src/gromacs/mdrun/rerun.cpp

   1 /*
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   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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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 "config.h"
  45
  46 #include <cinttypes>
  47 #include <cmath>
  48 #include <cstdio>
  49 #include <cstdlib>
  50
  51 #include <algorithm>
  52 #include <memory>
  53
  54 #include "gromacs/awh/awh.h"
  55 #include "gromacs/commandline/filenm.h"
  56 #include "gromacs/compat/make_unique.h"
  57 #include "gromacs/domdec/collect.h"
  58 #include "gromacs/domdec/domdec.h"
  59 #include "gromacs/domdec/domdec_network.h"
  60 #include "gromacs/domdec/domdec_struct.h"
  61 #include "gromacs/domdec/partition.h"
  62 #include "gromacs/essentialdynamics/edsam.h"
  63 #include "gromacs/ewald/pme.h"
  64 #include "gromacs/ewald/pme-load-balancing.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/imd/imd.h"
  70 #include "gromacs/listed-forces/manage-threading.h"
  71 #include "gromacs/math/functions.h"
  72 #include "gromacs/math/utilities.h"
  73 #include "gromacs/math/vec.h"
  74 #include "gromacs/math/vectypes.h"
  75 #include "gromacs/mdlib/checkpointhandler.h"
  76 #include "gromacs/mdlib/compute_io.h"
  77 #include "gromacs/mdlib/constr.h"
  78 #include "gromacs/mdlib/ebin.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/md_support.h"
  84 #include "gromacs/mdlib/mdatoms.h"
  85 #include "gromacs/mdlib/mdebin.h"
  86 #include "gromacs/mdlib/mdoutf.h"
  87 #include "gromacs/mdlib/mdrun.h"
  88 #include "gromacs/mdlib/mdsetup.h"
  89 #include "gromacs/mdlib/membed.h"
  90 #include "gromacs/mdlib/nb_verlet.h"
  91 #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
  92 #include "gromacs/mdlib/ns.h"
  93 #include "gromacs/mdlib/resethandler.h"
  94 #include "gromacs/mdlib/shellfc.h"
  95 #include "gromacs/mdlib/sighandler.h"
  96 #include "gromacs/mdlib/sim_util.h"
  97 #include "gromacs/mdlib/simulationsignal.h"
  98 #include "gromacs/mdlib/stophandler.h"
  99 #include "gromacs/mdlib/tgroup.h"
 100 #include "gromacs/mdlib/trajectory_writing.h"
 101 #include "gromacs/mdlib/update.h"
 102 #include "gromacs/mdlib/vcm.h"
 103 #include "gromacs/mdlib/vsite.h"
 104 #include "gromacs/mdtypes/awh-history.h"
 105 #include "gromacs/mdtypes/awh-params.h"
 106 #include "gromacs/mdtypes/commrec.h"
 107 #include "gromacs/mdtypes/df_history.h"
 108 #include "gromacs/mdtypes/energyhistory.h"
 109 #include "gromacs/mdtypes/fcdata.h"
 110 #include "gromacs/mdtypes/forcerec.h"
 111 #include "gromacs/mdtypes/group.h"
 112 #include "gromacs/mdtypes/inputrec.h"
 113 #include "gromacs/mdtypes/interaction_const.h"
 114 #include "gromacs/mdtypes/md_enums.h"
 115 #include "gromacs/mdtypes/mdatom.h"
 116 #include "gromacs/mdtypes/observableshistory.h"
 117 #include "gromacs/mdtypes/state.h"
 118 #include "gromacs/mimic/MimicUtils.h"
 119 #include "gromacs/pbcutil/mshift.h"
 120 #include "gromacs/pbcutil/pbc.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 #include "gromacs/utility/smalloc.h"
 136
 137 #include "integrator.h"
 138 #include "replicaexchange.h"
 139
 140 using gmx::SimulationSignaller;
 141
 142 /*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
 143  *
 144  * \param[in]     rerunFrame      The trajectory frame to compute energy/forces for
 145  * \param[in,out] globalState     The global state container
 146  * \param[in]     constructVsites When true, vsite coordinates are constructed
 147  * \param[in]     vsite           Vsite setup, can be nullptr when \p constructVsites = false
 148  * \param[in]     idef            Topology parameters, used for constructing vsites
 149  * \param[in]     timeStep        Time step, used for constructing vsites
 150  * \param[in]     forceRec        Force record, used for constructing vsites
 151  * \param[in,out] graph           The molecular graph, used for constructing vsites when != nullptr
 152  */
 153 static void prepareRerunState(const t_trxframe  &rerunFrame,
 154                               t_state           *globalState,
 155                               bool               constructVsites,
 156                               const gmx_vsite_t *vsite,
 157                               const t_idef      &idef,
 158                               double             timeStep,
 159                               const t_forcerec  &forceRec,
 160                               t_graph           *graph)
 161 {
 162     auto x      = makeArrayRef(globalState->x);
 163     auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec *>(rerunFrame.x), globalState->natoms);
 164     std::copy(rerunX.begin(), rerunX.end(), x.begin());
 165     copy_mat(rerunFrame.box, globalState->box);
 166
 167     if (constructVsites)
 168     {
 169         GMX_ASSERT(vsite, "Need valid vsite for constructing vsites");
 170
 171         if (graph)
 172         {
 173             /* Following is necessary because the graph may get out of sync
 174              * with the coordinates if we only have every N'th coordinate set
 175              */
 176             mk_mshift(nullptr, graph, forceRec.ePBC, globalState->box, globalState->x.rvec_array());
 177             shift_self(graph, globalState->box, as_rvec_array(globalState->x.data()));
 178         }
 179         construct_vsites(vsite, globalState->x.rvec_array(), timeStep, globalState->v.rvec_array(),
 180                          idef.iparams, idef.il,
 181                          forceRec.ePBC, forceRec.bMolPBC, nullptr, globalState->box);
 182         if (graph)
 183         {
 184             unshift_self(graph, globalState->box, globalState->x.rvec_array());
 185         }
 186     }
 187 }
 188
 189 void gmx::Integrator::do_rerun()
 190 {
 191     // TODO Historically, the EM and MD "integrators" used different
 192     // names for the t_inputrec *parameter, but these must have the
 193     // same name, now that it's a member of a struct. We use this ir
 194     // alias to avoid a large ripple of nearly useless changes.
 195     // t_inputrec is being replaced by IMdpOptionsProvider, so this
 196     // will go away eventually.
 197     t_inputrec             *ir   = inputrec;
 198     gmx_mdoutf             *outf = nullptr;
 199     int64_t                 step, step_rel;
 200     double                  t, lam0[efptNR];
 201     bool                    isLastStep               = false;
 202     bool                    doFreeEnergyPerturbation = false;
 203     int                     force_flags;
 204     tensor                  force_vir, shake_vir, total_vir, pres;
 205     t_trxstatus            *status;
 206     rvec                    mu_tot;
 207     t_trxframe              rerun_fr;
 208     gmx_localtop_t          top;
 209     t_mdebin               *mdebin   = nullptr;
 210     gmx_enerdata_t         *enerd;
 211     PaddedVector<gmx::RVec> f {};
 212     gmx_global_stat_t       gstat;
 213     t_graph                *graph = nullptr;
 214     gmx_groups_t           *groups;
 215     gmx_shellfc_t          *shellfc;
 216
 217     double                  cycles;
 218
 219     /* Domain decomposition could incorrectly miss a bonded
 220        interaction, but checking for that requires a global
 221        communication stage, which does not otherwise happen in DD
 222        code. So we do that alongside the first global energy reduction
 223        after a new DD is made. These variables handle whether the
 224        check happens, and the result it returns. */
 225     bool              shouldCheckNumberOfBondedInteractions = false;
 226     int               totalNumberOfBondedInteractions       = -1;
 227
 228     SimulationSignals signals;
 229     // Most global communnication stages don't propagate mdrun
 230     // signals, and will use this object to achieve that.
 231     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 232
 233     GMX_LOG(mdlog.info).asParagraph().
 234         appendText("Note that it is planned that the command gmx mdrun -rerun will "
 235                    "be available in a different form in a future version of GROMACS, "
 236                    "e.g. gmx rerun -f.");
 237
 238     if (ir->bExpanded)
 239     {
 240         gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
 241     }
 242     if (ir->bSimTemp)
 243     {
 244         gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
 245     }
 246     if (ir->bDoAwh)
 247     {
 248         gmx_fatal(FARGS, "AWH not supported by rerun.");
 249     }
 250     if (replExParams.exchangeInterval > 0)
 251     {
 252         gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
 253     }
 254     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 255     {
 256         gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
 257     }
 258     if (ir->bIMD)
 259     {
 260         gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
 261     }
 262     if (isMultiSim(ms))
 263     {
 264         gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
 265     }
 266     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
 267                     [](int i){return i != eannNO; }))
 268     {
 269         gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
 270     }
 271
 272     /* Rerun can't work if an output file name is the same as the input file name.
 273      * If this is the case, the user will get an error telling them what the issue is.
 274      */
 275     if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0 ||
 276         strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
 277     {
 278         gmx_fatal(FARGS, "When using mdrun -rerun, the name of the input trajectory file "
 279                   "%s cannot be identical to the name of an output file (whether "
 280                   "given explicitly with -o or -x, or by default)",
 281                   opt2fn("-rerun", nfile, fnm));
 282     }
 283
 284     /* Settings for rerun */
 285     ir->nstlist       = 1;
 286     ir->nstcalcenergy = 1;
 287     int        nstglobalcomm = 1;
 288     const bool bNS           = true;
 289
 290     ir->nstxout_compressed = 0;
 291     groups                 = &top_global->groups;
 292     if (ir->eI == eiMimic)
 293     {
 294         top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 295     }
 296
 297     /* Initial values */
 298     init_rerun(fplog, cr, outputProvider, ir, oenv, mdrunOptions,
 299                state_global, lam0, nrnb, top_global,
 300                nfile, fnm, &outf, &mdebin, wcycle);
 301
 302     /* Energy terms and groups */
 303     snew(enerd, 1);
 304     init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
 305                   enerd);
 306
 307     /* Kinetic energy data */
 308     std::unique_ptr<gmx_ekindata_t> eKinData = compat::make_unique<gmx_ekindata_t>();
 309     gmx_ekindata_t                 *ekind    = eKinData.get();
 310     init_ekindata(fplog, top_global, &(ir->opts), ekind);
 311     /* Copy the cos acceleration to the groups struct */
 312     ekind->cosacc.cos_accel = ir->cos_accel;
 313
 314     gstat = global_stat_init(ir);
 315
 316     /* Check for polarizable models and flexible constraints */
 317     shellfc = init_shell_flexcon(fplog,
 318                                  top_global, constr ? constr->numFlexibleConstraints() : 0,
 319                                  ir->nstcalcenergy, DOMAINDECOMP(cr));
 320
 321     {
 322         double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
 323         if ((io > 2000) && MASTER(cr))
 324         {
 325             fprintf(stderr,
 326                     "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
 327                     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         dd_init_local_top(*top_global, &top);
 338
 339         stateInstance = compat::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, mdlog, ir->init_step, cr, TRUE, 1,
 345                             state_global, *top_global, ir,
 346                             state, &f, mdAtoms, &top, fr,
 347                             vsite, constr,
 348                             nrnb, nullptr, FALSE);
 349         shouldCheckNumberOfBondedInteractions = true;
 350     }
 351     else
 352     {
 353         state_change_natoms(state_global, state_global->natoms);
 354         /* We need to allocate one element extra, since we might use
 355          * (unaligned) 4-wide SIMD loads to access rvec entries.
 356          */
 357         f.resizeWithPadding(state_global->natoms);
 358         /* Copy the pointer to the global state */
 359         state = state_global;
 360
 361         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
 362                                   &graph, mdAtoms, constr, vsite, shellfc);
 363     }
 364
 365     auto mdatoms = mdAtoms->mdatoms();
 366
 367     // NOTE: The global state is no longer used at this point.
 368     // But state_global is still used as temporary storage space for writing
 369     // the global state to file and potentially for replica exchange.
 370     // (Global topology should persist.)
 371
 372     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 373
 374     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 375     {
 376         doFreeEnergyPerturbation = true;
 377     }
 378
 379     {
 380         int    cglo_flags = (CGLO_INITIALIZATION | CGLO_GSTAT |
 381                              (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 382         bool   bSumEkinhOld = false;
 383         t_vcm *vcm          = nullptr;
 384         compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 385                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
 386                         constr, &nullSignaller, state->box,
 387                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 388     }
 389     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 390                                     top_global, &top, state,
 391                                     &shouldCheckNumberOfBondedInteractions);
 392
 393     if (MASTER(cr))
 394     {
 395         fprintf(stderr, "starting md rerun '%s', reading coordinates from"
 396                 " input trajectory '%s'\n\n",
 397                 *(top_global->name), opt2fn("-rerun", nfile, fnm));
 398         if (mdrunOptions.verbose)
 399         {
 400             fprintf(stderr, "Calculated time to finish depends on nsteps from "
 401                     "run input file,\nwhich may not correspond to the time "
 402                     "needed to process input trajectory.\n\n");
 403         }
 404         fprintf(fplog, "\n");
 405     }
 406
 407     walltime_accounting_start_time(walltime_accounting);
 408     wallcycle_start(wcycle, ewcRUN);
 409     print_start(fplog, cr, walltime_accounting, "mdrun");
 410
 411     /***********************************************************
 412      *
 413      *             Loop over MD steps
 414      *
 415      ************************************************************/
 416
 417     if (constr)
 418     {
 419         GMX_LOG(mdlog.info).asParagraph().
 420             appendText("Simulations has constraints. Rerun does not recalculate constraints.");
 421     }
 422
 423     rerun_fr.natoms = 0;
 424     if (MASTER(cr))
 425     {
 426         isLastStep = !read_first_frame(oenv, &status,
 427                                        opt2fn("-rerun", nfile, fnm),
 428                                        &rerun_fr, TRX_NEED_X);
 429         if (rerun_fr.natoms != top_global->natoms)
 430         {
 431             gmx_fatal(FARGS,
 432                       "Number of atoms in trajectory (%d) does not match the "
 433                       "run input file (%d)\n",
 434                       rerun_fr.natoms, top_global->natoms);
 435         }
 436
 437         if (ir->ePBC != epbcNONE)
 438         {
 439             if (!rerun_fr.bBox)
 440             {
 441                 gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
 442                           "does not contain a box, while pbc is used",
 443                           rerun_fr.step, rerun_fr.time);
 444             }
 445             if (max_cutoff2(ir->ePBC, rerun_fr.box) < gmx::square(fr->rlist))
 446             {
 447                 gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
 448                           "has too small box dimensions", rerun_fr.step, rerun_fr.time);
 449             }
 450         }
 451     }
 452
 453     GMX_LOG(mdlog.info).asParagraph().
 454         appendText("Rerun does not report kinetic energy, total energy, temperature, virial and pressure.");
 455
 456     if (PAR(cr))
 457     {
 458         rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 459     }
 460
 461     if (ir->ePBC != epbcNONE)
 462     {
 463         /* Set the shift vectors.
 464          * Necessary here when have a static box different from the tpr box.
 465          */
 466         calc_shifts(rerun_fr.box, fr->shift_vec);
 467     }
 468
 469     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 470                 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
 471                 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
 472                 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 473
 474     // we don't do counter resetting in rerun - finish will always be valid
 475     walltime_accounting_set_valid_finish(walltime_accounting);
 476
 477     DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion   = (DOMAINDECOMP(cr) ? DdOpenBalanceRegionBeforeForceComputation::yes : DdOpenBalanceRegionBeforeForceComputation::no);
 478     DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion  = (DOMAINDECOMP(cr) ? DdCloseBalanceRegionAfterForceComputation::yes : DdCloseBalanceRegionAfterForceComputation::no);
 479
 480     step     = ir->init_step;
 481     step_rel = 0;
 482
 483     /* and stop now if we should */
 484     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 485     while (!isLastStep)
 486     {
 487         wallcycle_start(wcycle, ewcSTEP);
 488
 489         if (rerun_fr.bStep)
 490         {
 491             step     = rerun_fr.step;
 492             step_rel = step - ir->init_step;
 493         }
 494         if (rerun_fr.bTime)
 495         {
 496             t = rerun_fr.time;
 497         }
 498         else
 499         {
 500             t = step;
 501         }
 502
 503         if (ir->efep != efepNO && MASTER(cr))
 504         {
 505             setCurrentLambdasRerun(step, ir->fepvals, &rerun_fr, lam0, state_global);
 506         }
 507
 508         if (MASTER(cr))
 509         {
 510             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 511             if (constructVsites && DOMAINDECOMP(cr))
 512             {
 513                 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
 514                           "use a single rank");
 515             }
 516             prepareRerunState(rerun_fr, state_global, constructVsites, vsite, top.idef, ir->delta_t, *fr, graph);
 517         }
 518
 519         isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
 520
 521         if (DOMAINDECOMP(cr))
 522         {
 523             /* Repartition the domain decomposition */
 524             const bool bMasterState = true;
 525             dd_partition_system(fplog, mdlog, step, cr,
 526                                 bMasterState, nstglobalcomm,
 527                                 state_global, *top_global, ir,
 528                                 state, &f, mdAtoms, &top, fr,
 529                                 vsite, constr,
 530                                 nrnb, wcycle,
 531                                 mdrunOptions.verbose);
 532             shouldCheckNumberOfBondedInteractions = true;
 533         }
 534
 535         if (MASTER(cr))
 536         {
 537             print_ebin_header(fplog, step, t); /* can we improve the information printed here? */
 538         }
 539
 540         if (ir->efep != efepNO)
 541         {
 542             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 543         }
 544
 545         force_flags = (GMX_FORCE_STATECHANGED |
 546                        GMX_FORCE_DYNAMICBOX |
 547                        GMX_FORCE_ALLFORCES |
 548                        (GMX_GPU ? GMX_FORCE_VIRIAL : 0) |  // TODO: Get rid of this once #2649 is solved
 549                        GMX_FORCE_ENERGY |
 550                        (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 551
 552         if (shellfc)
 553         {
 554             /* Now is the time to relax the shells */
 555             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
 556                                 enforcedRotation, step,
 557                                 ir, bNS, force_flags, &top,
 558                                 constr, enerd, fcd,
 559                                 state, f.arrayRefWithPadding(), force_vir, mdatoms,
 560                                 nrnb, wcycle, graph, groups,
 561                                 shellfc, fr, ppForceWorkload, t, mu_tot,
 562                                 vsite,
 563                                 ddOpenBalanceRegion, ddCloseBalanceRegion);
 564         }
 565         else
 566         {
 567             /* The coordinates (x) are shifted (to get whole molecules)
 568              * in do_force.
 569              * This is parallellized as well, and does communication too.
 570              * Check comments in sim_util.c
 571              */
 572             Awh       *awh = nullptr;
 573             gmx_edsam *ed  = nullptr;
 574             do_force(fplog, cr, ms, ir, awh, enforcedRotation,
 575                      step, nrnb, wcycle, &top, groups,
 576                      state->box, state->x.arrayRefWithPadding(), &state->hist,
 577                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
 578                      state->lambda, graph,
 579                      fr, ppForceWorkload, vsite, mu_tot, t, ed,
 580                      GMX_FORCE_NS | force_flags,
 581                      ddOpenBalanceRegion, ddCloseBalanceRegion);
 582         }
 583
 584         /* Now we have the energies and forces corresponding to the
 585          * coordinates at time t.
 586          */
 587         {
 588             const bool isCheckpointingStep = false;
 589             const bool doRerun             = true;
 590             const bool bSumEkinhOld        = false;
 591             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
 592                                      ir, state, state_global, observablesHistory,
 593                                      top_global, fr,
 594                                      outf, mdebin, ekind, f,
 595                                      isCheckpointingStep, doRerun, isLastStep,
 596                                      mdrunOptions.writeConfout,
 597                                      bSumEkinhOld);
 598         }
 599
 600         stopHandler->setSignal();
 601
 602         if (graph)
 603         {
 604             /* Need to unshift here */
 605             unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 606         }
 607
 608         if (vsite != nullptr)
 609         {
 610             wallcycle_start(wcycle, ewcVSITECONSTR);
 611             if (graph != nullptr)
 612             {
 613                 shift_self(graph, state->box, as_rvec_array(state->x.data()));
 614             }
 615             construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
 616                              top.idef.iparams, top.idef.il,
 617                              fr->ePBC, fr->bMolPBC, cr, state->box);
 618
 619             if (graph != nullptr)
 620             {
 621                 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 622             }
 623             wallcycle_stop(wcycle, ewcVSITECONSTR);
 624         }
 625
 626         {
 627             const bool          doInterSimSignal = false;
 628             const bool          doIntraSimSignal = true;
 629             bool                bSumEkinhOld     = false;
 630             t_vcm              *vcm              = nullptr;
 631             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 632
 633             compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 634                             wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
 635                             constr, &signaller,
 636                             state->box,
 637                             &totalNumberOfBondedInteractions, &bSumEkinhOld,
 638                             CGLO_GSTAT | CGLO_ENERGY
 639                             | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
 640                             );
 641             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 642                                             top_global, &top, state,
 643                                             &shouldCheckNumberOfBondedInteractions);
 644         }
 645
 646         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 647            the virial that should probably be addressed eventually. state->veta has better properies,
 648            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 649            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 650
 651         if (ir->efep != efepNO)
 652         {
 653             /* Sum up the foreign energy and dhdl terms for md and sd.
 654                Currently done every step so that dhdl is correct in the .edr */
 655             sum_dhdl(enerd, state->lambda, ir->fepvals);
 656         }
 657
 658         /* Output stuff */
 659         if (MASTER(cr))
 660         {
 661             const bool bCalcEnerStep = true;
 662             upd_mdebin(mdebin, doFreeEnergyPerturbation, bCalcEnerStep,
 663                        t, mdatoms->tmass, enerd, state,
 664                        ir->fepvals, ir->expandedvals, rerun_fr.box,
 665                        shake_vir, force_vir, total_vir, pres,
 666                        ekind, mu_tot, constr);
 667
 668             const bool do_ene = true;
 669             const bool do_log = true;
 670             Awh       *awh    = nullptr;
 671             const bool do_dr  = ir->nstdisreout != 0;
 672             const bool do_or  = ir->nstorireout != 0;
 673
 674             print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : nullptr,
 675                        step, t,
 676                        eprNORMAL, mdebin, fcd, groups, &(ir->opts), awh);
 677
 678             if (do_per_step(step, ir->nstlog))
 679             {
 680                 if (fflush(fplog) != 0)
 681                 {
 682                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 683                 }
 684             }
 685         }
 686
 687         /* Print the remaining wall clock time for the run */
 688         if (isMasterSimMasterRank(ms, cr) &&
 689             (mdrunOptions.verbose || gmx_got_usr_signal()))
 690         {
 691             if (shellfc)
 692             {
 693                 fprintf(stderr, "\n");
 694             }
 695             print_time(stderr, walltime_accounting, step, ir, cr);
 696         }
 697
 698         /* Ion/water position swapping.
 699          * Not done in last step since trajectory writing happens before this call
 700          * in the MD loop and exchanges would be lost anyway. */
 701         if ((ir->eSwapCoords != eswapNO) && (step > 0) && !isLastStep &&
 702             do_per_step(step, ir->swap->nstswap))
 703         {
 704             const bool doRerun = true;
 705             do_swapcoords(cr, step, t, ir, wcycle,
 706                           rerun_fr.x,
 707                           rerun_fr.box,
 708                           MASTER(cr) && mdrunOptions.verbose,
 709                           doRerun);
 710         }
 711
 712         if (MASTER(cr))
 713         {
 714             /* read next frame from input trajectory */
 715             isLastStep = !read_next_frame(oenv, status, &rerun_fr);
 716         }
 717
 718         if (PAR(cr))
 719         {
 720             rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 721         }
 722
 723         cycles = wallcycle_stop(wcycle, ewcSTEP);
 724         if (DOMAINDECOMP(cr) && wcycle)
 725         {
 726             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 727         }
 728
 729         if (!rerun_fr.bStep)
 730         {
 731             /* increase the MD step number */
 732             step++;
 733             step_rel++;
 734         }
 735     }
 736     /* End of main MD loop */
 737
 738     /* Closing TNG files can include compressing data. Therefore it is good to do that
 739      * before stopping the time measurements. */
 740     mdoutf_tng_close(outf);
 741
 742     /* Stop measuring walltime */
 743     walltime_accounting_end_time(walltime_accounting);
 744
 745     if (MASTER(cr))
 746     {
 747         close_trx(status);
 748     }
 749
 750     if (!thisRankHasDuty(cr, DUTY_PME))
 751     {
 752         /* Tell the PME only node to finish */
 753         gmx_pme_send_finish(cr);
 754     }
 755
 756     done_mdebin(mdebin);
 757     done_mdoutf(outf);
 758
 759     done_shellfc(fplog, shellfc, step_rel);
 760
 761     // Clean up swapcoords
 762     if (ir->eSwapCoords != eswapNO)
 763     {
 764         finish_swapcoords(ir->swap);
 765     }
 766
 767     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 768
 769     destroy_enerdata(enerd);
 770     sfree(enerd);
 771 }