Make relax_shell_flexcon independent of t_state

[gromacs.git] / src / gromacs / mdrun / rerun.cpp

/*
 * 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.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
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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;
    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);
    init_nrnb(nrnb);
    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, 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,
                                    &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, 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,
                                            &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);
}