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/dlbtiming.h"
  57 #include "gromacs/domdec/domdec.h"
  58 #include "gromacs/domdec/domdec_network.h"
  59 #include "gromacs/domdec/domdec_struct.h"
  60 #include "gromacs/domdec/mdsetup.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/listed_forces/manage_threading.h"
  70 #include "gromacs/math/functions.h"
  71 #include "gromacs/math/utilities.h"
  72 #include "gromacs/math/vec.h"
  73 #include "gromacs/math/vectypes.h"
  74 #include "gromacs/mdlib/checkpointhandler.h"
  75 #include "gromacs/mdlib/compute_io.h"
  76 #include "gromacs/mdlib/constr.h"
  77 #include "gromacs/mdlib/ebin.h"
  78 #include "gromacs/mdlib/enerdata_utils.h"
  79 #include "gromacs/mdlib/energyoutput.h"
  80 #include "gromacs/mdlib/expanded.h"
  81 #include "gromacs/mdlib/force.h"
  82 #include "gromacs/mdlib/force_flags.h"
  83 #include "gromacs/mdlib/forcerec.h"
  84 #include "gromacs/mdlib/md_support.h"
  85 #include "gromacs/mdlib/mdatoms.h"
  86 #include "gromacs/mdlib/mdoutf.h"
  87 #include "gromacs/mdlib/membed.h"
  88 #include "gromacs/mdlib/resethandler.h"
  89 #include "gromacs/mdlib/sighandler.h"
  90 #include "gromacs/mdlib/simulationsignal.h"
  91 #include "gromacs/mdlib/stat.h"
  92 #include "gromacs/mdlib/stophandler.h"
  93 #include "gromacs/mdlib/tgroup.h"
  94 #include "gromacs/mdlib/trajectory_writing.h"
  95 #include "gromacs/mdlib/update.h"
  96 #include "gromacs/mdlib/vcm.h"
  97 #include "gromacs/mdlib/vsite.h"
  98 #include "gromacs/mdrunutility/handlerestart.h"
  99 #include "gromacs/mdrunutility/multisim.h"
 100 #include "gromacs/mdrunutility/printtime.h"
 101 #include "gromacs/mdtypes/awh_history.h"
 102 #include "gromacs/mdtypes/awh_params.h"
 103 #include "gromacs/mdtypes/commrec.h"
 104 #include "gromacs/mdtypes/df_history.h"
 105 #include "gromacs/mdtypes/enerdata.h"
 106 #include "gromacs/mdtypes/energyhistory.h"
 107 #include "gromacs/mdtypes/fcdata.h"
 108 #include "gromacs/mdtypes/forcerec.h"
 109 #include "gromacs/mdtypes/group.h"
 110 #include "gromacs/mdtypes/inputrec.h"
 111 #include "gromacs/mdtypes/interaction_const.h"
 112 #include "gromacs/mdtypes/md_enums.h"
 113 #include "gromacs/mdtypes/mdatom.h"
 114 #include "gromacs/mdtypes/mdrunoptions.h"
 115 #include "gromacs/mdtypes/observableshistory.h"
 116 #include "gromacs/mdtypes/state.h"
 117 #include "gromacs/mimic/communicator.h"
 118 #include "gromacs/mimic/utilities.h"
 119 #include "gromacs/pbcutil/mshift.h"
 120 #include "gromacs/pbcutil/pbc.h"
 121 #include "gromacs/pulling/pull.h"
 122 #include "gromacs/timing/wallcycle.h"
 123 #include "gromacs/timing/walltime_accounting.h"
 124 #include "gromacs/topology/atoms.h"
 125 #include "gromacs/topology/idef.h"
 126 #include "gromacs/topology/mtop_util.h"
 127 #include "gromacs/topology/topology.h"
 128 #include "gromacs/trajectory/trajectoryframe.h"
 129 #include "gromacs/utility/basedefinitions.h"
 130 #include "gromacs/utility/cstringutil.h"
 131 #include "gromacs/utility/fatalerror.h"
 132 #include "gromacs/utility/logger.h"
 133 #include "gromacs/utility/real.h"
 134 #include "gromacs/utility/smalloc.h"
 135
 136 #include "legacysimulator.h"
 137 #include "replicaexchange.h"
 138 #include "shellfc.h"
 139
 140 using gmx::SimulationSignaller;
 141
 142 void gmx::LegacySimulator::do_mimic()
 143 {
 144     t_inputrec              *ir   = inputrec;
 145     int64_t                  step, step_rel;
 146     double                   t, lam0[efptNR];
 147     bool                     isLastStep               = false;
 148     bool                     doFreeEnergyPerturbation = false;
 149     unsigned int             force_flags;
 150     tensor                   force_vir, shake_vir, total_vir, pres;
 151     rvec                     mu_tot;
 152     gmx_localtop_t           top;
 153     PaddedVector<gmx::RVec>  f {};
 154     gmx_global_stat_t        gstat;
 155     t_graph                 *graph = nullptr;
 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     SimulationGroups *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
 229     gmx_mdoutf        *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle,
 230                                           StartingBehavior::NewSimulation);
 231     gmx::EnergyOutput  energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, mdoutf_get_fp_dhdl(outf), true);
 232
 233     /* Kinetic energy data */
 234     std::unique_ptr<gmx_ekindata_t> eKinData = std::make_unique<gmx_ekindata_t>();
 235     gmx_ekindata_t                 *ekind    = eKinData.get();
 236     init_ekindata(fplog, top_global, &(ir->opts), ekind);
 237     /* Copy the cos acceleration to the groups struct */
 238     ekind->cosacc.cos_accel = ir->cos_accel;
 239
 240     gstat = global_stat_init(ir);
 241
 242     /* Check for polarizable models and flexible constraints */
 243     shellfc = init_shell_flexcon(fplog,
 244                                  top_global, constr ? constr->numFlexibleConstraints() : 0,
 245                                  ir->nstcalcenergy, DOMAINDECOMP(cr));
 246
 247     {
 248         double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
 249         if ((io > 2000) && MASTER(cr))
 250         {
 251             fprintf(stderr,
 252                     "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
 253                     io);
 254         }
 255     }
 256
 257     // Local state only becomes valid now.
 258     std::unique_ptr<t_state> stateInstance;
 259     t_state *                state;
 260
 261     if (DOMAINDECOMP(cr))
 262     {
 263         dd_init_local_top(*top_global, &top);
 264
 265         stateInstance = std::make_unique<t_state>();
 266         state         = stateInstance.get();
 267         dd_init_local_state(cr->dd, state_global, state);
 268
 269         /* Distribute the charge groups over the nodes from the master node */
 270         dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
 271                             state_global, *top_global, ir, imdSession,
 272                             pull_work,
 273                             state, &f, mdAtoms, &top, fr,
 274                             vsite, constr,
 275                             nrnb, nullptr, FALSE);
 276         shouldCheckNumberOfBondedInteractions = true;
 277         gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr);
 278     }
 279     else
 280     {
 281         state_change_natoms(state_global, state_global->natoms);
 282         /* We need to allocate one element extra, since we might use
 283          * (unaligned) 4-wide SIMD loads to access rvec entries.
 284          */
 285         f.resizeWithPadding(state_global->natoms);
 286         /* Copy the pointer to the global state */
 287         state = state_global;
 288
 289         mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
 290                                   &graph, mdAtoms, constr, vsite, shellfc);
 291     }
 292
 293     auto mdatoms = mdAtoms->mdatoms();
 294
 295     // NOTE: The global state is no longer used at this point.
 296     // But state_global is still used as temporary storage space for writing
 297     // the global state to file and potentially for replica exchange.
 298     // (Global topology should persist.)
 299
 300     update_mdatoms(mdatoms, state->lambda[efptMASS]);
 301
 302     if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
 303     {
 304         doFreeEnergyPerturbation = true;
 305     }
 306
 307     {
 308         int    cglo_flags = (CGLO_GSTAT |
 309                              (shouldCheckNumberOfBondedInteractions ?
 310                               CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 311         bool   bSumEkinhOld = false;
 312         t_vcm *vcm          = nullptr;
 313         compute_globals(gstat, cr, ir, fr, ekind,
 314                         state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
 315                         mdatoms, nrnb, vcm,
 316                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
 317                         constr, &nullSignaller, state->box,
 318                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 319     }
 320     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 321                                     top_global, &top, state->x.rvec_array(), state->box,
 322                                     &shouldCheckNumberOfBondedInteractions);
 323
 324     if (MASTER(cr))
 325     {
 326         fprintf(stderr, "starting MiMiC MD run '%s'\n\n",
 327                 *(top_global->name));
 328         if (mdrunOptions.verbose)
 329         {
 330             fprintf(stderr, "Calculated time to finish depends on nsteps from "
 331                     "run input file,\nwhich may not correspond to the time "
 332                     "needed to process input trajectory.\n\n");
 333         }
 334         fprintf(fplog, "\n");
 335     }
 336
 337     walltime_accounting_start_time(walltime_accounting);
 338     wallcycle_start(wcycle, ewcRUN);
 339     print_start(fplog, cr, walltime_accounting, "mdrun");
 340
 341     /***********************************************************
 342      *
 343      *             Loop over MD steps
 344      *
 345      ************************************************************/
 346
 347     if (constr)
 348     {
 349         GMX_LOG(mdlog.info).asParagraph().
 350             appendText("Simulations has constraints. Constraints will "
 351                        "be handled by CPMD.");
 352     }
 353
 354     GMX_LOG(mdlog.info).asParagraph().
 355         appendText("MiMiC does not report kinetic energy, total energy, temperature, virial and pressure.");
 356
 357     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 358                 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
 359                 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
 360                 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 361
 362     // we don't do counter resetting in rerun - finish will always be valid
 363     walltime_accounting_set_valid_finish(walltime_accounting);
 364
 365     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 366
 367     step     = ir->init_step;
 368     step_rel = 0;
 369
 370     /* and stop now if we should */
 371     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 372     while (!isLastStep)
 373     {
 374         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 375         wallcycle_start(wcycle, ewcSTEP);
 376
 377         t = step;
 378
 379         if (MASTER(cr))
 380         {
 381             mimicCommunicator.getCoords(&state_global->x, state_global->natoms);
 382         }
 383
 384         if (ir->efep != efepNO)
 385         {
 386             setCurrentLambdasLocal(step, ir->fepvals, lam0, state);
 387         }
 388
 389         if (MASTER(cr))
 390         {
 391             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 392             if (constructVsites && DOMAINDECOMP(cr))
 393             {
 394                 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
 395                           "use a single rank");
 396             }
 397         }
 398
 399         if (DOMAINDECOMP(cr))
 400         {
 401             /* Repartition the domain decomposition */
 402             const bool bMasterState = true;
 403             dd_partition_system(fplog, mdlog, step, cr,
 404                                 bMasterState, nstglobalcomm,
 405                                 state_global, *top_global, ir, imdSession,
 406                                 pull_work,
 407                                 state, &f, mdAtoms, &top, fr,
 408                                 vsite, constr,
 409                                 nrnb, wcycle,
 410                                 mdrunOptions.verbose);
 411             shouldCheckNumberOfBondedInteractions = true;
 412         }
 413
 414         if (MASTER(cr))
 415         {
 416             energyOutput.printHeader(fplog, step, t); /* can we improve the information printed here? */
 417         }
 418
 419         if (ir->efep != efepNO)
 420         {
 421             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 422         }
 423
 424         force_flags = (GMX_FORCE_STATECHANGED |
 425                        GMX_FORCE_DYNAMICBOX |
 426                        GMX_FORCE_ALLFORCES |
 427                        GMX_FORCE_VIRIAL |  // TODO: Get rid of this once #2649 is solved
 428                        GMX_FORCE_ENERGY |
 429                        (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 430
 431         if (shellfc)
 432         {
 433             /* Now is the time to relax the shells */
 434             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
 435                                 enforcedRotation, step,
 436                                 ir, imdSession, pull_work, bNS, force_flags, &top,
 437                                 constr, enerd, fcd,
 438                                 state->natoms,
 439                                 state->x.arrayRefWithPadding(),
 440                                 state->v.arrayRefWithPadding(),
 441                                 state->box,
 442                                 state->lambda,
 443                                 &state->hist,
 444                                 f.arrayRefWithPadding(), force_vir, mdatoms,
 445                                 nrnb, wcycle, graph,
 446                                 shellfc, fr, ppForceWorkload, t, mu_tot,
 447                                 vsite,
 448                                 ddBalanceRegionHandler);
 449         }
 450         else
 451         {
 452             /* The coordinates (x) are shifted (to get whole molecules)
 453              * in do_force.
 454              * This is parallellized as well, and does communication too.
 455              * Check comments in sim_util.c
 456              */
 457             Awh       *awh = nullptr;
 458             gmx_edsam *ed  = nullptr;
 459             do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession,
 460                      pull_work,
 461                      step, nrnb, wcycle, &top,
 462                      state->box, state->x.arrayRefWithPadding(), &state->hist,
 463                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
 464                      state->lambda, graph,
 465                      fr, ppForceWorkload, vsite, mu_tot, t, ed,
 466                      GMX_FORCE_NS | force_flags,
 467                      ddBalanceRegionHandler);
 468         }
 469
 470         /* Now we have the energies and forces corresponding to the
 471          * coordinates at time t.
 472          */
 473         {
 474             const bool isCheckpointingStep = false;
 475             const bool doRerun             = false;
 476             const bool bSumEkinhOld        = false;
 477             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
 478                                      ir, state, state_global, observablesHistory,
 479                                      top_global, fr,
 480                                      outf, energyOutput, ekind, f,
 481                                      isCheckpointingStep, doRerun, isLastStep,
 482                                      mdrunOptions.writeConfout,
 483                                      bSumEkinhOld);
 484         }
 485
 486         stopHandler->setSignal();
 487
 488         if (graph)
 489         {
 490             /* Need to unshift here */
 491             unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 492         }
 493
 494         if (vsite != nullptr)
 495         {
 496             wallcycle_start(wcycle, ewcVSITECONSTR);
 497             if (graph != nullptr)
 498             {
 499                 shift_self(graph, state->box, as_rvec_array(state->x.data()));
 500             }
 501             construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
 502                              top.idef.iparams, top.idef.il,
 503                              fr->ePBC, fr->bMolPBC, cr, state->box);
 504
 505             if (graph != nullptr)
 506             {
 507                 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 508             }
 509             wallcycle_stop(wcycle, ewcVSITECONSTR);
 510         }
 511
 512         {
 513             const bool          doInterSimSignal = false;
 514             const bool          doIntraSimSignal = true;
 515             bool                bSumEkinhOld     = false;
 516             t_vcm              *vcm              = nullptr;
 517             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 518
 519             compute_globals(gstat, cr, ir, fr, ekind,
 520                             state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
 521                             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->x.rvec_array(), state->box,
 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.printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
 586             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
 587                                                do_log ? fplog : nullptr,
 588                                                step, t,
 589                                                fcd, awh);
 590
 591             if (do_per_step(step, ir->nstlog))
 592             {
 593                 if (fflush(fplog) != 0)
 594                 {
 595                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 596                 }
 597             }
 598         }
 599
 600         /* Print the remaining wall clock time for the run */
 601         if (isMasterSimMasterRank(ms, MASTER(cr)) &&
 602             (mdrunOptions.verbose || gmx_got_usr_signal()))
 603         {
 604             if (shellfc)
 605             {
 606                 fprintf(stderr, "\n");
 607             }
 608             print_time(stderr, walltime_accounting, step, ir, cr);
 609         }
 610
 611         cycles = wallcycle_stop(wcycle, ewcSTEP);
 612         if (DOMAINDECOMP(cr) && wcycle)
 613         {
 614             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 615         }
 616
 617         /* increase the MD step number */
 618         step++;
 619         step_rel++;
 620     }
 621     /* End of main MD loop */
 622
 623     /* Closing TNG files can include compressing data. Therefore it is good to do that
 624      * before stopping the time measurements. */
 625     mdoutf_tng_close(outf);
 626
 627     /* Stop measuring walltime */
 628     walltime_accounting_end_time(walltime_accounting);
 629
 630     if (MASTER(cr))
 631     {
 632         mimicCommunicator.finalize();
 633     }
 634
 635     if (!thisRankHasDuty(cr, DUTY_PME))
 636     {
 637         /* Tell the PME only node to finish */
 638         gmx_pme_send_finish(cr);
 639     }
 640
 641     done_mdoutf(outf);
 642
 643     done_shellfc(fplog, shellfc, step_rel);
 644
 645     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 646 }