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/partition.h"
  61 #include "gromacs/essentialdynamics/edsam.h"
  62 #include "gromacs/ewald/pme.h"
  63 #include "gromacs/ewald/pme_load_balancing.h"
  64 #include "gromacs/fileio/trxio.h"
  65 #include "gromacs/gmxlib/network.h"
  66 #include "gromacs/gmxlib/nrnb.h"
  67 #include "gromacs/gpu_utils/gpu_utils.h"
  68 #include "gromacs/imd/imd.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/energyoutput.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/mdoutf.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/simulationsignal.h"
  93 #include "gromacs/mdlib/stat.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/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/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 void gmx::Integrator::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     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     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     /* Kinetic energy data */
 235     std::unique_ptr<gmx_ekindata_t> eKinData = std::make_unique<gmx_ekindata_t>();
 236     gmx_ekindata_t                 *ekind    = eKinData.get();
 237     init_ekindata(fplog, top_global, &(ir->opts), ekind);
 238     /* Copy the cos acceleration to the groups struct */
 239     ekind->cosacc.cos_accel = ir->cos_accel;
 240
 241     gstat = global_stat_init(ir);
 242
 243     /* Check for polarizable models and flexible constraints */
 244     shellfc = init_shell_flexcon(fplog,
 245                                  top_global, constr ? constr->numFlexibleConstraints() : 0,
 246                                  ir->nstcalcenergy, DOMAINDECOMP(cr));
 247
 248     {
 249         double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
 250         if ((io > 2000) && MASTER(cr))
 251         {
 252             fprintf(stderr,
 253                     "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
 254                     io);
 255         }
 256     }
 257
 258     // Local state only becomes valid now.
 259     std::unique_ptr<t_state> stateInstance;
 260     t_state *                state;
 261
 262     if (DOMAINDECOMP(cr))
 263     {
 264         dd_init_local_top(*top_global, &top);
 265
 266         stateInstance = std::make_unique<t_state>();
 267         state         = stateInstance.get();
 268         dd_init_local_state(cr->dd, state_global, state);
 269
 270         /* Distribute the charge groups over the nodes from the master node */
 271         dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
 272                             state_global, *top_global, ir,
 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_INITIALIZATION | CGLO_GSTAT |
 309                              (shouldCheckNumberOfBondedInteractions ?
 310                               CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
 311         bool   bSumEkinhOld = false;
 312         t_vcm *vcm          = nullptr;
 313         compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 314                         nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
 315                         constr, &nullSignaller, state->box,
 316                         &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
 317     }
 318     checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 319                                     top_global, &top, state,
 320                                     &shouldCheckNumberOfBondedInteractions);
 321
 322     if (MASTER(cr))
 323     {
 324         fprintf(stderr, "starting MiMiC MD run '%s'\n\n",
 325                 *(top_global->name));
 326         if (mdrunOptions.verbose)
 327         {
 328             fprintf(stderr, "Calculated time to finish depends on nsteps from "
 329                     "run input file,\nwhich may not correspond to the time "
 330                     "needed to process input trajectory.\n\n");
 331         }
 332         fprintf(fplog, "\n");
 333     }
 334
 335     walltime_accounting_start_time(walltime_accounting);
 336     wallcycle_start(wcycle, ewcRUN);
 337     print_start(fplog, cr, walltime_accounting, "mdrun");
 338
 339     /***********************************************************
 340      *
 341      *             Loop over MD steps
 342      *
 343      ************************************************************/
 344
 345     if (constr)
 346     {
 347         GMX_LOG(mdlog.info).asParagraph().
 348             appendText("Simulations has constraints. Constraints will "
 349                        "be handled by CPMD.");
 350     }
 351
 352     GMX_LOG(mdlog.info).asParagraph().
 353         appendText("MiMiC does not report kinetic energy, total energy, temperature, virial and pressure.");
 354
 355     auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
 356                 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
 357                 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
 358                 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
 359
 360     // we don't do counter resetting in rerun - finish will always be valid
 361     walltime_accounting_set_valid_finish(walltime_accounting);
 362
 363     const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
 364
 365     step     = ir->init_step;
 366     step_rel = 0;
 367
 368     /* and stop now if we should */
 369     isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
 370     while (!isLastStep)
 371     {
 372         isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
 373         wallcycle_start(wcycle, ewcSTEP);
 374
 375         t = step;
 376
 377         if (MASTER(cr))
 378         {
 379             mimicCommunicator.getCoords(&state_global->x, state_global->natoms);
 380         }
 381
 382         if (ir->efep != efepNO)
 383         {
 384             setCurrentLambdasLocal(step, ir->fepvals, lam0, state);
 385         }
 386
 387         if (MASTER(cr))
 388         {
 389             const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
 390             if (constructVsites && DOMAINDECOMP(cr))
 391             {
 392                 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
 393                           "use a single rank");
 394             }
 395         }
 396
 397         if (DOMAINDECOMP(cr))
 398         {
 399             /* Repartition the domain decomposition */
 400             const bool bMasterState = true;
 401             dd_partition_system(fplog, mdlog, step, cr,
 402                                 bMasterState, nstglobalcomm,
 403                                 state_global, *top_global, ir,
 404                                 state, &f, mdAtoms, &top, fr,
 405                                 vsite, constr,
 406                                 nrnb, wcycle,
 407                                 mdrunOptions.verbose);
 408             shouldCheckNumberOfBondedInteractions = true;
 409         }
 410
 411         if (MASTER(cr))
 412         {
 413             print_ebin_header(fplog, step, t); /* can we improve the information printed here? */
 414         }
 415
 416         if (ir->efep != efepNO)
 417         {
 418             update_mdatoms(mdatoms, state->lambda[efptMASS]);
 419         }
 420
 421         force_flags = (GMX_FORCE_STATECHANGED |
 422                        GMX_FORCE_DYNAMICBOX |
 423                        GMX_FORCE_ALLFORCES |
 424                        GMX_FORCE_VIRIAL |  // TODO: Get rid of this once #2649 is solved
 425                        GMX_FORCE_ENERGY |
 426                        (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
 427
 428         if (shellfc)
 429         {
 430             /* Now is the time to relax the shells */
 431             relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
 432                                 enforcedRotation, step,
 433                                 ir, bNS, force_flags, &top,
 434                                 constr, enerd, fcd,
 435                                 state, f.arrayRefWithPadding(), force_vir, mdatoms,
 436                                 nrnb, wcycle, graph,
 437                                 shellfc, fr, ppForceWorkload, t, mu_tot,
 438                                 vsite,
 439                                 ddBalanceRegionHandler);
 440         }
 441         else
 442         {
 443             /* The coordinates (x) are shifted (to get whole molecules)
 444              * in do_force.
 445              * This is parallellized as well, and does communication too.
 446              * Check comments in sim_util.c
 447              */
 448             Awh       *awh = nullptr;
 449             gmx_edsam *ed  = nullptr;
 450             do_force(fplog, cr, ms, ir, awh, enforcedRotation,
 451                      step, nrnb, wcycle, &top,
 452                      state->box, state->x.arrayRefWithPadding(), &state->hist,
 453                      f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
 454                      state->lambda, graph,
 455                      fr, ppForceWorkload, vsite, mu_tot, t, ed,
 456                      GMX_FORCE_NS | force_flags,
 457                      ddBalanceRegionHandler);
 458         }
 459
 460         /* Now we have the energies and forces corresponding to the
 461          * coordinates at time t.
 462          */
 463         {
 464             const bool isCheckpointingStep = false;
 465             const bool doRerun             = false;
 466             const bool bSumEkinhOld        = false;
 467             do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
 468                                      ir, state, state_global, observablesHistory,
 469                                      top_global, fr,
 470                                      outf, energyOutput, ekind, f,
 471                                      isCheckpointingStep, doRerun, isLastStep,
 472                                      mdrunOptions.writeConfout,
 473                                      bSumEkinhOld);
 474         }
 475
 476         stopHandler->setSignal();
 477
 478         if (graph)
 479         {
 480             /* Need to unshift here */
 481             unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 482         }
 483
 484         if (vsite != nullptr)
 485         {
 486             wallcycle_start(wcycle, ewcVSITECONSTR);
 487             if (graph != nullptr)
 488             {
 489                 shift_self(graph, state->box, as_rvec_array(state->x.data()));
 490             }
 491             construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
 492                              top.idef.iparams, top.idef.il,
 493                              fr->ePBC, fr->bMolPBC, cr, state->box);
 494
 495             if (graph != nullptr)
 496             {
 497                 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
 498             }
 499             wallcycle_stop(wcycle, ewcVSITECONSTR);
 500         }
 501
 502         {
 503             const bool          doInterSimSignal = false;
 504             const bool          doIntraSimSignal = true;
 505             bool                bSumEkinhOld     = false;
 506             t_vcm              *vcm              = nullptr;
 507             SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
 508
 509             compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
 510                             wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
 511                             constr, &signaller,
 512                             state->box,
 513                             &totalNumberOfBondedInteractions, &bSumEkinhOld,
 514                             CGLO_GSTAT | CGLO_ENERGY
 515                             | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
 516                             );
 517             checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
 518                                             top_global, &top, state,
 519                                             &shouldCheckNumberOfBondedInteractions);
 520         }
 521
 522         {
 523             gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
 524             gmx::ArrayRef<gmx::RVec>       ftemp;
 525             gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
 526             if (DOMAINDECOMP(cr))
 527             {
 528                 ftemp = gmx::makeArrayRef(fglobal);
 529                 dd_collect_vec(cr->dd, state, flocal, ftemp);
 530             }
 531             else
 532             {
 533                 ftemp = gmx::makeArrayRef(f);
 534             }
 535
 536             if (MASTER(cr))
 537             {
 538                 mimicCommunicator.sendEnergies(enerd->term[F_EPOT]);
 539                 mimicCommunicator.sendForces(ftemp, state_global->natoms);
 540             }
 541         }
 542
 543
 544
 545         /* Note: this is OK, but there are some numerical precision issues with using the convergence of
 546            the virial that should probably be addressed eventually. state->veta has better properies,
 547            but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
 548            generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
 549
 550         if (ir->efep != efepNO)
 551         {
 552             /* Sum up the foreign energy and dhdl terms for md and sd.
 553                Currently done every step so that dhdl is correct in the .edr */
 554             sum_dhdl(enerd, state->lambda, ir->fepvals);
 555         }
 556
 557         /* Output stuff */
 558         if (MASTER(cr))
 559         {
 560             const bool bCalcEnerStep = true;
 561             energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep,
 562                                              t, mdatoms->tmass, enerd, state,
 563                                              ir->fepvals, ir->expandedvals, state->box,
 564                                              shake_vir, force_vir, total_vir, pres,
 565                                              ekind, mu_tot, constr);
 566
 567             const bool do_ene = true;
 568             const bool do_log = true;
 569             Awh       *awh    = nullptr;
 570             const bool do_dr  = ir->nstdisreout != 0;
 571             const bool do_or  = ir->nstorireout != 0;
 572
 573             energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
 574                                                do_log ? fplog : nullptr,
 575                                                step, t,
 576                                                eprNORMAL, fcd, groups, &(ir->opts), awh);
 577
 578             if (do_per_step(step, ir->nstlog))
 579             {
 580                 if (fflush(fplog) != 0)
 581                 {
 582                     gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
 583                 }
 584             }
 585         }
 586
 587         /* Print the remaining wall clock time for the run */
 588         if (isMasterSimMasterRank(ms, cr) &&
 589             (mdrunOptions.verbose || gmx_got_usr_signal()))
 590         {
 591             if (shellfc)
 592             {
 593                 fprintf(stderr, "\n");
 594             }
 595             print_time(stderr, walltime_accounting, step, ir, cr);
 596         }
 597
 598         cycles = wallcycle_stop(wcycle, ewcSTEP);
 599         if (DOMAINDECOMP(cr) && wcycle)
 600         {
 601             dd_cycles_add(cr->dd, cycles, ddCyclStep);
 602         }
 603
 604         /* increase the MD step number */
 605         step++;
 606         step_rel++;
 607     }
 608     /* End of main MD loop */
 609
 610     /* Closing TNG files can include compressing data. Therefore it is good to do that
 611      * before stopping the time measurements. */
 612     mdoutf_tng_close(outf);
 613
 614     /* Stop measuring walltime */
 615     walltime_accounting_end_time(walltime_accounting);
 616
 617     if (MASTER(cr))
 618     {
 619         mimicCommunicator.finalize();
 620     }
 621
 622     if (!thisRankHasDuty(cr, DUTY_PME))
 623     {
 624         /* Tell the PME only node to finish */
 625         gmx_pme_send_finish(cr);
 626     }
 627
 628     done_mdoutf(outf);
 629
 630     done_shellfc(fplog, shellfc, step_rel);
 631
 632     // Clean up swapcoords
 633     if (ir->eSwapCoords != eswapNO)
 634     {
 635         finish_swapcoords(ir->swap);
 636     }
 637
 638     walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
 639 }