src/gromacs/mdrun/rerun.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
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  17  * Lesser General Public License for more details.
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  34  */
  35 /*! \internal \file
  36  *
  37  * \brief Implements the loop for simulation reruns
  38  *
  39  * \author Pascal Merz <pascal.merz@colorado.edu>
  40  * \ingroup module_mdrun
  41  */
  42 #include "gmxpre.h"
  43
  44 #include <cinttypes>
  45 #include <cmath>
  46 #include <cstdio>
  47 #include <cstdlib>
  48
  49 #include <algorithm>
  50 #include <memory>
  51
  52 #include "gromacs/applied_forces/awh/awh.h"
  53 #include "gromacs/commandline/filenm.h"
  54 #include "gromacs/domdec/collect.h"
  55 #include "gromacs/domdec/dlbtiming.h"
  56 #include "gromacs/domdec/domdec.h"
  57 #include "gromacs/domdec/domdec_network.h"
  58 #include "gromacs/domdec/domdec_struct.h"
  59 #include "gromacs/domdec/localtopologychecker.h"
  60 #include "gromacs/domdec/mdsetup.h"
  61 #include "gromacs/domdec/partition.h"
  62 #include "gromacs/essentialdynamics/edsam.h"
  63 #include "gromacs/ewald/pme_load_balancing.h"
  64 #include "gromacs/ewald/pme_pp.h"
  65 #include "gromacs/fileio/trxio.h"
  66 #include "gromacs/gmxlib/network.h"
  67 #include "gromacs/gmxlib/nrnb.h"
  68 #include "gromacs/gpu_utils/gpu_utils.h"
  69 #include "gromacs/listed_forces/listed_forces.h"
  70 #include "gromacs/math/functions.h"
  71 #include "gromacs/math/utilities.h"
  72 #include "gromacs/math/vec.h"
  73 #include "gromacs/math/vectypes.h"
  74 #include "gromacs/mdlib/checkpointhandler.h"
  75 #include "gromacs/mdlib/compute_io.h"
  76 #include "gromacs/mdlib/constr.h"
  77 #include "gromacs/mdlib/ebin.h"
  78 #include "gromacs/mdlib/enerdata_utils.h"
  79 #include "gromacs/mdlib/energyoutput.h"
  80 #include "gromacs/mdlib/expanded.h"
  81 #include "gromacs/mdlib/force.h"
  82 #include "gromacs/mdlib/force_flags.h"
  83 #include "gromacs/mdlib/forcerec.h"
  84 #include "gromacs/mdlib/freeenergyparameters.h"
  85 #include "gromacs/mdlib/md_support.h"
  86 #include "gromacs/mdlib/mdatoms.h"
  87 #include "gromacs/mdlib/mdoutf.h"
  88 #include "gromacs/mdlib/membed.h"
  89 #include "gromacs/mdlib/resethandler.h"
  90 #include "gromacs/mdlib/sighandler.h"
  91 #include "gromacs/mdlib/simulationsignal.h"
  92 #include "gromacs/mdlib/stat.h"
  93 #include "gromacs/mdlib/stophandler.h"
  94 #include "gromacs/mdlib/tgroup.h"
  95 #include "gromacs/mdlib/trajectory_writing.h"
  96 #include "gromacs/mdlib/update.h"
  97 #include "gromacs/mdlib/vcm.h"
  98 #include "gromacs/mdlib/vsite.h"
  99 #include "gromacs/mdrunutility/handlerestart.h"
 100 #include "gromacs/mdrunutility/multisim.h"
 101 #include "gromacs/mdrunutility/printtime.h"
 102 #include "gromacs/mdtypes/awh_history.h"
 103 #include "gromacs/mdtypes/awh_params.h"
 104 #include "gromacs/mdtypes/commrec.h"
 105 #include "gromacs/mdtypes/df_history.h"
 106 #include "gromacs/mdtypes/energyhistory.h"
 107 #include "gromacs/mdtypes/forcebuffers.h"
 108 #include "gromacs/mdtypes/forcerec.h"
 109 #include "gromacs/mdtypes/group.h"
 110 #include "gromacs/mdtypes/inputrec.h"
 111 #include "gromacs/mdtypes/interaction_const.h"
 112 #include "gromacs/mdtypes/md_enums.h"
 113 #include "gromacs/mdtypes/mdatom.h"
 114 #include "gromacs/mdtypes/mdrunoptions.h"
 115 #include "gromacs/mdtypes/observableshistory.h"
 116 #include "gromacs/mdtypes/simulation_workload.h"
 117 #include "gromacs/mdtypes/state.h"
 118 #include "gromacs/mimic/utilities.h"
 119 #include "gromacs/pbcutil/pbc.h"
 120 #include "gromacs/pulling/output.h"
 121 #include "gromacs/pulling/pull.h"
 122 #include "gromacs/swap/swapcoords.h"
 123 #include "gromacs/timing/wallcycle.h"
 124 #include "gromacs/timing/walltime_accounting.h"
 125 #include "gromacs/topology/atoms.h"
 126 #include "gromacs/topology/idef.h"
 127 #include "gromacs/topology/mtop_util.h"
 128 #include "gromacs/topology/topology.h"
 129 #include "gromacs/trajectory/trajectoryframe.h"
 130 #include "gromacs/utility/basedefinitions.h"
 131 #include "gromacs/utility/cstringutil.h"
 132 #include "gromacs/utility/fatalerror.h"
 133 #include "gromacs/utility/logger.h"
 134 #include "gromacs/utility/real.h"
 135
 136 #include "legacysimulator.h"
 137 #include "replicaexchange.h"
 138 #include "shellfc.h"
 139
 140 using gmx::SimulationSignaller;
 141 using gmx::VirtualSitesHandler;
 142
 143 /*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
 144  *
 145  * \param[in]     rerunFrame      The trajectory frame to compute energy/forces for
 146  * \param[in,out] globalState     The global state container
 147  * \param[in]     constructVsites When true, vsite coordinates are constructed
 148  * \param[in]     vsite           Vsite setup, can be nullptr when \p constructVsites = false
 149  */
 150 static void prepareRerunState(const t_trxframe&          rerunFrame,
 151                               t_state*                   globalState,
 152                               bool                       constructVsites,
 153                               const VirtualSitesHandler* vsite)
 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, globalState->v, globalState->box, gmx::VSiteOperation::PositionsAndVelocities);
 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     double            t;
 178     bool              isLastStep               = false;
 179     bool              doFreeEnergyPerturbation = false;
 180     unsigned int      force_flags;
 181     tensor            force_vir, shake_vir, total_vir, pres;
 182     t_trxstatus*      status = nullptr;
 183     rvec              mu_tot;
 184     t_trxframe        rerun_fr;
 185     gmx_localtop_t    top(top_global.ffparams);
 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     const SimulationGroups* groups = &top_global.groups;
 272     if (ir->eI == IntegrationAlgorithm::Mimic)
 273     {
 274         auto* nonConstGlobalTopology                         = const_cast<gmx_mtop_t*>(&top_global);
 275         nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
 276     }
 277     int*                fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
 278     gmx::ArrayRef<real> lambda    = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
 279     initialize_lambdas(fplog,
 280                        ir->efep,
 281                        ir->bSimTemp,
 282                        *ir->fepvals,
 283                        ir->simtempvals->temperatures,
 284                        gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
 285                        MASTER(cr),
 286                        fep_state,
 287                        lambda);
 288     const bool        simulationsShareState = false;
 289     gmx_mdoutf*       outf                  = init_mdoutf(fplog,
 290                                    nfile,
 291                                    fnm,
 292                                    mdrunOptions,
 293                                    cr,
 294                                    outputProvider,
 295                                    mdModulesNotifiers,
 296                                    ir,
 297                                    top_global,
 298                                    oenv,
 299                                    wcycle,
 300                                    StartingBehavior::NewSimulation,
 301                                    simulationsShareState,
 302                                    ms);
 303     gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
 304                                    top_global,
 305                                    *ir,
 306                                    pull_work,
 307                                    mdoutf_get_fp_dhdl(outf),
 308                                    true,
 309                                    StartingBehavior::NewSimulation,
 310                                    simulationsShareState,
 311                                    mdModulesNotifiers);
 312
 313     gstat = global_stat_init(ir);
 314
 315     /* Check for polarizable models and flexible constraints */
 316     shellfc = init_shell_flexcon(fplog,
 317                                  top_global,
 318                                  constr ? constr->numFlexibleConstraints() : 0,
 319                                  ir->nstcalcenergy,
 320                                  DOMAINDECOMP(cr),
 321                                  runScheduleWork->simulationWork.useGpuPme);
 322
 323     {
 324         double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
 325         if ((io > 2000) && MASTER(cr))
 326         {
 327             fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
 328         }
 329     }
 330
 331     // Local state only becomes valid now.
 332     std::unique_ptr<t_state> stateInstance;
 333     t_state*                 state;
 334
 335     if (DOMAINDECOMP(cr))
 336     {
 337         stateInstance = std::make_unique<t_state>();
 338         state         = stateInstance.get();
 339         dd_init_local_state(*cr->dd, state_global, state);
 340
 341         /* Distribute the charge groups over the nodes from the master node */
 342         dd_partition_system(fplog,
 343                             mdlog,
 344                             ir->init_step,
 345                             cr,
 346                             TRUE,
 347                             1,
 348                             state_global,
 349                             top_global,
 350                             *ir,
 351                             imdSession,
 352                             pull_work,
 353                             state,
 354                             &f,
 355                             mdAtoms,
 356                             &top,
 357                             fr,
 358                             vsite,
 359                             constr,
 360                             nrnb,
 361                             nullptr,
 362                             FALSE);
 363     }
 364     else
 365     {
 366         state_change_natoms(state_global, state_global->natoms);
 367         /* Copy the pointer to the global state */
 368         state = state_global;
 369
 370         mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
 371     }
 372
 373     auto* mdatoms = mdAtoms->mdatoms();
 374
 375     // NOTE: The global state is no longer used at this point.
 376     // But state_global is still used as temporary storage space for writing
 377     // the global state to file and potentially for replica exchange.
 378     // (Global topology should persist.)
 379
 380     update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 381
 382     if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
 383     {
 384         doFreeEnergyPerturbation = true;
 385     }
 386
 387     {
 388         int cglo_flags = CGLO_GSTAT;
 389         if (DOMAINDECOMP(cr) && dd_localTopologyChecker(*cr->dd).shouldCheckNumberOfBondedInteractions())
 390         {
 391             cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 392         }
 393         bool   bSumEkinhOld = false;
 394         t_vcm* vcm          = nullptr;
 395         compute_globals(gstat,
 396                         cr,
 397                         ir,
 398                         fr,
 399                         ekind,
 400                         makeConstArrayRef(state->x),
 401                         makeConstArrayRef(state->v),
 402                         state->box,
 403                         mdatoms,
 404                         nrnb,
 405                         vcm,
 406                         nullptr,
 407                         enerd,
 408                         force_vir,
 409                         shake_vir,
 410                         total_vir,
 411                         pres,
 412                         gmx::ArrayRef<real>{},
 413                         &nullSignaller,
 414                         state->box,
 415                         &bSumEkinhOld,
 416                         cglo_flags);
 417         if (DOMAINDECOMP(cr))
 418         {
 419             dd_localTopologyChecker(cr->dd)->checkNumberOfBondedInteractions(
 420                     &top, makeConstArrayRef(state->x), state->box);
 421         }
 422     }
 423
 424     if (MASTER(cr))
 425     {
 426         fprintf(stderr,
 427                 "starting md rerun '%s', reading coordinates from"
 428                 " input trajectory '%s'\n\n",
 429                 *(top_global.name),
 430                 opt2fn("-rerun", nfile, fnm));
 431         if (mdrunOptions.verbose)
 432         {
 433             fprintf(stderr,
 434                     "Calculated time to finish depends on nsteps from "
 435                     "run input file,\nwhich may not correspond to the time "
 436                     "needed to process input trajectory.\n\n");
 437         }
 438         fprintf(fplog, "\n");
 439     }
 440
 441     walltime_accounting_start_time(walltime_accounting);
 442     wallcycle_start(wcycle, WallCycleCounter::Run);
 443     print_start(fplog, cr, walltime_accounting, "mdrun");
 444
 445     /***********************************************************
 446      *
 447      *             Loop over MD steps
 448      *
 449      ************************************************************/
 450
 451     if (constr)
 452     {
 453         GMX_LOG(mdlog.info)
 454                 .asParagraph()
 455                 .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
 456     }
 457
 458     rerun_fr.natoms = 0;
 459     if (MASTER(cr))
 460     {
 461         isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
 462         if (rerun_fr.natoms != top_global.natoms)
 463         {
 464             gmx_fatal(FARGS,
 465                       "Number of atoms in trajectory (%d) does not match the "
 466                       "run input file (%d)\n",
 467                       rerun_fr.natoms,
 468                       top_global.natoms);
 469         }
 470
 471         if (ir->pbcType != PbcType::No)
 472         {
 473             if (!rerun_fr.bBox)
 474             {
 475                 gmx_fatal(FARGS,
 476                           "Rerun trajectory frame step %" PRId64
 477                           " time %f "
 478                           "does not contain a box, while pbc is used",
 479                           rerun_fr.step,
 480                           rerun_fr.time);
 481             }
 482             if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
 483             {
 484                 gmx_fatal(FARGS,
 485                           "Rerun trajectory frame step %" PRId64
 486                           " time %f "
 487                           "has too small box dimensions",
 488                           rerun_fr.step,
 489                           rerun_fr.time);
 490             }
 491         }
 492     }
 493
 494     GMX_LOG(mdlog.info)
 495             .asParagraph()
 496             .appendText(
 497                     "Rerun does not report kinetic energy, total energy, temperature, virial and "
 498                     "pressure.");
 499
 500     if (PAR(cr))
 501     {
 502         rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 503     }
 504
 505     if (ir->pbcType != PbcType::No)
 506     {
 507         /* Set the shift vectors.
 508          * Necessary here when have a static box different from the tpr box.
 509          */
 510         calc_shifts(rerun_fr.box, fr->shift_vec);
 511     }
 512
 513     int64_t step     = ir->init_step;
 514     int64_t step_rel = 0;
 515
 516     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 517             compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
 518             false,
 519             MASTER(cr),
 520             ir->nstlist,
 521             mdrunOptions.reproducible,
 522             nstglobalcomm,
 523             mdrunOptions.maximumHoursToRun,
 524             ir->nstlist == 0,
 525             fplog,
 526             step,
 527             bNS,
 528             walltime_accounting);
 529
 530     // we don't do counter resetting in rerun - finish will always be valid
 531     walltime_accounting_set_valid_finish(walltime_accounting);
 532
 533     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 534
 535     /* and stop now if we should */
 536     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 537     while (!isLastStep)
 538     {
 539         wallcycle_start(wcycle, WallCycleCounter::Step);
 540
 541         if (rerun_fr.bStep)
 542         {
 543             step     = rerun_fr.step;
 544             step_rel = step - ir->init_step;
 545         }
 546         if (rerun_fr.bTime)
 547         {
 548             t = rerun_fr.time;
 549         }
 550         else
 551         {
 552             t = step;
 553         }
 554
 555         if (ir->efep != FreeEnergyPerturbationType::No && MASTER(cr))
 556         {
 557             if (rerun_fr.bLambda)
 558             {
 559                 ir->fepvals->init_lambda = rerun_fr.lambda;
 560             }
 561             else
 562             {
 563                 if (rerun_fr.bFepState)
 564                 {
 565                     state->fep_state = rerun_fr.fep_state;
 566                 }
 567             }
 568
 569             state_global->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
 570         }
 571
 572         if (MASTER(cr))
 573         {
 574             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 575             if (constructVsites && DOMAINDECOMP(cr))
 576             {
 577                 gmx_fatal(FARGS,
 578                           "Vsite recalculation with -rerun is not implemented with domain "
 579                           "decomposition, "
 580                           "use a single rank");
 581             }
 582             prepareRerunState(rerun_fr, state_global, constructVsites, vsite);
 583         }
 584
 585         isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
 586
 587         if (DOMAINDECOMP(cr))
 588         {
 589             /* Repartition the domain decomposition */
 590             const bool bMasterState = true;
 591             dd_partition_system(fplog,
 592                                 mdlog,
 593                                 step,
 594                                 cr,
 595                                 bMasterState,
 596                                 nstglobalcomm,
 597                                 state_global,
 598                                 top_global,
 599                                 *ir,
 600                                 imdSession,
 601                                 pull_work,
 602                                 state,
 603                                 &f,
 604                                 mdAtoms,
 605                                 &top,
 606                                 fr,
 607                                 vsite,
 608                                 constr,
 609                                 nrnb,
 610                                 wcycle,
 611                                 mdrunOptions.verbose);
 612         }
 613
 614         if (MASTER(cr))
 615         {
 616             EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
 617         }
 618
 619         if (ir->efep != FreeEnergyPerturbationType::No)
 620         {
 621             update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
 622         }
 623
 624         force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
 625                        | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
 626                        GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 627
 628         if (shellfc)
 629         {
 630             /* Now is the time to relax the shells */
 631             relax_shell_flexcon(fplog,
 632                                 cr,
 633                                 ms,
 634                                 mdrunOptions.verbose,
 635                                 enforcedRotation,
 636                                 step,
 637                                 ir,
 638                                 imdSession,
 639                                 pull_work,
 640                                 bNS,
 641                                 force_flags,
 642                                 &top,
 643                                 constr,
 644                                 enerd,
 645                                 state->natoms,
 646                                 state->x.arrayRefWithPadding(),
 647                                 state->v.arrayRefWithPadding(),
 648                                 state->box,
 649                                 state->lambda,
 650                                 &state->hist,
 651                                 &f.view(),
 652                                 force_vir,
 653                                 *mdatoms,
 654                                 nrnb,
 655                                 wcycle,
 656                                 shellfc,
 657                                 fr,
 658                                 runScheduleWork,
 659                                 t,
 660                                 mu_tot,
 661                                 vsite,
 662                                 ddBalanceRegionHandler);
 663         }
 664         else
 665         {
 666             /* The coordinates (x) are shifted (to get whole molecules)
 667              * in do_force.
 668              * This is parallellized as well, and does communication too.
 669              * Check comments in sim_util.c
 670              */
 671             Awh*       awh = nullptr;
 672             gmx_edsam* ed  = nullptr;
 673             do_force(fplog,
 674                      cr,
 675                      ms,
 676                      *ir,
 677                      awh,
 678                      enforcedRotation,
 679                      imdSession,
 680                      pull_work,
 681                      step,
 682                      nrnb,
 683                      wcycle,
 684                      &top,
 685                      state->box,
 686                      state->x.arrayRefWithPadding(),
 687                      &state->hist,
 688                      &f.view(),
 689                      force_vir,
 690                      mdatoms,
 691                      enerd,
 692                      state->lambda,
 693                      fr,
 694                      runScheduleWork,
 695                      vsite,
 696                      mu_tot,
 697                      t,
 698                      ed,
 699                      GMX_FORCE_NS | force_flags,
 700                      ddBalanceRegionHandler);
 701         }
 702
 703         /* Now we have the energies and forces corresponding to the
 704          * coordinates at time t.
 705          */
 706         {
 707             const bool isCheckpointingStep = false;
 708             const bool doRerun             = true;
 709             const bool bSumEkinhOld        = false;
 710             do_md_trajectory_writing(fplog,
 711                                      cr,
 712                                      nfile,
 713                                      fnm,
 714                                      step,
 715                                      step_rel,
 716                                      t,
 717                                      ir,
 718                                      state,
 719                                      state_global,
 720                                      observablesHistory,
 721                                      top_global,
 722                                      fr,
 723                                      outf,
 724                                      energyOutput,
 725                                      ekind,
 726                                      f.view().force(),
 727                                      isCheckpointingStep,
 728                                      doRerun,
 729                                      isLastStep,
 730                                      mdrunOptions.writeConfout,
 731                                      bSumEkinhOld);
 732         }
 733
 734         stopHandler->setSignal();
 735
 736         {
 737             const bool          doInterSimSignal = false;
 738             const bool          doIntraSimSignal = true;
 739             bool                bSumEkinhOld     = false;
 740             t_vcm*              vcm              = nullptr;
 741             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 742
 743             int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
 744             if (DOMAINDECOMP(cr) && dd_localTopologyChecker(*cr->dd).shouldCheckNumberOfBondedInteractions())
 745             {
 746                 cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
 747             }
 748             compute_globals(gstat,
 749                             cr,
 750                             ir,
 751                             fr,
 752                             ekind,
 753                             makeConstArrayRef(state->x),
 754                             makeConstArrayRef(state->v),
 755                             state->box,
 756                             mdatoms,
 757                             nrnb,
 758                             vcm,
 759                             wcycle,
 760                             enerd,
 761                             force_vir,
 762                             shake_vir,
 763                             total_vir,
 764                             pres,
 765                             constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
 766                             &signaller,
 767                             state->box,
 768                             &bSumEkinhOld,
 769                             cglo_flags);
 770             if (DOMAINDECOMP(cr))
 771             {
 772                 dd_localTopologyChecker(cr->dd)->checkNumberOfBondedInteractions(
 773                         &top, makeConstArrayRef(state->x), state->box);
 774             }
 775         }
 776
 777         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 778            the virial that should probably be addressed eventually. state->veta has better properies,
 779            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 780            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 781
 782         /* Output stuff */
 783         if (MASTER(cr))
 784         {
 785             const bool bCalcEnerStep = true;
 786             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
 787                                              bCalcEnerStep,
 788                                              t,
 789                                              mdatoms->tmass,
 790                                              enerd,
 791                                              ir->fepvals.get(),
 792                                              ir->expandedvals.get(),
 793                                              state->box,
 794                                              PTCouplingArrays({ state->boxv,
 795                                                                 state->nosehoover_xi,
 796                                                                 state->nosehoover_vxi,
 797                                                                 state->nhpres_xi,
 798                                                                 state->nhpres_vxi }),
 799                                              state->fep_state,
 800                                              total_vir,
 801                                              pres,
 802                                              ekind,
 803                                              mu_tot,
 804                                              constr);
 805
 806             const bool do_ene = true;
 807             const bool do_log = true;
 808             Awh*       awh    = nullptr;
 809             const bool do_dr  = ir->nstdisreout != 0;
 810             const bool do_or  = ir->nstorireout != 0;
 811
 812             EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 813             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
 814                                                do_ene,
 815                                                do_dr,
 816                                                do_or,
 817                                                do_log ? fplog : nullptr,
 818                                                step,
 819                                                t,
 820                                                fr->fcdata.get(),
 821                                                awh);
 822
 823             if (ir->bPull)
 824             {
 825                 pull_print_output(pull_work, step, t);
 826             }
 827
 828             if (do_per_step(step, ir->nstlog))
 829             {
 830                 if (fflush(fplog) != 0)
 831                 {
 832                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 833                 }
 834             }
 835         }
 836
 837         /* Print the remaining wall clock time for the run */
 838         if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
 839         {
 840             if (shellfc)
 841             {
 842                 fprintf(stderr, "\n");
 843             }
 844             print_time(stderr, walltime_accounting, step, ir, cr);
 845         }
 846
 847         /* Ion/water position swapping.
 848          * Not done in last step since trajectory writing happens before this call
 849          * in the MD loop and exchanges would be lost anyway. */
 850         if ((ir->eSwapCoords != SwapType::No) && (step > 0) && !isLastStep
 851             && do_per_step(step, ir->swap->nstswap))
 852         {
 853             const bool doRerun = true;
 854             do_swapcoords(cr,
 855                           step,
 856                           t,
 857                           ir,
 858                           swap,
 859                           wcycle,
 860                           rerun_fr.x,
 861                           rerun_fr.box,
 862                           MASTER(cr) && mdrunOptions.verbose,
 863                           doRerun);
 864         }
 865
 866         if (MASTER(cr))
 867         {
 868             /* read next frame from input trajectory */
 869             isLastStep = !read_next_frame(oenv, status, &rerun_fr);
 870         }
 871
 872         if (PAR(cr))
 873         {
 874             rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 875         }
 876
 877         cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
 878         if (DOMAINDECOMP(cr) && wcycle)
 879         {
 880             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 881         }
 882
 883         if (!rerun_fr.bStep)
 884         {
 885             /* increase the MD step number */
 886             step++;
 887             step_rel++;
 888         }
 889     }
 890     /* End of main MD loop */
 891
 892     /* Closing TNG files can include compressing data. Therefore it is good to do that
 893      * before stopping the time measurements. */
 894     mdoutf_tng_close(outf);
 895
 896     /* Stop measuring walltime */
 897     walltime_accounting_end_time(walltime_accounting);
 898
 899     if (MASTER(cr))
 900     {
 901         close_trx(status);
 902     }
 903
 904     if (!thisRankHasDuty(cr, DUTY_PME))
 905     {
 906         /* Tell the PME only node to finish */
 907         gmx_pme_send_finish(cr);
 908     }
 909
 910     done_mdoutf(outf);
 911
 912     done_shellfc(fplog, shellfc, step_rel);
 913
 914     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 915 }