src/gromacs/mdrun/mimic.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018,2019, 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,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35
  36 /*! \internal \file
  37  *
  38  * \brief Declares the loop for MiMiC QM/MM
  39  *
  40  * \author Viacheslav Bolnykh <v.bolnykh@hpc-leap.eu>
  41  * \ingroup module_mdrun
  42  */
  43 #include "gmxpre.h"
  44
  45 #include <cinttypes>
  46 #include <cmath>
  47 #include <cstdio>
  48 #include <cstdlib>
  49
  50 #include <algorithm>
  51 #include <memory>
  52
  53 #include "gromacs/awh/awh.h"
  54 #include "gromacs/commandline/filenm.h"
  55 #include "gromacs/domdec/collect.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/partition.h"
  60 #include "gromacs/essentialdynamics/edsam.h"
  61 #include "gromacs/ewald/pme.h"
  62 #include "gromacs/ewald/pme_load_balancing.h"
  63 #include "gromacs/fileio/trxio.h"
  64 #include "gromacs/gmxlib/network.h"
  65 #include "gromacs/gmxlib/nrnb.h"
  66 #include "gromacs/gpu_utils/gpu_utils.h"
  67 #include "gromacs/imd/imd.h"
  68 #include "gromacs/listed_forces/manage_threading.h"
  69 #include "gromacs/math/functions.h"
  70 #include "gromacs/math/utilities.h"
  71 #include "gromacs/math/vec.h"
  72 #include "gromacs/math/vectypes.h"
  73 #include "gromacs/mdlib/checkpointhandler.h"
  74 #include "gromacs/mdlib/compute_io.h"
  75 #include "gromacs/mdlib/constr.h"
  76 #include "gromacs/mdlib/ebin.h"
  77 #include "gromacs/mdlib/energyoutput.h"
  78 #include "gromacs/mdlib/expanded.h"
  79 #include "gromacs/mdlib/force.h"
  80 #include "gromacs/mdlib/force_flags.h"
  81 #include "gromacs/mdlib/forcerec.h"
  82 #include "gromacs/mdlib/md_support.h"
  83 #include "gromacs/mdlib/mdatoms.h"
  84 #include "gromacs/mdlib/mdoutf.h"
  85 #include "gromacs/mdlib/mdrun.h"
  86 #include "gromacs/mdlib/mdsetup.h"
  87 #include "gromacs/mdlib/membed.h"
  88 #include "gromacs/mdlib/ns.h"
  89 #include "gromacs/mdlib/resethandler.h"
  90 #include "gromacs/mdlib/shellfc.h"
  91 #include "gromacs/mdlib/sighandler.h"
  92 #include "gromacs/mdlib/sim_util.h"
  93 #include "gromacs/mdlib/simulationsignal.h"
  94 #include "gromacs/mdlib/stophandler.h"
  95 #include "gromacs/mdlib/tgroup.h"
  96 #include "gromacs/mdlib/trajectory_writing.h"
  97 #include "gromacs/mdlib/update.h"
  98 #include "gromacs/mdlib/vcm.h"
  99 #include "gromacs/mdlib/vsite.h"
 100 #include "gromacs/mdtypes/awh_history.h"
 101 #include "gromacs/mdtypes/awh_params.h"
 102 #include "gromacs/mdtypes/commrec.h"
 103 #include "gromacs/mdtypes/df_history.h"
 104 #include "gromacs/mdtypes/enerdata.h"
 105 #include "gromacs/mdtypes/energyhistory.h"
 106 #include "gromacs/mdtypes/fcdata.h"
 107 #include "gromacs/mdtypes/forcerec.h"
 108 #include "gromacs/mdtypes/group.h"
 109 #include "gromacs/mdtypes/inputrec.h"
 110 #include "gromacs/mdtypes/interaction_const.h"
 111 #include "gromacs/mdtypes/md_enums.h"
 112 #include "gromacs/mdtypes/mdatom.h"
 113 #include "gromacs/mdtypes/observableshistory.h"
 114 #include "gromacs/mdtypes/state.h"
 115 #include "gromacs/mimic/MimicCommunicator.h"
 116 #include "gromacs/mimic/MimicUtils.h"
 117 #include "gromacs/pbcutil/mshift.h"
 118 #include "gromacs/pbcutil/pbc.h"
 119 #include "gromacs/pulling/pull.h"
 120 #include "gromacs/swap/swapcoords.h"
 121 #include "gromacs/timing/wallcycle.h"
 122 #include "gromacs/timing/walltime_accounting.h"
 123 #include "gromacs/topology/atoms.h"
 124 #include "gromacs/topology/idef.h"
 125 #include "gromacs/topology/mtop_util.h"
 126 #include "gromacs/topology/topology.h"
 127 #include "gromacs/trajectory/trajectoryframe.h"
 128 #include "gromacs/utility/basedefinitions.h"
 129 #include "gromacs/utility/cstringutil.h"
 130 #include "gromacs/utility/fatalerror.h"
 131 #include "gromacs/utility/logger.h"
 132 #include "gromacs/utility/real.h"
 133 #include "gromacs/utility/smalloc.h"
 134
 135 #include "integrator.h"
 136 #include "replicaexchange.h"
 137
 138 using gmx::SimulationSignaller;
 139
 140 void gmx::Integrator::do_mimic()
 141 {
 142     t_inputrec              *ir   = inputrec;
 143     int64_t                  step, step_rel;
 144     double                   t, lam0[efptNR];
 145     bool                     isLastStep               = false;
 146     bool                     doFreeEnergyPerturbation = false;
 147     int                      force_flags;
 148     tensor                   force_vir, shake_vir, total_vir, pres;
 149     rvec                     mu_tot;
 150     gmx_localtop_t           top;
 151     gmx_enerdata_t          *enerd;
 152     PaddedVector<gmx::RVec>  f {};
 153     gmx_global_stat_t        gstat;
 154     t_graph                 *graph = nullptr;
 155     gmx_groups_t            *groups;
 156     gmx_shellfc_t           *shellfc;
 157
 158     double                   cycles;
 159
 160     /* Domain decomposition could incorrectly miss a bonded
 161        interaction, but checking for that requires a global
 162        communication stage, which does not otherwise happen in DD
 163        code. So we do that alongside the first global energy reduction
 164        after a new DD is made. These variables handle whether the
 165        check happens, and the result it returns. */
 166     bool              shouldCheckNumberOfBondedInteractions = false;
 167     int               totalNumberOfBondedInteractions       = -1;
 168
 169     SimulationSignals signals;
 170     // Most global communnication stages don't propagate mdrun
 171     // signals, and will use this object to achieve that.
 172     SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
 173
 174     if (ir->bExpanded)
 175     {
 176         gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
 177     }
 178     if (ir->bSimTemp)
 179     {
 180         gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
 181     }
 182     if (ir->bDoAwh)
 183     {
 184         gmx_fatal(FARGS, "AWH not supported by MiMiC.");
 185     }
 186     if (replExParams.exchangeInterval > 0)
 187     {
 188         gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
 189     }
 190     if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
 191     {
 192         gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
 193     }
 194     if (ir->bIMD)
 195     {
 196         gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
 197     }
 198     if (isMultiSim(ms))
 199     {
 200         gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
 201     }
 202     if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
 203                     [](int i){return i != eannNO; }))
 204     {
 205         gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
 206     }
 207
 208     /* Settings for rerun */
 209     ir->nstlist       = 1;
 210     ir->nstcalcenergy = 1;
 211     int        nstglobalcomm = 1;
 212     const bool bNS           = true;
 213
 214     // Communicator to interact with MiMiC
 215     MimicCommunicator mimicCommunicator {};
 216     if (MASTER(cr))
 217     {
 218         mimicCommunicator.init();
 219         mimicCommunicator.sendInitData(top_global, state_global->x);
 220         ir->nsteps = mimicCommunicator.getStepNumber();
 221     }
 222
 223     ir->nstxout_compressed                   = 0;
 224     groups                                   = &top_global->groups;
 225     top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
 226
 227     initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
 228     init_nrnb(nrnb);
 229
 230     gmx_mdoutf       *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle);
 231     gmx::EnergyOutput energyOutput;
 232     energyOutput.prepare(mdoutf_get_fp_ene(outf), top_global, ir, mdoutf_get_fp_dhdl(outf), true);
 233
 234     /* Energy terms and groups */
 235     snew(enerd, 1);
 236     init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
 237                   enerd);
 238
 239     /* Kinetic energy data */
 240     std::unique_ptr<gmx_ekindata_t> eKinData = std::make_unique<gmx_ekindata_t>();
 241     gmx_ekindata_t                 *ekind    = eKinData.get();
 242     init_ekindata(fplog, top_global, &(ir->opts), ekind);
 243     /* Copy the cos acceleration to the groups struct */
 244     ekind->cosacc.cos_accel = ir->cos_accel;
 245
 246     gstat = global_stat_init(ir);
 247
 248     /* Check for polarizable models and flexible constraints */
 249     shellfc = init_shell_flexcon(fplog,
 250                                  top_global, constr ? constr->numFlexibleConstraints() : 0,
 251                                  ir->nstcalcenergy, DOMAINDECOMP(cr));
 252
 253     {
 254         double io = compute_io(ir, top_global->natoms, groups, energyOutput.numEnergyTerms(), 1);
 255         if ((io > 2000) && MASTER(cr))
 256         {
 257             fprintf(stderr,
 258                     "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
 259                     io);
 260         }
 261     }
 262
 263     // Local state only becomes valid now.
 264     std::unique_ptr<t_state> stateInstance;
 265     t_state *                state;
 266
 267     if (DOMAINDECOMP(cr))
 268     {
 269         dd_init_local_top(*top_global, &top);
 270
 271         stateInstance = std::make_unique<t_state>();
 272         state         = stateInstance.get();
 273         dd_init_local_state(cr->dd, state_global, state);
 274
 275         /* Distribute the charge groups over the nodes from the master node */
 276         dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
 277                             state_global, *top_global, ir,
 278                             state, &f, mdAtoms, &top, fr,
 279                             vsite, constr,
 280                             nrnb, nullptr, FALSE);
 281         shouldCheckNumberOfBondedInteractions = true;
 282         gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr);
 283     }
 284     else
 285     {
 286         state_change_natoms(state_global, state_global->natoms);
 287         /* We need to allocate one element extra, since we might use
 288          * (unaligned) 4-wide SIMD loads to access rvec entries.
 289          */
 290         f.resizeWithPadding(state_global->natoms);
 291         /* Copy the pointer to the global state */
 292         state = state_global;
 293
 294         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
 295                                   &graph, mdAtoms, constr, vsite, shellfc);
 296     }
 297
 298     auto mdatoms = mdAtoms->mdatoms();
 299
 300     // NOTE: The global state is no longer used at this point.
 301     // But state_global is still used as temporary storage space for writing
 302     // the global state to file and potentially for replica exchange.
 303     // (Global topology should persist.)
 304
 305     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 306
 307     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 308     {
 309         doFreeEnergyPerturbation = true;
 310     }
 311
 312     {
 313         int    cglo_flags = (CGLO_INITIALIZATION | CGLO_GSTAT |
 314                              (shouldCheckNumberOfBondedInteractions ?
 315                               CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 316         bool   bSumEkinhOld = false;
 317         t_vcm *vcm          = nullptr;
 318         compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 319                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
 320                         constr, &nullSignaller, state->box,
 321                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 322     }
 323     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 324                                     top_global, &top, state,
 325                                     &shouldCheckNumberOfBondedInteractions);
 326
 327     if (MASTER(cr))
 328     {
 329         fprintf(stderr, "starting MiMiC MD run '%s'\n\n",
 330                 *(top_global->name));
 331         if (mdrunOptions.verbose)
 332         {
 333             fprintf(stderr, "Calculated time to finish depends on nsteps from "
 334                     "run input file,\nwhich may not correspond to the time "
 335                     "needed to process input trajectory.\n\n");
 336         }
 337         fprintf(fplog, "\n");
 338     }
 339
 340     walltime_accounting_start_time(walltime_accounting);
 341     wallcycle_start(wcycle, ewcRUN);
 342     print_start(fplog, cr, walltime_accounting, "mdrun");
 343
 344     /***********************************************************
 345      *
 346      *             Loop over MD steps
 347      *
 348      ************************************************************/
 349
 350     if (constr)
 351     {
 352         GMX_LOG(mdlog.info).asParagraph().
 353             appendText("Simulations has constraints. Constraints will "
 354                        "be handled by CPMD.");
 355     }
 356
 357     GMX_LOG(mdlog.info).asParagraph().
 358         appendText("MiMiC does not report kinetic energy, total energy, temperature, virial and pressure.");
 359
 360     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 361                 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
 362                 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
 363                 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 364
 365     // we don't do counter resetting in rerun - finish will always be valid
 366     walltime_accounting_set_valid_finish(walltime_accounting);
 367
 368     DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion   =
 369         (DOMAINDECOMP(cr) ?
 370          DdOpenBalanceRegionBeforeForceComputation::yes :
 371          DdOpenBalanceRegionBeforeForceComputation::no);
 372     DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion  =
 373         (DOMAINDECOMP(cr) ?
 374          DdCloseBalanceRegionAfterForceComputation::yes :
 375          DdCloseBalanceRegionAfterForceComputation::no);
 376
 377     step     = ir->init_step;
 378     step_rel = 0;
 379
 380     /* and stop now if we should */
 381     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 382     while (!isLastStep)
 383     {
 384         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 385         wallcycle_start(wcycle, ewcSTEP);
 386
 387         t = step;
 388
 389         if (MASTER(cr))
 390         {
 391             mimicCommunicator.getCoords(&state_global->x, state_global->natoms);
 392         }
 393
 394         if (ir->efep != efepNO)
 395         {
 396             setCurrentLambdasLocal(step, ir->fepvals, lam0, state);
 397         }
 398
 399         if (MASTER(cr))
 400         {
 401             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 402             if (constructVsites && DOMAINDECOMP(cr))
 403             {
 404                 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
 405                           "use a single rank");
 406             }
 407         }
 408
 409         if (DOMAINDECOMP(cr))
 410         {
 411             /* Repartition the domain decomposition */
 412             const bool bMasterState = true;
 413             dd_partition_system(fplog, mdlog, step, cr,
 414                                 bMasterState, nstglobalcomm,
 415                                 state_global, *top_global, ir,
 416                                 state, &f, mdAtoms, &top, fr,
 417                                 vsite, constr,
 418                                 nrnb, wcycle,
 419                                 mdrunOptions.verbose);
 420             shouldCheckNumberOfBondedInteractions = true;
 421         }
 422
 423         if (MASTER(cr))
 424         {
 425             print_ebin_header(fplog, step, t); /* can we improve the information printed here? */
 426         }
 427
 428         if (ir->efep != efepNO)
 429         {
 430             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 431         }
 432
 433         force_flags = (GMX_FORCE_STATECHANGED |
 434                        GMX_FORCE_DYNAMICBOX |
 435                        GMX_FORCE_ALLFORCES |
 436                        GMX_FORCE_VIRIAL |  // TODO: Get rid of this once #2649 is solved
 437                        GMX_FORCE_ENERGY |
 438                        (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 439
 440         if (shellfc)
 441         {
 442             /* Now is the time to relax the shells */
 443             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
 444                                 enforcedRotation, step,
 445                                 ir, bNS, force_flags, &top,
 446                                 constr, enerd, fcd,
 447                                 state, f.arrayRefWithPadding(), force_vir, mdatoms,
 448                                 nrnb, wcycle, graph, groups,
 449                                 shellfc, fr, ppForceWorkload, t, mu_tot,
 450                                 vsite,
 451                                 ddOpenBalanceRegion, ddCloseBalanceRegion);
 452         }
 453         else
 454         {
 455             /* The coordinates (x) are shifted (to get whole molecules)
 456              * in do_force.
 457              * This is parallellized as well, and does communication too.
 458              * Check comments in sim_util.c
 459              */
 460             Awh       *awh = nullptr;
 461             gmx_edsam *ed  = nullptr;
 462             do_force(fplog, cr, ms, ir, awh, enforcedRotation,
 463                      step, nrnb, wcycle, &top, groups,
 464                      state->box, state->x.arrayRefWithPadding(), &state->hist,
 465                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
 466                      state->lambda, graph,
 467                      fr, ppForceWorkload, vsite, mu_tot, t, ed,
 468                      GMX_FORCE_NS | force_flags,
 469                      ddOpenBalanceRegion, ddCloseBalanceRegion);
 470         }
 471
 472         /* Now we have the energies and forces corresponding to the
 473          * coordinates at time t.
 474          */
 475         {
 476             const bool isCheckpointingStep = false;
 477             const bool doRerun             = false;
 478             const bool bSumEkinhOld        = false;
 479             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
 480                                      ir, state, state_global, observablesHistory,
 481                                      top_global, fr,
 482                                      outf, energyOutput, ekind, f,
 483                                      isCheckpointingStep, doRerun, isLastStep,
 484                                      mdrunOptions.writeConfout,
 485                                      bSumEkinhOld);
 486         }
 487
 488         stopHandler->setSignal();
 489
 490         if (graph)
 491         {
 492             /* Need to unshift here */
 493             unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 494         }
 495
 496         if (vsite != nullptr)
 497         {
 498             wallcycle_start(wcycle, ewcVSITECONSTR);
 499             if (graph != nullptr)
 500             {
 501                 shift_self(graph, state->box, as_rvec_array(state->x.data()));
 502             }
 503             construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
 504                              top.idef.iparams, top.idef.il,
 505                              fr->ePBC, fr->bMolPBC, cr, state->box);
 506
 507             if (graph != nullptr)
 508             {
 509                 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 510             }
 511             wallcycle_stop(wcycle, ewcVSITECONSTR);
 512         }
 513
 514         {
 515             const bool          doInterSimSignal = false;
 516             const bool          doIntraSimSignal = true;
 517             bool                bSumEkinhOld     = false;
 518             t_vcm              *vcm              = nullptr;
 519             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 520
 521             compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 522                             wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
 523                             constr, &signaller,
 524                             state->box,
 525                             &totalNumberOfBondedInteractions, &bSumEkinhOld,
 526                             CGLO_GSTAT | CGLO_ENERGY
 527                             | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
 528                             );
 529             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 530                                             top_global, &top, state,
 531                                             &shouldCheckNumberOfBondedInteractions);
 532         }
 533
 534         {
 535             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 536             gmx::ArrayRef<gmx::RVec>       ftemp;
 537             gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
 538             if (DOMAINDECOMP(cr))
 539             {
 540                 ftemp = gmx::makeArrayRef(fglobal);
 541                 dd_collect_vec(cr->dd, state, flocal, ftemp);
 542             }
 543             else
 544             {
 545                 ftemp = gmx::makeArrayRef(f);
 546             }
 547
 548             if (MASTER(cr))
 549             {
 550                 mimicCommunicator.sendEnergies(enerd->term[F_EPOT]);
 551                 mimicCommunicator.sendForces(ftemp, state_global->natoms);
 552             }
 553         }
 554
 555
 556
 557         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 558            the virial that should probably be addressed eventually. state->veta has better properies,
 559            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 560            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 561
 562         if (ir->efep != efepNO)
 563         {
 564             /* Sum up the foreign energy and dhdl terms for md and sd.
 565                Currently done every step so that dhdl is correct in the .edr */
 566             sum_dhdl(enerd, state->lambda, ir->fepvals);
 567         }
 568
 569         /* Output stuff */
 570         if (MASTER(cr))
 571         {
 572             const bool bCalcEnerStep = true;
 573             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep,
 574                                              t, mdatoms->tmass, enerd, state,
 575                                              ir->fepvals, ir->expandedvals, state->box,
 576                                              shake_vir, force_vir, total_vir, pres,
 577                                              ekind, mu_tot, constr);
 578
 579             const bool do_ene = true;
 580             const bool do_log = true;
 581             Awh       *awh    = nullptr;
 582             const bool do_dr  = ir->nstdisreout != 0;
 583             const bool do_or  = ir->nstorireout != 0;
 584
 585             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
 586                                                do_log ? fplog : nullptr,
 587                                                step, t,
 588                                                eprNORMAL, fcd, groups, &(ir->opts), awh);
 589
 590             if (do_per_step(step, ir->nstlog))
 591             {
 592                 if (fflush(fplog) != 0)
 593                 {
 594                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 595                 }
 596             }
 597         }
 598
 599         /* Print the remaining wall clock time for the run */
 600         if (isMasterSimMasterRank(ms, cr) &&
 601             (mdrunOptions.verbose || gmx_got_usr_signal()))
 602         {
 603             if (shellfc)
 604             {
 605                 fprintf(stderr, "\n");
 606             }
 607             print_time(stderr, walltime_accounting, step, ir, cr);
 608         }
 609
 610         cycles = wallcycle_stop(wcycle, ewcSTEP);
 611         if (DOMAINDECOMP(cr) && wcycle)
 612         {
 613             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 614         }
 615
 616         /* increase the MD step number */
 617         step++;
 618         step_rel++;
 619     }
 620     /* End of main MD loop */
 621
 622     /* Closing TNG files can include compressing data. Therefore it is good to do that
 623      * before stopping the time measurements. */
 624     mdoutf_tng_close(outf);
 625
 626     /* Stop measuring walltime */
 627     walltime_accounting_end_time(walltime_accounting);
 628
 629     if (MASTER(cr))
 630     {
 631         mimicCommunicator.finalize();
 632     }
 633
 634     if (!thisRankHasDuty(cr, DUTY_PME))
 635     {
 636         /* Tell the PME only node to finish */
 637         gmx_pme_send_finish(cr);
 638     }
 639
 640     done_mdoutf(outf);
 641
 642     done_shellfc(fplog, shellfc, step_rel);
 643
 644     // Clean up swapcoords
 645     if (ir->eSwapCoords != eswapNO)
 646     {
 647         finish_swapcoords(ir->swap);
 648     }
 649
 650     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 651
 652     destroy_enerdata(enerd);
 653     sfree(enerd);
 654 }