src/gromacs/mdrun/rerun.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
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   4  * Copyright (c) 2018, by the GROMACS development team, led by
   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_ekindata_t         *ekind;
 216     gmx_shellfc_t          *shellfc;
 217
 218     double                  cycles;
 219
 220     /* Domain decomposition could incorrectly miss a bonded
 221        interaction, but checking for that requires a global
 222        communication stage, which does not otherwise happen in DD
 223        code. So we do that alongside the first global energy reduction
 224        after a new DD is made. These variables handle whether the
 225        check happens, and the result it returns. */
 226     bool              shouldCheckNumberOfBondedInteractions = false;
 227     int               totalNumberOfBondedInteractions       = -1;
 228
 229     SimulationSignals signals;
 230     // Most global communnication stages don't propagate mdrun
 231     // signals, and will use this object to achieve that.
 232     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 233
 234     GMX_LOG(mdlog.info).asParagraph().
 235         appendText("Note that it is planned that the command gmx mdrun -rerun will "
 236                    "be available in a different form in a future version of GROMACS, "
 237                    "e.g. gmx rerun -f.");
 238
 239     if (ir->bExpanded)
 240     {
 241         gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
 242     }
 243     if (ir->bSimTemp)
 244     {
 245         gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
 246     }
 247     if (ir->bDoAwh)
 248     {
 249         gmx_fatal(FARGS, "AWH not supported by rerun.");
 250     }
 251     if (replExParams.exchangeInterval > 0)
 252     {
 253         gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
 254     }
 255     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 256     {
 257         gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
 258     }
 259     if (ir->bIMD)
 260     {
 261         gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
 262     }
 263     if (isMultiSim(ms))
 264     {
 265         gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
 266     }
 267     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
 268                     [](int i){return i != eannNO; }))
 269     {
 270         gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
 271     }
 272
 273     /* Rerun can't work if an output file name is the same as the input file name.
 274      * If this is the case, the user will get an error telling them what the issue is.
 275      */
 276     if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0 ||
 277         strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
 278     {
 279         gmx_fatal(FARGS, "When using mdrun -rerun, the name of the input trajectory file "
 280                   "%s cannot be identical to the name of an output file (whether "
 281                   "given explicitly with -o or -x, or by default)",
 282                   opt2fn("-rerun", nfile, fnm));
 283     }
 284
 285     /* Settings for rerun */
 286     ir->nstlist       = 1;
 287     ir->nstcalcenergy = 1;
 288     int        nstglobalcomm = 1;
 289     const bool bNS           = true;
 290
 291     ir->nstxout_compressed = 0;
 292     groups                 = &top_global->groups;
 293     if (ir->eI == eiMimic)
 294     {
 295         top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 296     }
 297
 298     /* Initial values */
 299     init_rerun(fplog, cr, outputProvider, ir, oenv, mdrunOptions,
 300                state_global, lam0, nrnb, top_global,
 301                nfile, fnm, &outf, &mdebin, wcycle);
 302
 303     /* Energy terms and groups */
 304     snew(enerd, 1);
 305     init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
 306                   enerd);
 307
 308     /* Kinetic energy data */
 309     snew(ekind, 1);
 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         top = dd_init_local_top(top_global);
 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         snew(top, 1);
 362         mdAlgorithmsSetupAtomData(cr, ir, top_global, top, fr,
 363                                   &graph, mdAtoms, constr, vsite, shellfc);
 364     }
 365
 366     auto mdatoms = mdAtoms->mdatoms();
 367
 368     // NOTE: The global state is no longer used at this point.
 369     // But state_global is still used as temporary storage space for writing
 370     // the global state to file and potentially for replica exchange.
 371     // (Global topology should persist.)
 372
 373     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 374
 375     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 376     {
 377         doFreeEnergyPerturbation = true;
 378     }
 379
 380     {
 381         int    cglo_flags = (CGLO_INITIALIZATION | CGLO_GSTAT |
 382                              (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 383         bool   bSumEkinhOld = false;
 384         t_vcm *vcm          = nullptr;
 385         compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 386                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
 387                         constr, &nullSignaller, state->box,
 388                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 389     }
 390     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 391                                     top_global, top, state,
 392                                     &shouldCheckNumberOfBondedInteractions);
 393
 394     if (MASTER(cr))
 395     {
 396         fprintf(stderr, "starting md rerun '%s', reading coordinates from"
 397                 " input trajectory '%s'\n\n",
 398                 *(top_global->name), opt2fn("-rerun", nfile, fnm));
 399         if (mdrunOptions.verbose)
 400         {
 401             fprintf(stderr, "Calculated time to finish depends on nsteps from "
 402                     "run input file,\nwhich may not correspond to the time "
 403                     "needed to process input trajectory.\n\n");
 404         }
 405         fprintf(fplog, "\n");
 406     }
 407
 408     walltime_accounting_start_time(walltime_accounting);
 409     wallcycle_start(wcycle, ewcRUN);
 410     print_start(fplog, cr, walltime_accounting, "mdrun");
 411
 412     /***********************************************************
 413      *
 414      *             Loop over MD steps
 415      *
 416      ************************************************************/
 417
 418     if (constr)
 419     {
 420         GMX_LOG(mdlog.info).asParagraph().
 421             appendText("Simulations has constraints. Rerun does not recalculate constraints.");
 422     }
 423
 424     rerun_fr.natoms = 0;
 425     if (MASTER(cr))
 426     {
 427         isLastStep = !read_first_frame(oenv, &status,
 428                                        opt2fn("-rerun", nfile, fnm),
 429                                        &rerun_fr, TRX_NEED_X);
 430         if (rerun_fr.natoms != top_global->natoms)
 431         {
 432             gmx_fatal(FARGS,
 433                       "Number of atoms in trajectory (%d) does not match the "
 434                       "run input file (%d)\n",
 435                       rerun_fr.natoms, top_global->natoms);
 436         }
 437
 438         if (ir->ePBC != epbcNONE)
 439         {
 440             if (!rerun_fr.bBox)
 441             {
 442                 gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
 443                           "does not contain a box, while pbc is used",
 444                           rerun_fr.step, rerun_fr.time);
 445             }
 446             if (max_cutoff2(ir->ePBC, rerun_fr.box) < gmx::square(fr->rlist))
 447             {
 448                 gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
 449                           "has too small box dimensions", rerun_fr.step, rerun_fr.time);
 450             }
 451         }
 452     }
 453
 454     GMX_LOG(mdlog.info).asParagraph().
 455         appendText("Rerun does not report kinetic energy, total energy, temperature, virial and pressure.");
 456
 457     if (PAR(cr))
 458     {
 459         rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 460     }
 461
 462     if (ir->ePBC != epbcNONE)
 463     {
 464         /* Set the shift vectors.
 465          * Necessary here when have a static box different from the tpr box.
 466          */
 467         calc_shifts(rerun_fr.box, fr->shift_vec);
 468     }
 469
 470     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 471                 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
 472                 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
 473                 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 474
 475     // we don't do counter resetting in rerun - finish will always be valid
 476     walltime_accounting_set_valid_finish(walltime_accounting);
 477
 478     DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion   = (DOMAINDECOMP(cr) ? DdOpenBalanceRegionBeforeForceComputation::yes : DdOpenBalanceRegionBeforeForceComputation::no);
 479     DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion  = (DOMAINDECOMP(cr) ? DdCloseBalanceRegionAfterForceComputation::yes : DdCloseBalanceRegionAfterForceComputation::no);
 480
 481     step     = ir->init_step;
 482     step_rel = 0;
 483
 484     /* and stop now if we should */
 485     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 486     while (!isLastStep)
 487     {
 488         wallcycle_start(wcycle, ewcSTEP);
 489
 490         if (rerun_fr.bStep)
 491         {
 492             step     = rerun_fr.step;
 493             step_rel = step - ir->init_step;
 494         }
 495         if (rerun_fr.bTime)
 496         {
 497             t = rerun_fr.time;
 498         }
 499         else
 500         {
 501             t = step;
 502         }
 503
 504         if (ir->efep != efepNO && MASTER(cr))
 505         {
 506             setCurrentLambdasRerun(step, ir->fepvals, &rerun_fr, lam0, state_global);
 507         }
 508
 509         if (MASTER(cr))
 510         {
 511             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 512             if (constructVsites && DOMAINDECOMP(cr))
 513             {
 514                 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
 515                           "use a single rank");
 516             }
 517             prepareRerunState(rerun_fr, state_global, constructVsites, vsite, top->idef, ir->delta_t, *fr, graph);
 518         }
 519
 520         isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
 521
 522         if (DOMAINDECOMP(cr))
 523         {
 524             /* Repartition the domain decomposition */
 525             const bool bMasterState = true;
 526             dd_partition_system(fplog, mdlog, step, cr,
 527                                 bMasterState, nstglobalcomm,
 528                                 state_global, top_global, ir,
 529                                 state, &f, mdAtoms, top, fr,
 530                                 vsite, constr,
 531                                 nrnb, wcycle,
 532                                 mdrunOptions.verbose);
 533             shouldCheckNumberOfBondedInteractions = true;
 534         }
 535
 536         if (MASTER(cr))
 537         {
 538             print_ebin_header(fplog, step, t); /* can we improve the information printed here? */
 539         }
 540
 541         if (ir->efep != efepNO)
 542         {
 543             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 544         }
 545
 546         force_flags = (GMX_FORCE_STATECHANGED |
 547                        GMX_FORCE_DYNAMICBOX |
 548                        GMX_FORCE_ALLFORCES |
 549                        (GMX_GPU ? GMX_FORCE_VIRIAL : 0) |  // TODO: Get rid of this once #2649 is solved
 550                        GMX_FORCE_ENERGY |
 551                        (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 552
 553         if (shellfc)
 554         {
 555             /* Now is the time to relax the shells */
 556             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
 557                                 enforcedRotation, step,
 558                                 ir, bNS, force_flags, top,
 559                                 constr, enerd, fcd,
 560                                 state, f.arrayRefWithPadding(), force_vir, mdatoms,
 561                                 nrnb, wcycle, graph, groups,
 562                                 shellfc, fr, ppForceWorkload, t, mu_tot,
 563                                 vsite,
 564                                 ddOpenBalanceRegion, ddCloseBalanceRegion);
 565         }
 566         else
 567         {
 568             /* The coordinates (x) are shifted (to get whole molecules)
 569              * in do_force.
 570              * This is parallellized as well, and does communication too.
 571              * Check comments in sim_util.c
 572              */
 573             Awh       *awh = nullptr;
 574             gmx_edsam *ed  = nullptr;
 575             do_force(fplog, cr, ms, ir, awh, enforcedRotation,
 576                      step, nrnb, wcycle, top, groups,
 577                      state->box, state->x.arrayRefWithPadding(), &state->hist,
 578                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
 579                      state->lambda, graph,
 580                      fr, ppForceWorkload, vsite, mu_tot, t, ed,
 581                      GMX_FORCE_NS | force_flags,
 582                      ddOpenBalanceRegion, ddCloseBalanceRegion);
 583         }
 584
 585         /* Now we have the energies and forces corresponding to the
 586          * coordinates at time t.
 587          */
 588         {
 589             const bool isCheckpointingStep = false;
 590             const bool doRerun             = true;
 591             const bool bSumEkinhOld        = false;
 592             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
 593                                      ir, state, state_global, observablesHistory,
 594                                      top_global, fr,
 595                                      outf, mdebin, ekind, f,
 596                                      isCheckpointingStep, doRerun, isLastStep,
 597                                      mdrunOptions.writeConfout,
 598                                      bSumEkinhOld);
 599         }
 600
 601         stopHandler->setSignal();
 602
 603         if (graph)
 604         {
 605             /* Need to unshift here */
 606             unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 607         }
 608
 609         if (vsite != nullptr)
 610         {
 611             wallcycle_start(wcycle, ewcVSITECONSTR);
 612             if (graph != nullptr)
 613             {
 614                 shift_self(graph, state->box, as_rvec_array(state->x.data()));
 615             }
 616             construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
 617                              top->idef.iparams, top->idef.il,
 618                              fr->ePBC, fr->bMolPBC, cr, state->box);
 619
 620             if (graph != nullptr)
 621             {
 622                 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 623             }
 624             wallcycle_stop(wcycle, ewcVSITECONSTR);
 625         }
 626
 627         {
 628             const bool          doInterSimSignal = false;
 629             const bool          doIntraSimSignal = true;
 630             bool                bSumEkinhOld     = false;
 631             t_vcm              *vcm              = nullptr;
 632             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 633
 634             compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 635                             wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
 636                             constr, &signaller,
 637                             state->box,
 638                             &totalNumberOfBondedInteractions, &bSumEkinhOld,
 639                             CGLO_GSTAT | CGLO_ENERGY
 640                             | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
 641                             );
 642             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 643                                             top_global, top, state,
 644                                             &shouldCheckNumberOfBondedInteractions);
 645         }
 646
 647         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 648            the virial that should probably be addressed eventually. state->veta has better properies,
 649            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 650            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 651
 652         if (ir->efep != efepNO)
 653         {
 654             /* Sum up the foreign energy and dhdl terms for md and sd.
 655                Currently done every step so that dhdl is correct in the .edr */
 656             sum_dhdl(enerd, state->lambda, ir->fepvals);
 657         }
 658
 659         /* Output stuff */
 660         if (MASTER(cr))
 661         {
 662             const bool bCalcEnerStep = true;
 663             upd_mdebin(mdebin, doFreeEnergyPerturbation, bCalcEnerStep,
 664                        t, mdatoms->tmass, enerd, state,
 665                        ir->fepvals, ir->expandedvals, rerun_fr.box,
 666                        shake_vir, force_vir, total_vir, pres,
 667                        ekind, mu_tot, constr);
 668
 669             const bool do_ene = true;
 670             const bool do_log = true;
 671             Awh       *awh    = nullptr;
 672             const bool do_dr  = ir->nstdisreout != 0;
 673             const bool do_or  = ir->nstorireout != 0;
 674
 675             print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : nullptr,
 676                        step, t,
 677                        eprNORMAL, mdebin, fcd, groups, &(ir->opts), awh);
 678
 679             if (do_per_step(step, ir->nstlog))
 680             {
 681                 if (fflush(fplog) != 0)
 682                 {
 683                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 684                 }
 685             }
 686         }
 687
 688         /* Print the remaining wall clock time for the run */
 689         if (isMasterSimMasterRank(ms, cr) &&
 690             (mdrunOptions.verbose || gmx_got_usr_signal()))
 691         {
 692             if (shellfc)
 693             {
 694                 fprintf(stderr, "\n");
 695             }
 696             print_time(stderr, walltime_accounting, step, ir, cr);
 697         }
 698
 699         /* Ion/water position swapping.
 700          * Not done in last step since trajectory writing happens before this call
 701          * in the MD loop and exchanges would be lost anyway. */
 702         if ((ir->eSwapCoords != eswapNO) && (step > 0) && !isLastStep &&
 703             do_per_step(step, ir->swap->nstswap))
 704         {
 705             const bool doRerun = true;
 706             do_swapcoords(cr, step, t, ir, wcycle,
 707                           rerun_fr.x,
 708                           rerun_fr.box,
 709                           MASTER(cr) && mdrunOptions.verbose,
 710                           doRerun);
 711         }
 712
 713         if (MASTER(cr))
 714         {
 715             /* read next frame from input trajectory */
 716             isLastStep = !read_next_frame(oenv, status, &rerun_fr);
 717         }
 718
 719         if (PAR(cr))
 720         {
 721             rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
 722         }
 723
 724         cycles = wallcycle_stop(wcycle, ewcSTEP);
 725         if (DOMAINDECOMP(cr) && wcycle)
 726         {
 727             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 728         }
 729
 730         if (!rerun_fr.bStep)
 731         {
 732             /* increase the MD step number */
 733             step++;
 734             step_rel++;
 735         }
 736     }
 737     /* End of main MD loop */
 738
 739     /* Closing TNG files can include compressing data. Therefore it is good to do that
 740      * before stopping the time measurements. */
 741     mdoutf_tng_close(outf);
 742
 743     /* Stop measuring walltime */
 744     walltime_accounting_end_time(walltime_accounting);
 745
 746     if (MASTER(cr))
 747     {
 748         close_trx(status);
 749     }
 750
 751     if (!thisRankHasDuty(cr, DUTY_PME))
 752     {
 753         /* Tell the PME only node to finish */
 754         gmx_pme_send_finish(cr);
 755     }
 756
 757     done_mdebin(mdebin);
 758     done_mdoutf(outf);
 759
 760     done_shellfc(fplog, shellfc, step_rel);
 761
 762     // Clean up swapcoords
 763     if (ir->eSwapCoords != eswapNO)
 764     {
 765         finish_swapcoords(ir->swap);
 766     }
 767
 768     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 769
 770     destroy_enerdata(enerd);
 771     sfree(enerd);
 772     sfree(top);
 773 }