text: /*
   * This file is part of the GROMACS molecular simulation package.
   *
   * Copyright (c) 2018,2019, by the GROMACS development team, led by
   * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   * and including many others, as listed in the AUTHORS file in the
   * top-level source directory and at http://www.gromacs.org.
   *
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   * modify it under the terms of the GNU Lesser General Public License
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  /*! \internal \file
   *
   * \brief Implements the loop for simulation reruns
   *
   * \author Pascal Merz <pascal.merz@colorado.edu>
   * \ingroup module_mdrun
   */
  #include "gmxpre.h"
  
  #include "config.h"
  
  #include <cinttypes>
  #include <cmath>
  #include <cstdio>
  #include <cstdlib>
  
  #include <algorithm>
  #include <memory>
  
  #include "gromacs/awh/awh.h"
  #include "gromacs/commandline/filenm.h"
  #include "gromacs/domdec/collect.h"
  #include "gromacs/domdec/dlbtiming.h"
  #include "gromacs/domdec/domdec.h"
  #include "gromacs/domdec/domdec_network.h"
  #include "gromacs/domdec/domdec_struct.h"
  #include "gromacs/domdec/mdsetup.h"
  #include "gromacs/domdec/partition.h"
  #include "gromacs/essentialdynamics/edsam.h"
  #include "gromacs/ewald/pme.h"
  #include "gromacs/ewald/pme_load_balancing.h"
  #include "gromacs/fileio/trxio.h"
  #include "gromacs/gmxlib/network.h"
  #include "gromacs/gmxlib/nrnb.h"
  #include "gromacs/gpu_utils/gpu_utils.h"
  #include "gromacs/listed_forces/manage_threading.h"
  #include "gromacs/math/functions.h"
  #include "gromacs/math/utilities.h"
  #include "gromacs/math/vec.h"
  #include "gromacs/math/vectypes.h"
  #include "gromacs/mdlib/checkpointhandler.h"
  #include "gromacs/mdlib/compute_io.h"
  #include "gromacs/mdlib/constr.h"
  #include "gromacs/mdlib/ebin.h"
  #include "gromacs/mdlib/enerdata_utils.h"
  #include "gromacs/mdlib/energyoutput.h"
  #include "gromacs/mdlib/expanded.h"
  #include "gromacs/mdlib/force.h"
  #include "gromacs/mdlib/force_flags.h"
  #include "gromacs/mdlib/forcerec.h"
  #include "gromacs/mdlib/md_support.h"
  #include "gromacs/mdlib/mdatoms.h"
  #include "gromacs/mdlib/mdoutf.h"
  #include "gromacs/mdlib/membed.h"
  #include "gromacs/mdlib/resethandler.h"
  #include "gromacs/mdlib/sighandler.h"
  #include "gromacs/mdlib/simulationsignal.h"
  #include "gromacs/mdlib/stat.h"
  #include "gromacs/mdlib/stophandler.h"
  #include "gromacs/mdlib/tgroup.h"
  #include "gromacs/mdlib/trajectory_writing.h"
  #include "gromacs/mdlib/update.h"
  #include "gromacs/mdlib/vcm.h"
  #include "gromacs/mdlib/vsite.h"
  #include "gromacs/mdrunutility/handlerestart.h"
  #include "gromacs/mdrunutility/multisim.h"
  #include "gromacs/mdrunutility/printtime.h"
  #include "gromacs/mdtypes/awh_history.h"
  #include "gromacs/mdtypes/awh_params.h"
  #include "gromacs/mdtypes/commrec.h"
  #include "gromacs/mdtypes/df_history.h"
  #include "gromacs/mdtypes/energyhistory.h"
  #include "gromacs/mdtypes/fcdata.h"
  #include "gromacs/mdtypes/forcerec.h"
  #include "gromacs/mdtypes/group.h"
  #include "gromacs/mdtypes/inputrec.h"
  #include "gromacs/mdtypes/interaction_const.h"
  #include "gromacs/mdtypes/md_enums.h"
  #include "gromacs/mdtypes/mdatom.h"
  #include "gromacs/mdtypes/mdrunoptions.h"
  #include "gromacs/mdtypes/observableshistory.h"
  #include "gromacs/mdtypes/state.h"
  #include "gromacs/mimic/utilities.h"
  #include "gromacs/pbcutil/mshift.h"
  #include "gromacs/pbcutil/pbc.h"
  #include "gromacs/pulling/pull.h"
  #include "gromacs/swap/swapcoords.h"
  #include "gromacs/timing/wallcycle.h"
  #include "gromacs/timing/walltime_accounting.h"
  #include "gromacs/topology/atoms.h"
  #include "gromacs/topology/idef.h"
  #include "gromacs/topology/mtop_util.h"
  #include "gromacs/topology/topology.h"
  #include "gromacs/trajectory/trajectoryframe.h"
  #include "gromacs/utility/basedefinitions.h"
  #include "gromacs/utility/cstringutil.h"
  #include "gromacs/utility/fatalerror.h"
  #include "gromacs/utility/logger.h"
  #include "gromacs/utility/real.h"
  #include "gromacs/utility/smalloc.h"
  
  #include "replicaexchange.h"
  #include "shellfc.h"
  #include "simulator.h"
  
  using gmx::SimulationSignaller;
  
  /*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
   *
   * \param[in]     rerunFrame      The trajectory frame to compute energy/forces for
   * \param[in,out] globalState     The global state container
   * \param[in]     constructVsites When true, vsite coordinates are constructed
   * \param[in]     vsite           Vsite setup, can be nullptr when \p constructVsites = false
   * \param[in]     idef            Topology parameters, used for constructing vsites
   * \param[in]     timeStep        Time step, used for constructing vsites
   * \param[in]     forceRec        Force record, used for constructing vsites
   * \param[in,out] graph           The molecular graph, used for constructing vsites when != nullptr
   */
  static void prepareRerunState(const t_trxframe  &rerunFrame,
                                t_state           *globalState,
                                bool               constructVsites,
                                const gmx_vsite_t *vsite,
                                const t_idef      &idef,
                                double             timeStep,
                                const t_forcerec  &forceRec,
                                t_graph           *graph)
  {
      auto x      = makeArrayRef(globalState->x);
      auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec *>(rerunFrame.x), globalState->natoms);
      std::copy(rerunX.begin(), rerunX.end(), x.begin());
      copy_mat(rerunFrame.box, globalState->box);
  
      if (constructVsites)
      {
          GMX_ASSERT(vsite, "Need valid vsite for constructing vsites");
  
          if (graph)
          {
              /* Following is necessary because the graph may get out of sync
               * with the coordinates if we only have every N'th coordinate set
               */
              mk_mshift(nullptr, graph, forceRec.ePBC, globalState->box, globalState->x.rvec_array());
              shift_self(graph, globalState->box, as_rvec_array(globalState->x.data()));
          }
          construct_vsites(vsite, globalState->x.rvec_array(), timeStep, globalState->v.rvec_array(),
                           idef.iparams, idef.il,
                           forceRec.ePBC, forceRec.bMolPBC, nullptr, globalState->box);
          if (graph)
          {
              unshift_self(graph, globalState->box, globalState->x.rvec_array());
          }
      }
  }
  
  void gmx::Simulator::do_rerun()
  {
      // TODO Historically, the EM and MD "integrators" used different
      // names for the t_inputrec *parameter, but these must have the
      // same name, now that it's a member of a struct. We use this ir
      // alias to avoid a large ripple of nearly useless changes.
      // t_inputrec is being replaced by IMdpOptionsProvider, so this
      // will go away eventually.
      t_inputrec             *ir   = inputrec;
      int64_t                 step, step_rel;
      double                  t, lam0[efptNR];
      bool                    isLastStep               = false;
      bool                    doFreeEnergyPerturbation = false;
      unsigned int            force_flags;
      tensor                  force_vir, shake_vir, total_vir, pres;
      t_trxstatus            *status;
      rvec                    mu_tot;
      t_trxframe              rerun_fr;
      gmx_localtop_t          top;
      PaddedVector<gmx::RVec> f {};
      gmx_global_stat_t       gstat;
      t_graph                *graph = nullptr;
      gmx_shellfc_t          *shellfc;
  
      double                  cycles;
  
      /* Domain decomposition could incorrectly miss a bonded
         interaction, but checking for that requires a global
         communication stage, which does not otherwise happen in DD
         code. So we do that alongside the first global energy reduction
         after a new DD is made. These variables handle whether the
         check happens, and the result it returns. */
      bool              shouldCheckNumberOfBondedInteractions = false;
      int               totalNumberOfBondedInteractions       = -1;
  
      SimulationSignals signals;
      // Most global communnication stages don't propagate mdrun
      // signals, and will use this object to achieve that.
      SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
  
      GMX_LOG(mdlog.info).asParagraph().
          appendText("Note that it is planned that the command gmx mdrun -rerun will "
                     "be available in a different form in a future version of GROMACS, "
                     "e.g. gmx rerun -f.");
  
      if (ir->efep != efepNO && (mdAtoms->mdatoms()->nMassPerturbed > 0 ||
                                 (constr && constr->havePerturbedConstraints())))
      {
          gmx_fatal(FARGS, "Perturbed masses or constraints are not supported by rerun. "
                    "Either make a .tpr without mass and constraint perturbation, "
                    "or use GROMACS 2018.4, 2018.5 or later 2018 version.");
      }
      if (ir->bExpanded)
      {
          gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
      }
      if (ir->bSimTemp)
      {
          gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
      }
      if (ir->bDoAwh)
      {
          gmx_fatal(FARGS, "AWH not supported by rerun.");
      }
      if (replExParams.exchangeInterval > 0)
      {
          gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
      }
      if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
      {
          gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
      }
      if (ir->bIMD)
      {
          gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
      }
      if (isMultiSim(ms))
      {
          gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
      }
      if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
                      [](int i){return i != eannNO; }))
      {
          gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
      }
  
      /* Rerun can't work if an output file name is the same as the input file name.
       * If this is the case, the user will get an error telling them what the issue is.
       */
      if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0 ||
          strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
      {
          gmx_fatal(FARGS, "When using mdrun -rerun, the name of the input trajectory file "
                    "%s cannot be identical to the name of an output file (whether "
                    "given explicitly with -o or -x, or by default)",
                    opt2fn("-rerun", nfile, fnm));
      }
  
      /* Settings for rerun */
      ir->nstlist       = 1;
      ir->nstcalcenergy = 1;
      int        nstglobalcomm = 1;
      const bool bNS           = true;
  
      ir->nstxout_compressed = 0;
      SimulationGroups *groups                 = &top_global->groups;
      if (ir->eI == eiMimic)
      {
          top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
      }
  
      initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
      gmx_mdoutf       *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle,
                                           StartingBehavior::NewSimulation);
      gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work, mdoutf_get_fp_dhdl(outf), true);
  
      /* Kinetic energy data */
      std::unique_ptr<gmx_ekindata_t> eKinData = std::make_unique<gmx_ekindata_t>();
      gmx_ekindata_t                 *ekind    = eKinData.get();
      init_ekindata(fplog, top_global, &(ir->opts), ekind);
      /* Copy the cos acceleration to the groups struct */
      ekind->cosacc.cos_accel = ir->cos_accel;
  
      gstat = global_stat_init(ir);
  
      /* Check for polarizable models and flexible constraints */
      shellfc = init_shell_flexcon(fplog,
                                   top_global, constr ? constr->numFlexibleConstraints() : 0,
                                   ir->nstcalcenergy, DOMAINDECOMP(cr));
  
      {
          double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
          if ((io > 2000) && MASTER(cr))
          {
              fprintf(stderr,
                      "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
                      io);
          }
      }
  
      // Local state only becomes valid now.
      std::unique_ptr<t_state> stateInstance;
      t_state *                state;
  
      if (DOMAINDECOMP(cr))
      {
          dd_init_local_top(*top_global, &top);
  
          stateInstance = std::make_unique<t_state>();
          state         = stateInstance.get();
          dd_init_local_state(cr->dd, state_global, state);
  
          /* Distribute the charge groups over the nodes from the master node */
          dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
                              state_global, *top_global, ir, imdSession,
                              pull_work,
                              state, &f, mdAtoms, &top, fr,
                              vsite, constr,
                              nrnb, nullptr, FALSE);
          shouldCheckNumberOfBondedInteractions = true;
      }
      else
      {
          state_change_natoms(state_global, state_global->natoms);
          /* We need to allocate one element extra, since we might use
           * (unaligned) 4-wide SIMD loads to access rvec entries.
           */
          f.resizeWithPadding(state_global->natoms);
          /* Copy the pointer to the global state */
          state = state_global;
  
          mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
                                    &graph, mdAtoms, constr, vsite, shellfc);
      }
  
      auto mdatoms = mdAtoms->mdatoms();
  
      // NOTE: The global state is no longer used at this point.
      // But state_global is still used as temporary storage space for writing
      // the global state to file and potentially for replica exchange.
      // (Global topology should persist.)
  
      update_mdatoms(mdatoms, state->lambda[efptMASS]);
  
      if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
      {
          doFreeEnergyPerturbation = true;
      }
  
      {
          int    cglo_flags = (CGLO_INITIALIZATION | CGLO_GSTAT |
                               (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
          bool   bSumEkinhOld = false;
          t_vcm *vcm          = nullptr;
          compute_globals(fplog, gstat, cr, ir, fr, ekind,
                          state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
                          mdatoms, nrnb, vcm,
                          nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                          constr, &nullSignaller, state->box,
                          &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
      }
      checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
                                      top_global, &top, state->x.rvec_array(), state->box,
                                      &shouldCheckNumberOfBondedInteractions);
  
      if (MASTER(cr))
      {
          fprintf(stderr, "starting md rerun '%s', reading coordinates from"
                  " input trajectory '%s'\n\n",
                  *(top_global->name), opt2fn("-rerun", nfile, fnm));
          if (mdrunOptions.verbose)
          {
              fprintf(stderr, "Calculated time to finish depends on nsteps from "
                      "run input file,\nwhich may not correspond to the time "
                      "needed to process input trajectory.\n\n");
          }
          fprintf(fplog, "\n");
      }
  
      walltime_accounting_start_time(walltime_accounting);
      wallcycle_start(wcycle, ewcRUN);
      print_start(fplog, cr, walltime_accounting, "mdrun");
  
      /***********************************************************
       *
       *             Loop over MD steps
       *
       ************************************************************/
  
      if (constr)
      {
          GMX_LOG(mdlog.info).asParagraph().
              appendText("Simulations has constraints. Rerun does not recalculate constraints.");
      }
  
      rerun_fr.natoms = 0;
      if (MASTER(cr))
      {
          isLastStep = !read_first_frame(oenv, &status,
                                         opt2fn("-rerun", nfile, fnm),
                                         &rerun_fr, TRX_NEED_X);
          if (rerun_fr.natoms != top_global->natoms)
          {
              gmx_fatal(FARGS,
                        "Number of atoms in trajectory (%d) does not match the "
                        "run input file (%d)\n",
                        rerun_fr.natoms, top_global->natoms);
          }
  
          if (ir->ePBC != epbcNONE)
          {
              if (!rerun_fr.bBox)
              {
                  gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
                            "does not contain a box, while pbc is used",
                            rerun_fr.step, rerun_fr.time);
              }
              if (max_cutoff2(ir->ePBC, rerun_fr.box) < gmx::square(fr->rlist))
              {
                  gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
                            "has too small box dimensions", rerun_fr.step, rerun_fr.time);
              }
          }
      }
  
      GMX_LOG(mdlog.info).asParagraph().
          appendText("Rerun does not report kinetic energy, total energy, temperature, virial and pressure.");
  
      if (PAR(cr))
      {
          rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
      }
  
      if (ir->ePBC != epbcNONE)
      {
          /* Set the shift vectors.
           * Necessary here when have a static box different from the tpr box.
           */
          calc_shifts(rerun_fr.box, fr->shift_vec);
      }
  
      auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
                  compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
                  MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
                  mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
  
      // we don't do counter resetting in rerun - finish will always be valid
      walltime_accounting_set_valid_finish(walltime_accounting);
  
      const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
  
      step     = ir->init_step;
      step_rel = 0;
  
      /* and stop now if we should */
      isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
      while (!isLastStep)
      {
          wallcycle_start(wcycle, ewcSTEP);
  
          if (rerun_fr.bStep)
          {
              step     = rerun_fr.step;
              step_rel = step - ir->init_step;
          }
          if (rerun_fr.bTime)
          {
              t = rerun_fr.time;
          }
          else
          {
              t = step;
          }
  
          if (ir->efep != efepNO && MASTER(cr))
          {
              setCurrentLambdasRerun(step, ir->fepvals, &rerun_fr, lam0, state_global);
          }
  
          if (MASTER(cr))
          {
              const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
              if (constructVsites && DOMAINDECOMP(cr))
              {
                  gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
                            "use a single rank");
              }
              prepareRerunState(rerun_fr, state_global, constructVsites, vsite, top.idef, ir->delta_t, *fr, graph);
          }
  
          isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
  
          if (DOMAINDECOMP(cr))
          {
              /* Repartition the domain decomposition */
              const bool bMasterState = true;
              dd_partition_system(fplog, mdlog, step, cr,
                                  bMasterState, nstglobalcomm,
                                  state_global, *top_global, ir, imdSession,
                                  pull_work,
                                  state, &f, mdAtoms, &top, fr,
                                  vsite, constr,
                                  nrnb, wcycle,
                                  mdrunOptions.verbose);
              shouldCheckNumberOfBondedInteractions = true;
          }
  
          if (MASTER(cr))
          {
              energyOutput.printHeader(fplog, step, t); /* can we improve the information printed here? */
          }
  
          if (ir->efep != efepNO)
          {
              update_mdatoms(mdatoms, state->lambda[efptMASS]);
          }
  
          force_flags = (GMX_FORCE_STATECHANGED |
                         GMX_FORCE_DYNAMICBOX |
                         GMX_FORCE_ALLFORCES |
                         (GMX_GPU ? GMX_FORCE_VIRIAL : 0) |  // TODO: Get rid of this once #2649 is solved
                         GMX_FORCE_ENERGY |
                         (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
  
          if (shellfc)
          {
              /* Now is the time to relax the shells */
              relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
                                  enforcedRotation, step,
                                  ir, imdSession, pull_work, bNS, force_flags, &top,
                                  constr, enerd, fcd,
                                  state->natoms,
                                  state->x.arrayRefWithPadding(),
                                  state->v.arrayRefWithPadding(),
                                  state->box,
                                  state->lambda,
                                  &state->hist,
                                  f.arrayRefWithPadding(), force_vir, mdatoms,
                                  nrnb, wcycle, graph,
                                  shellfc, fr, ppForceWorkload, t, mu_tot,
                                  vsite,
                                  ddBalanceRegionHandler);
          }
          else
          {
              /* The coordinates (x) are shifted (to get whole molecules)
               * in do_force.
               * This is parallellized as well, and does communication too.
               * Check comments in sim_util.c
               */
              Awh       *awh = nullptr;
              gmx_edsam *ed  = nullptr;
              do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession,
                       pull_work,
                       step, nrnb, wcycle, &top,
                       state->box, state->x.arrayRefWithPadding(), &state->hist,
                       f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
                       state->lambda, graph,
                       fr, ppForceWorkload, vsite, mu_tot, t, ed,
                       GMX_FORCE_NS | force_flags,
                       ddBalanceRegionHandler);
          }
  
          /* Now we have the energies and forces corresponding to the
           * coordinates at time t.
           */
          {
              const bool isCheckpointingStep = false;
              const bool doRerun             = true;
              const bool bSumEkinhOld        = false;
              do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
                                       ir, state, state_global, observablesHistory,
                                       top_global, fr,
                                       outf, energyOutput, ekind, f,
                                       isCheckpointingStep, doRerun, isLastStep,
                                       mdrunOptions.writeConfout,
                                       bSumEkinhOld);
          }
  
          stopHandler->setSignal();
  
          if (graph)
          {
              /* Need to unshift here */
              unshift_self(graph, state->box, as_rvec_array(state->x.data()));
          }
  
          if (vsite != nullptr)
          {
              wallcycle_start(wcycle, ewcVSITECONSTR);
              if (graph != nullptr)
              {
                  shift_self(graph, state->box, as_rvec_array(state->x.data()));
              }
              construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
                               top.idef.iparams, top.idef.il,
                               fr->ePBC, fr->bMolPBC, cr, state->box);
  
              if (graph != nullptr)
              {
                  unshift_self(graph, state->box, as_rvec_array(state->x.data()));
              }
              wallcycle_stop(wcycle, ewcVSITECONSTR);
          }
  
          {
              const bool          doInterSimSignal = false;
              const bool          doIntraSimSignal = true;
              bool                bSumEkinhOld     = false;
              t_vcm              *vcm              = nullptr;
              SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
  
              compute_globals(fplog, gstat, cr, ir, fr, ekind,
                              state->x.rvec_array(), state->v.rvec_array(), state->box, state->lambda[efptVDW],
                              mdatoms, nrnb, vcm,
                              wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
                              constr, &signaller,
                              state->box,
                              &totalNumberOfBondedInteractions, &bSumEkinhOld,
                              CGLO_GSTAT | CGLO_ENERGY
                              | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
                              );
              checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
                                              top_global, &top, state->x.rvec_array(), state->box,
                                              &shouldCheckNumberOfBondedInteractions);
          }
  
          /* Note: this is OK, but there are some numerical precision issues with using the convergence of
             the virial that should probably be addressed eventually. state->veta has better properies,
             but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
             generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
  
          if (ir->efep != efepNO)
          {
              /* Sum up the foreign energy and dhdl terms for md and sd.
                 Currently done every step so that dhdl is correct in the .edr */
              sum_dhdl(enerd, state->lambda, ir->fepvals);
          }
  
          /* Output stuff */
          if (MASTER(cr))
          {
              const bool bCalcEnerStep = true;
              energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep,
                                               t, mdatoms->tmass, enerd, state,
                                               ir->fepvals, ir->expandedvals, state->box,
                                               shake_vir, force_vir, total_vir, pres,
                                               ekind, mu_tot,
                                               constr);
  
              const bool do_ene = true;
              const bool do_log = true;
              Awh       *awh    = nullptr;
              const bool do_dr  = ir->nstdisreout != 0;
              const bool do_or  = ir->nstorireout != 0;
  
              energyOutput.printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
              energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
                                                 do_log ? fplog : nullptr,
                                                 step, t,
                                                 fcd, awh);
  
              if (do_per_step(step, ir->nstlog))
              {
                  if (fflush(fplog) != 0)
                  {
                      gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
                  }
              }
          }
  
          /* Print the remaining wall clock time for the run */
          if (isMasterSimMasterRank(ms, MASTER(cr)) &&
              (mdrunOptions.verbose || gmx_got_usr_signal()))
          {
              if (shellfc)
              {
                  fprintf(stderr, "\n");
              }
              print_time(stderr, walltime_accounting, step, ir, cr);
          }
  
          /* Ion/water position swapping.
           * Not done in last step since trajectory writing happens before this call
           * in the MD loop and exchanges would be lost anyway. */
          if ((ir->eSwapCoords != eswapNO) && (step > 0) && !isLastStep &&
              do_per_step(step, ir->swap->nstswap))
          {
              const bool doRerun = true;
              do_swapcoords(cr, step, t, ir, swap, wcycle,
                            rerun_fr.x,
                            rerun_fr.box,
                            MASTER(cr) && mdrunOptions.verbose,
                            doRerun);
          }
  
          if (MASTER(cr))
          {
              /* read next frame from input trajectory */
              isLastStep = !read_next_frame(oenv, status, &rerun_fr);
          }
  
          if (PAR(cr))
          {
              rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
          }
  
          cycles = wallcycle_stop(wcycle, ewcSTEP);
          if (DOMAINDECOMP(cr) && wcycle)
          {
              dd_cycles_add(cr->dd, cycles, ddCyclStep);
          }
  
          if (!rerun_fr.bStep)
          {
              /* increase the MD step number */
              step++;
              step_rel++;
          }
      }
      /* End of main MD loop */
  
      /* Closing TNG files can include compressing data. Therefore it is good to do that
       * before stopping the time measurements. */
      mdoutf_tng_close(outf);
  
      /* Stop measuring walltime */
      walltime_accounting_end_time(walltime_accounting);
  
      if (MASTER(cr))
      {
          close_trx(status);
      }
  
      if (!thisRankHasDuty(cr, DUTY_PME))
      {
          /* Tell the PME only node to finish */
          gmx_pme_send_finish(cr);
      }
  
      done_mdoutf(outf);
  
      done_shellfc(fplog, shellfc, step_rel);
  
      walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
  }
  