONSTR);
 581         }
 582
 583         {
 584             const bool          doInterSimSignal = false;
 585             const bool          doIntraSimSignal = true;
 586             bool                bSumEkinhOld     = false;
 587             t_vcm*              vcm              = nullptr;
 588             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 589
 590             compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
 591                             makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
 592                             enerd, force_vir, shake_vir, total_vir, pres, constr, &signaller,
 593                             state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
 594                             CGLO_GSTAT | CGLO_ENERGY
 595                                     | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
 596                                                                              : 0));
 597             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
 598                                             &top, makeConstArrayRef(state->x), state->box,
 599                                             &shouldCheckNumberOfBondedInteractions);
 600         }
 601
 602         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 603            the virial that should probably be addressed eventually. state->veta has better properies,
 604            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 605            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 606
 607         /* Output stuff */
 608         if (MASTER(cr))
 609         {
 610             const bool bCalcEnerStep = true;
 611             energyOutput.addDataAtEnergyStep(
 612                     doFreeEnergyPerturbation, bCalcEnerStep, t, mdatoms->tmass, enerd, ir->fepvals,
 613                     ir->expandedvals, state->box,
 614                     PTCouplingArrays({ state->boxv, state->nosehoover_xi, state->nosehoover_vxi,
 615                                        state->nhpres_xi, state->nhpres_vxi }),
 616                     state->fep_state, shake_vir, force_vir, total_vir, pres, ekind, mu_tot, constr);
 617
 618             const bool do_ene = true;
 619             const bool do_log = true;
 620             Awh*       awh    = nullptr;
 621             const bool do_dr  = ir->nstdisreout != 0;
 622             const bool do_or  = ir->nstorireout != 0;
 623
 624             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 625             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
 626                                                do_log ? fplog : nullptr, step, t, fr->fcdata.get(), awh);
 627
 628             if (do_per_step(step, ir->nstlog))
 629             {
 630                 if (fflush(fplog) != 0)
 631                 {
 632                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 633                 }
 634             }
 635         }
 636
 637         /* Print the remaining wall clock time for the run */
 638         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 639         {
 640             if (shellfc)
 641             {
 642                 fprintf(stderr, "\n");
 643             }
 644             print_time(stderr, walltime_accounting, step, ir, cr);
 645         }
 646
 647         /* Ion/water position swapping.
 648          * Not done in last step since trajectory writing happens before this call
 649          * in the MD loop and exchanges would be lost anyway. */
 650         if ((ir->eSwapCoords != eswapNO) && (step > 0) && !isLastStep && do_per_step(step, ir->swap->nstswap))
 651         {
 652             const bool doRerun = true;
 653             do_swapcoords(cr, step, t, ir, swap, wcycle, rerun_fr.x, rerun_fr.box,
 654                           MASTER(cr) && mdrunOptions.verbose, doRerun);
 655         }
 656
 657         if (MASTER(cr))
 658         {
 659             /* read next frame from input trajectory */
 660             isLastStep = !read_next_frame(oenv, status, &rerun_fr);
 661         }
 662
 663         if (PAR(cr))
 664         {
 665             rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 666         }
 667
 668         cycles = wallcycle_stop(wcycle, ewcSTEP);
 669         if (DOMAINDECOMP(cr) && wcycle)
 670         {
 671             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 672         }
 673
 674         if (!rerun_fr.bStep)
 675         {
 676             /* increase the MD step number */
 677             step++;
 678             step_rel++;
 679         }
 680     }
 681     /* End of main MD loop */
 682
 683     /* Closing TNG files can include compressing data. Therefore it is good to do that
 684      * before stopping the time measurements. */
 685     mdoutf_tng_close(outf);
 686
 687     /* Stop measuring walltime */
 688     walltime_accounting_end_time(walltime_accounting);
 689
 690     if (MASTER(cr))
 691     {
 692         close_trx(status);
 693     }
 694
 695     if (!thisRankHasDuty(cr, DUTY_PME))
 696     {
 697         /* Tell the PME only node to finish */
 698         gmx_pme_send_finish(cr);
 699     }
 700
 701     done_mdoutf(outf);
 702
 703     done_shellfc(fplog, shellfc, step_rel);
 704
 705     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 706 }