Use ArrayRef in signatures of constraints and some pulling

[alexxy/gromacs.git] / src / gromacs / mdlib / sim_util.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013-2019,2020,2021, 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
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#include "gmxpre.h"

#include "config.h"

#include <cmath>
#include <cstdint>
#include <cstdio>
#include <cstring>

#include <array>
#include <optional>

#include "gromacs/applied_forces/awh/awh.h"
#include "gromacs/domdec/dlbtiming.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/gpuhaloexchange.h"
#include "gromacs/domdec/partition.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/ewald/pme_pp.h"
#include "gromacs/ewald/pme_pp_comm_gpu.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
#include "gromacs/gmxlib/nonbonded/nonbonded.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/imd/imd.h"
#include "gromacs/listed_forces/disre.h"
#include "gromacs/listed_forces/gpubonded.h"
#include "gromacs/listed_forces/listed_forces.h"
#include "gromacs/listed_forces/orires.h"
#include "gromacs/math/arrayrefwithpadding.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vecdump.h"
#include "gromacs/mdlib/calcmu.h"
#include "gromacs/mdlib/calcvir.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/dispersioncorrection.h"
#include "gromacs/mdlib/enerdata_utils.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdlib/wall.h"
#include "gromacs/mdlib/wholemoleculetransform.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/forcebuffers.h"
#include "gromacs/mdtypes/forceoutput.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/iforceprovider.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/multipletimestepping.h"
#include "gromacs/mdtypes/simulation_workload.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/mdtypes/state_propagator_data_gpu.h"
#include "gromacs/nbnxm/gpu_data_mgmt.h"
#include "gromacs/nbnxm/nbnxm.h"
#include "gromacs/nbnxm/nbnxm_gpu.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/pulling/pull_rotation.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/timing/gpu_timing.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/wallcyclereporting.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/fixedcapacityvector.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/sysinfo.h"

#include "gpuforcereduction.h"

using gmx::ArrayRef;
using gmx::AtomLocality;
using gmx::DomainLifetimeWorkload;
using gmx::ForceOutputs;
using gmx::ForceWithShiftForces;
using gmx::InteractionLocality;
using gmx::RVec;
using gmx::SimulationWorkload;
using gmx::StepWorkload;

// TODO: this environment variable allows us to verify before release
// that on less common architectures the total cost of polling is not larger than
// a blocking wait (so polling does not introduce overhead when the static
// PME-first ordering would suffice).
static const bool c_disableAlternatingWait = (getenv("GMX_DISABLE_ALTERNATING_GPU_WAIT") != nullptr);

static void sum_forces(ArrayRef<RVec> f, ArrayRef<const RVec> forceToAdd)
{
    GMX_ASSERT(f.size() >= forceToAdd.size(), "Accumulation buffer should be sufficiently large");
    const int end = forceToAdd.size();

    int gmx_unused nt = gmx_omp_nthreads_get(emntDefault);
#pragma omp parallel for num_threads(nt) schedule(static)
    for (int i = 0; i < end; i++)
    {
        rvec_inc(f[i], forceToAdd[i]);
    }
}

static void calc_virial(int                              start,
                        int                              homenr,
                        const rvec                       x[],
                        const gmx::ForceWithShiftForces& forceWithShiftForces,
                        tensor                           vir_part,
                        const matrix                     box,
                        t_nrnb*                          nrnb,
                        const t_forcerec*                fr,
                        PbcType                          pbcType)
{
    /* The short-range virial from surrounding boxes */
    const rvec* fshift = as_rvec_array(forceWithShiftForces.shiftForces().data());
    calc_vir(SHIFTS, fr->shift_vec, fshift, vir_part, pbcType == PbcType::Screw, box);
    inc_nrnb(nrnb, eNR_VIRIAL, SHIFTS);

    /* Calculate partial virial, for local atoms only, based on short range.
     * Total virial is computed in global_stat, called from do_md
     */
    const rvec* f = as_rvec_array(forceWithShiftForces.force().data());
    f_calc_vir(start, start + homenr, x, f, vir_part, box);
    inc_nrnb(nrnb, eNR_VIRIAL, homenr);

    if (debug)
    {
        pr_rvecs(debug, 0, "vir_part", vir_part, DIM);
    }
}

static void pull_potential_wrapper(const t_commrec*               cr,
                                   const t_inputrec&              ir,
                                   const matrix                   box,
                                   gmx::ArrayRef<const gmx::RVec> x,
                                   gmx::ForceWithVirial*          force,
                                   const t_mdatoms*               mdatoms,
                                   gmx_enerdata_t*                enerd,
                                   pull_t*                        pull_work,
                                   const real*                    lambda,
                                   double                         t,
                                   gmx_wallcycle_t                wcycle)
{
    t_pbc pbc;
    real  dvdl;

    /* Calculate the center of mass forces, this requires communication,
     * which is why pull_potential is called close to other communication.
     */
    wallcycle_start(wcycle, ewcPULLPOT);
    set_pbc(&pbc, ir.pbcType, box);
    dvdl = 0;
    enerd->term[F_COM_PULL] +=
            pull_potential(pull_work,
                           gmx::arrayRefFromArray(mdatoms->massT, mdatoms->nr),
                           &pbc,
                           cr,
                           t,
                           lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Restraint)],
                           x,
                           force,
                           &dvdl);
    enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Restraint] += dvdl;
    wallcycle_stop(wcycle, ewcPULLPOT);
}

static void pme_receive_force_ener(t_forcerec*           fr,
                                   const t_commrec*      cr,
                                   gmx::ForceWithVirial* forceWithVirial,
                                   gmx_enerdata_t*       enerd,
                                   bool                  useGpuPmePpComms,
                                   bool                  receivePmeForceToGpu,
                                   gmx_wallcycle_t       wcycle)
{
    real  e_q, e_lj, dvdl_q, dvdl_lj;
    float cycles_ppdpme, cycles_seppme;

    cycles_ppdpme = wallcycle_stop(wcycle, ewcPPDURINGPME);
    dd_cycles_add(cr->dd, cycles_ppdpme, ddCyclPPduringPME);

    /* In case of node-splitting, the PP nodes receive the long-range
     * forces, virial and energy from the PME nodes here.
     */
    wallcycle_start(wcycle, ewcPP_PMEWAITRECVF);
    dvdl_q  = 0;
    dvdl_lj = 0;
    gmx_pme_receive_f(fr->pmePpCommGpu.get(),
                      cr,
                      forceWithVirial,
                      &e_q,
                      &e_lj,
                      &dvdl_q,
                      &dvdl_lj,
                      useGpuPmePpComms,
                      receivePmeForceToGpu,
                      &cycles_seppme);
    enerd->term[F_COUL_RECIP] += e_q;
    enerd->term[F_LJ_RECIP] += e_lj;
    enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Coul] += dvdl_q;
    enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Vdw] += dvdl_lj;

    if (wcycle)
    {
        dd_cycles_add(cr->dd, cycles_seppme, ddCyclPME);
    }
    wallcycle_stop(wcycle, ewcPP_PMEWAITRECVF);
}

static void print_large_forces(FILE*                fp,
                               const t_mdatoms*     md,
                               const t_commrec*     cr,
                               int64_t              step,
                               real                 forceTolerance,
                               ArrayRef<const RVec> x,
                               ArrayRef<const RVec> f)
{
    real       force2Tolerance = gmx::square(forceTolerance);
    gmx::index numNonFinite    = 0;
    for (int i = 0; i < md->homenr; i++)
    {
        real force2    = norm2(f[i]);
        bool nonFinite = !std::isfinite(force2);
        if (force2 >= force2Tolerance || nonFinite)
        {
            fprintf(fp,
                    "step %" PRId64 " atom %6d  x %8.3f %8.3f %8.3f  force %12.5e\n",
                    step,
                    ddglatnr(cr->dd, i),
                    x[i][XX],
                    x[i][YY],
                    x[i][ZZ],
                    std::sqrt(force2));
        }
        if (nonFinite)
        {
            numNonFinite++;
        }
    }
    if (numNonFinite > 0)
    {
        /* Note that with MPI this fatal call on one rank might interrupt
         * the printing on other ranks. But we can only avoid that with
         * an expensive MPI barrier that we would need at each step.
         */
        gmx_fatal(FARGS, "At step %" PRId64 " detected non-finite forces on %td atoms", step, numNonFinite);
    }
}

//! When necessary, spreads forces on vsites and computes the virial for \p forceOutputs->forceWithShiftForces()
static void postProcessForceWithShiftForces(t_nrnb*                   nrnb,
                                            gmx_wallcycle_t           wcycle,
                                            const matrix              box,
                                            ArrayRef<const RVec>      x,
                                            ForceOutputs*             forceOutputs,
                                            tensor                    vir_force,
                                            const t_mdatoms&          mdatoms,
                                            const t_forcerec&         fr,
                                            gmx::VirtualSitesHandler* vsite,
                                            const StepWorkload&       stepWork)
{
    ForceWithShiftForces& forceWithShiftForces = forceOutputs->forceWithShiftForces();

    /* If we have NoVirSum forces, but we do not calculate the virial,
     * we later sum the forceWithShiftForces buffer together with
     * the noVirSum buffer and spread the combined vsite forces at once.
     */
    if (vsite && (!forceOutputs->haveForceWithVirial() || stepWork.computeVirial))
    {
        using VirialHandling = gmx::VirtualSitesHandler::VirialHandling;

        auto                 f      = forceWithShiftForces.force();
        auto                 fshift = forceWithShiftForces.shiftForces();
        const VirialHandling virialHandling =
                (stepWork.computeVirial ? VirialHandling::Pbc : VirialHandling::None);
        vsite->spreadForces(x, f, virialHandling, fshift, nullptr, nrnb, box, wcycle);
        forceWithShiftForces.haveSpreadVsiteForces() = true;
    }

    if (stepWork.computeVirial)
    {
        /* Calculation of the virial must be done after vsites! */
        calc_virial(
                0, mdatoms.homenr, as_rvec_array(x.data()), forceWithShiftForces, vir_force, box, nrnb, &fr, fr.pbcType);
    }
}

//! Spread, compute virial for and sum forces, when necessary
static void postProcessForces(const t_commrec*          cr,
                              int64_t                   step,
                              t_nrnb*                   nrnb,
                              gmx_wallcycle_t           wcycle,
                              const matrix              box,
                              ArrayRef<const RVec>      x,
                              ForceOutputs*             forceOutputs,
                              tensor                    vir_force,
                              const t_mdatoms*          mdatoms,
                              const t_forcerec*         fr,
                              gmx::VirtualSitesHandler* vsite,
                              const StepWorkload&       stepWork)
{
    // Extract the final output force buffer, which is also the buffer for forces with shift forces
    ArrayRef<RVec> f = forceOutputs->forceWithShiftForces().force();

    if (forceOutputs->haveForceWithVirial())
    {
        auto& forceWithVirial = forceOutputs->forceWithVirial();

        if (vsite)
        {
            /* Spread the mesh force on virtual sites to the other particles...
             * This is parallellized. MPI communication is performed
             * if the constructing atoms aren't local.
             */
            GMX_ASSERT(!stepWork.computeVirial || f.data() != forceWithVirial.force_.data(),
                       "We need separate force buffers for shift and virial forces when "
                       "computing the virial");
            GMX_ASSERT(!stepWork.computeVirial
                               || forceOutputs->forceWithShiftForces().haveSpreadVsiteForces(),
                       "We should spread the force with shift forces separately when computing "
                       "the virial");
            const gmx::VirtualSitesHandler::VirialHandling virialHandling =
                    (stepWork.computeVirial ? gmx::VirtualSitesHandler::VirialHandling::NonLinear
                                            : gmx::VirtualSitesHandler::VirialHandling::None);
            matrix virial = { { 0 } };
            vsite->spreadForces(x, forceWithVirial.force_, virialHandling, {}, virial, nrnb, box, wcycle);
            forceWithVirial.addVirialContribution(virial);
        }

        if (stepWork.computeVirial)
        {
            /* Now add the forces, this is local */
            sum_forces(f, forceWithVirial.force_);

            /* Add the direct virial contributions */
            GMX_ASSERT(
                    forceWithVirial.computeVirial_,
                    "forceWithVirial should request virial computation when we request the virial");
            m_add(vir_force, forceWithVirial.getVirial(), vir_force);

            if (debug)
            {
                pr_rvecs(debug, 0, "vir_force", vir_force, DIM);
            }
        }
    }
    else
    {
        GMX_ASSERT(vsite == nullptr || forceOutputs->forceWithShiftForces().haveSpreadVsiteForces(),
                   "We should have spread the vsite forces (earlier)");
    }

    if (fr->print_force >= 0)
    {
        print_large_forces(stderr, mdatoms, cr, step, fr->print_force, x, f);
    }
}

static void do_nb_verlet(t_forcerec*                fr,
                         const interaction_const_t* ic,
                         gmx_enerdata_t*            enerd,
                         const StepWorkload&        stepWork,
                         const InteractionLocality  ilocality,
                         const int                  clearF,
                         const int64_t              step,
                         t_nrnb*                    nrnb,
                         gmx_wallcycle_t            wcycle)
{
    if (!stepWork.computeNonbondedForces)
    {
        /* skip non-bonded calculation */
        return;
    }

    nonbonded_verlet_t* nbv = fr->nbv.get();

    /* GPU kernel launch overhead is already timed separately */
    if (!nbv->useGpu())
    {
        /* When dynamic pair-list  pruning is requested, we need to prune
         * at nstlistPrune steps.
         */
        if (nbv->isDynamicPruningStepCpu(step))
        {
            /* Prune the pair-list beyond fr->ic->rlistPrune using
             * the current coordinates of the atoms.
             */
            wallcycle_sub_start(wcycle, ewcsNONBONDED_PRUNING);
            nbv->dispatchPruneKernelCpu(ilocality, fr->shift_vec);
            wallcycle_sub_stop(wcycle, ewcsNONBONDED_PRUNING);
        }
    }

    nbv->dispatchNonbondedKernel(ilocality, *ic, stepWork, clearF, *fr, enerd, nrnb);
}

static inline void clearRVecs(ArrayRef<RVec> v, const bool useOpenmpThreading)
{
    int nth = gmx_omp_nthreads_get_simple_rvec_task(emntDefault, v.ssize());

    /* Note that we would like to avoid this conditional by putting it
     * into the omp pragma instead, but then we still take the full
     * omp parallel for overhead (at least with gcc5).
     */
    if (!useOpenmpThreading || nth == 1)
    {
        for (RVec& elem : v)
        {
            clear_rvec(elem);
        }
    }
    else
    {
#pragma omp parallel for num_threads(nth) schedule(static)
        for (gmx::index i = 0; i < v.ssize(); i++)
        {
            clear_rvec(v[i]);
        }
    }
}

/*! \brief Return an estimate of the average kinetic energy or 0 when unreliable
 *
 * \param groupOptions  Group options, containing T-coupling options
 */
static real averageKineticEnergyEstimate(const t_grpopts& groupOptions)
{
    real nrdfCoupled   = 0;
    real nrdfUncoupled = 0;
    real kineticEnergy = 0;
    for (int g = 0; g < groupOptions.ngtc; g++)
    {
        if (groupOptions.tau_t[g] >= 0)
        {
            nrdfCoupled += groupOptions.nrdf[g];
            kineticEnergy += groupOptions.nrdf[g] * 0.5 * groupOptions.ref_t[g] * gmx::c_boltz;
        }
        else
        {
            nrdfUncoupled += groupOptions.nrdf[g];
        }
    }

    /* This conditional with > also catches nrdf=0 */
    if (nrdfCoupled > nrdfUncoupled)
    {
        return kineticEnergy * (nrdfCoupled + nrdfUncoupled) / nrdfCoupled;
    }
    else
    {
        return 0;
    }
}

/*! \brief This routine checks that the potential energy is finite.
 *
 * Always checks that the potential energy is finite. If step equals
 * inputrec.init_step also checks that the magnitude of the potential energy
 * is reasonable. Terminates with a fatal error when a check fails.
 * Note that passing this check does not guarantee finite forces,
 * since those use slightly different arithmetics. But in most cases
 * there is just a narrow coordinate range where forces are not finite
 * and energies are finite.
 *
 * \param[in] step      The step number, used for checking and printing
 * \param[in] enerd     The energy data; the non-bonded group energies need to be added to
 * enerd.term[F_EPOT] before calling this routine \param[in] inputrec  The input record
 */
static void checkPotentialEnergyValidity(int64_t step, const gmx_enerdata_t& enerd, const t_inputrec& inputrec)
{
    /* Threshold valid for comparing absolute potential energy against
     * the kinetic energy. Normally one should not consider absolute
     * potential energy values, but with a factor of one million
     * we should never get false positives.
     */
    constexpr real c_thresholdFactor = 1e6;

    bool energyIsNotFinite    = !std::isfinite(enerd.term[F_EPOT]);
    real averageKineticEnergy = 0;
    /* We only check for large potential energy at the initial step,
     * because that is by far the most likely step for this too occur
     * and because computing the average kinetic energy is not free.
     * Note: nstcalcenergy >> 1 often does not allow to catch large energies
     * before they become NaN.
     */
    if (step == inputrec.init_step && EI_DYNAMICS(inputrec.eI))
    {
        averageKineticEnergy = averageKineticEnergyEstimate(inputrec.opts);
    }

    if (energyIsNotFinite
        || (averageKineticEnergy > 0 && enerd.term[F_EPOT] > c_thresholdFactor * averageKineticEnergy))
    {
        gmx_fatal(
                FARGS,
                "Step %" PRId64
                ": The total potential energy is %g, which is %s. The LJ and electrostatic "
                "contributions to the energy are %g and %g, respectively. A %s potential energy "
                "can be caused by overlapping interactions in bonded interactions or very large%s "
                "coordinate values. Usually this is caused by a badly- or non-equilibrated initial "
                "configuration, incorrect interactions or parameters in the topology.",
                step,
                enerd.term[F_EPOT],
                energyIsNotFinite ? "not finite" : "extremely high",
                enerd.term[F_LJ],
                enerd.term[F_COUL_SR],
                energyIsNotFinite ? "non-finite" : "very high",
                energyIsNotFinite ? " or Nan" : "");
    }
}

/*! \brief Return true if there are special forces computed this step.
 *
 * The conditionals exactly correspond to those in computeSpecialForces().
 */
static bool haveSpecialForces(const t_inputrec&          inputrec,
                              const gmx::ForceProviders& forceProviders,
                              const pull_t*              pull_work,
                              const bool                 computeForces,
                              const gmx_edsam*           ed)
{

    return ((computeForces && forceProviders.hasForceProvider()) || // forceProviders
            (inputrec.bPull && pull_have_potential(*pull_work)) ||  // pull
            inputrec.bRot ||                                        // enforced rotation
            (ed != nullptr) ||                                      // flooding
            (inputrec.bIMD && computeForces));                      // IMD
}

/*! \brief Compute forces and/or energies for special algorithms
 *
 * The intention is to collect all calls to algorithms that compute
 * forces on local atoms only and that do not contribute to the local
 * virial sum (but add their virial contribution separately).
 * Eventually these should likely all become ForceProviders.
 * Within this function the intention is to have algorithms that do
 * global communication at the end, so global barriers within the MD loop
 * are as close together as possible.
 *
 * \param[in]     fplog            The log file
 * \param[in]     cr               The communication record
 * \param[in]     inputrec         The input record
 * \param[in]     awh              The Awh module (nullptr if none in use).
 * \param[in]     enforcedRotation Enforced rotation module.
 * \param[in]     imdSession       The IMD session
 * \param[in]     pull_work        The pull work structure.
 * \param[in]     step             The current MD step
 * \param[in]     t                The current time
 * \param[in,out] wcycle           Wallcycle accounting struct
 * \param[in,out] forceProviders   Pointer to a list of force providers
 * \param[in]     box              The unit cell
 * \param[in]     x                The coordinates
 * \param[in]     mdatoms          Per atom properties
 * \param[in]     lambda           Array of free-energy lambda values
 * \param[in]     stepWork         Step schedule flags
 * \param[in,out] forceWithVirialMtsLevel0  Force and virial for MTS level0 forces
 * \param[in,out] forceWithVirialMtsLevel1  Force and virial for MTS level1 forces, can be nullptr
 * \param[in,out] enerd            Energy buffer
 * \param[in,out] ed               Essential dynamics pointer
 * \param[in]     didNeighborSearch Tells if we did neighbor searching this step, used for ED sampling
 *
 * \todo Remove didNeighborSearch, which is used incorrectly.
 * \todo Convert all other algorithms called here to ForceProviders.
 */
static void computeSpecialForces(FILE*                          fplog,
                                 const t_commrec*               cr,
                                 const t_inputrec&              inputrec,
                                 gmx::Awh*                      awh,
                                 gmx_enfrot*                    enforcedRotation,
                                 gmx::ImdSession*               imdSession,
                                 pull_t*                        pull_work,
                                 int64_t                        step,
                                 double                         t,
                                 gmx_wallcycle_t                wcycle,
                                 gmx::ForceProviders*           forceProviders,
                                 const matrix                   box,
                                 gmx::ArrayRef<const gmx::RVec> x,
                                 const t_mdatoms*               mdatoms,
                                 gmx::ArrayRef<const real>      lambda,
                                 const StepWorkload&            stepWork,
                                 gmx::ForceWithVirial*          forceWithVirialMtsLevel0,
                                 gmx::ForceWithVirial*          forceWithVirialMtsLevel1,
                                 gmx_enerdata_t*                enerd,
                                 gmx_edsam*                     ed,
                                 bool                           didNeighborSearch)
{
    /* NOTE: Currently all ForceProviders only provide forces.
     *       When they also provide energies, remove this conditional.
     */
    if (stepWork.computeForces)
    {
        gmx::ForceProviderInput forceProviderInput(
                x,
                mdatoms->homenr,
                gmx::arrayRefFromArray(mdatoms->chargeA, mdatoms->homenr),
                gmx::arrayRefFromArray(mdatoms->massT, mdatoms->homenr),
                t,
                box,
                *cr);
        gmx::ForceProviderOutput forceProviderOutput(forceWithVirialMtsLevel0, enerd);

        /* Collect forces from modules */
        forceProviders->calculateForces(forceProviderInput, &forceProviderOutput);
    }

    if (inputrec.bPull && pull_have_potential(*pull_work))
    {
        const int mtsLevel = forceGroupMtsLevel(inputrec.mtsLevels, gmx::MtsForceGroups::Pull);
        if (mtsLevel == 0 || stepWork.computeSlowForces)
        {
            auto& forceWithVirial = (mtsLevel == 0) ? forceWithVirialMtsLevel0 : forceWithVirialMtsLevel1;
            pull_potential_wrapper(
                    cr, inputrec, box, x, forceWithVirial, mdatoms, enerd, pull_work, lambda.data(), t, wcycle);
        }
    }
    if (awh)
    {
        const int mtsLevel = forceGroupMtsLevel(inputrec.mtsLevels, gmx::MtsForceGroups::Pull);
        if (mtsLevel == 0 || stepWork.computeSlowForces)
        {
            const bool needForeignEnergyDifferences = awh->needForeignEnergyDifferences(step);
            std::vector<double> foreignLambdaDeltaH, foreignLambdaDhDl;
            if (needForeignEnergyDifferences)
            {
                enerd->foreignLambdaTerms.finalizePotentialContributions(
                        enerd->dvdl_lin, lambda, *inputrec.fepvals);
                std::tie(foreignLambdaDeltaH, foreignLambdaDhDl) = enerd->foreignLambdaTerms.getTerms(cr);
            }

            auto& forceWithVirial = (mtsLevel == 0) ? forceWithVirialMtsLevel0 : forceWithVirialMtsLevel1;
            enerd->term[F_COM_PULL] += awh->applyBiasForcesAndUpdateBias(
                    inputrec.pbcType,
                    gmx::arrayRefFromArray(mdatoms->massT, mdatoms->nr),
                    foreignLambdaDeltaH,
                    foreignLambdaDhDl,
                    box,
                    forceWithVirial,
                    t,
                    step,
                    wcycle,
                    fplog);
        }
    }

    rvec* f = as_rvec_array(forceWithVirialMtsLevel0->force_.data());

    /* Add the forces from enforced rotation potentials (if any) */
    if (inputrec.bRot)
    {
        wallcycle_start(wcycle, ewcROTadd);
        enerd->term[F_COM_PULL] += add_rot_forces(enforcedRotation, f, cr, step, t);
        wallcycle_stop(wcycle, ewcROTadd);
    }

    if (ed)
    {
        /* Note that since init_edsam() is called after the initialization
         * of forcerec, edsam doesn't request the noVirSum force buffer.
         * Thus if no other algorithm (e.g. PME) requires it, the forces
         * here will contribute to the virial.
         */
        do_flood(cr, inputrec, as_rvec_array(x.data()), f, ed, box, step, didNeighborSearch);
    }

    /* Add forces from interactive molecular dynamics (IMD), if any */
    if (inputrec.bIMD && stepWork.computeForces)
    {
        imdSession->applyForces(f);
    }
}

/*! \brief Launch the prepare_step and spread stages of PME GPU.
 *
 * \param[in]  pmedata              The PME structure
 * \param[in]  box                  The box matrix
 * \param[in]  stepWork             Step schedule flags
 * \param[in]  xReadyOnDevice       Event synchronizer indicating that the coordinates are ready in the device memory.
 * \param[in]  lambdaQ              The Coulomb lambda of the current state.
 * \param[in]  wcycle               The wallcycle structure
 */
static inline void launchPmeGpuSpread(gmx_pme_t*            pmedata,
                                      const matrix          box,
                                      const StepWorkload&   stepWork,
                                      GpuEventSynchronizer* xReadyOnDevice,
                                      const real            lambdaQ,
                                      gmx_wallcycle_t       wcycle)
{
    pme_gpu_prepare_computation(pmedata, box, wcycle, stepWork);
    pme_gpu_launch_spread(pmedata, xReadyOnDevice, wcycle, lambdaQ);
}

/*! \brief Launch the FFT and gather stages of PME GPU
 *
 * This function only implements setting the output forces (no accumulation).
 *
 * \param[in]  pmedata        The PME structure
 * \param[in]  lambdaQ        The Coulomb lambda of the current system state.
 * \param[in]  wcycle         The wallcycle structure
 * \param[in]  stepWork       Step schedule flags
 */
static void launchPmeGpuFftAndGather(gmx_pme_t*               pmedata,
                                     const real               lambdaQ,
                                     gmx_wallcycle_t          wcycle,
                                     const gmx::StepWorkload& stepWork)
{
    pme_gpu_launch_complex_transforms(pmedata, wcycle, stepWork);
    pme_gpu_launch_gather(pmedata, wcycle, lambdaQ);
}

/*! \brief
 *  Polling wait for either of the PME or nonbonded GPU tasks.
 *
 * Instead of a static order in waiting for GPU tasks, this function
 * polls checking which of the two tasks completes first, and does the
 * associated force buffer reduction overlapped with the other task.
 * By doing that, unlike static scheduling order, it can always overlap
 * one of the reductions, regardless of the GPU task completion order.
 *
 * \param[in]     nbv              Nonbonded verlet structure
 * \param[in,out] pmedata          PME module data
 * \param[in,out] forceOutputsNonbonded  Force outputs for the non-bonded forces and shift forces
 * \param[in,out] forceOutputsPme  Force outputs for the PME forces and virial
 * \param[in,out] enerd            Energy data structure results are reduced into
 * \param[in]     lambdaQ          The Coulomb lambda of the current system state.
 * \param[in]     stepWork         Step schedule flags
 * \param[in]     wcycle           The wallcycle structure
 */
static void alternatePmeNbGpuWaitReduce(nonbonded_verlet_t* nbv,
                                        gmx_pme_t*          pmedata,
                                        gmx::ForceOutputs*  forceOutputsNonbonded,
                                        gmx::ForceOutputs*  forceOutputsPme,
                                        gmx_enerdata_t*     enerd,
                                        const real          lambdaQ,
                                        const StepWorkload& stepWork,
                                        gmx_wallcycle_t     wcycle)
{
    bool isPmeGpuDone = false;
    bool isNbGpuDone  = false;

    gmx::ArrayRef<const gmx::RVec> pmeGpuForces;

    while (!isPmeGpuDone || !isNbGpuDone)
    {
        if (!isPmeGpuDone)
        {
            GpuTaskCompletion completionType =
                    (isNbGpuDone) ? GpuTaskCompletion::Wait : GpuTaskCompletion::Check;
            isPmeGpuDone = pme_gpu_try_finish_task(
                    pmedata, stepWork, wcycle, &forceOutputsPme->forceWithVirial(), enerd, lambdaQ, completionType);
        }

        if (!isNbGpuDone)
        {
            auto&             forceBuffersNonbonded = forceOutputsNonbonded->forceWithShiftForces();
            GpuTaskCompletion completionType =
                    (isPmeGpuDone) ? GpuTaskCompletion::Wait : GpuTaskCompletion::Check;
            isNbGpuDone = Nbnxm::gpu_try_finish_task(
                    nbv->gpu_nbv,
                    stepWork,
                    AtomLocality::Local,
                    enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR].data(),
                    enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR].data(),
                    forceBuffersNonbonded.shiftForces(),
                    completionType,
                    wcycle);

            if (isNbGpuDone)
            {
                nbv->atomdata_add_nbat_f_to_f(AtomLocality::Local, forceBuffersNonbonded.force());
            }
        }
    }
}

/*! \brief Set up the different force buffers; also does clearing.
 *
 * \param[in] forceHelperBuffers  Helper force buffers
 * \param[in] force     force array
 * \param[in] stepWork  Step schedule flags
 * \param[out] wcycle   wallcycle recording structure
 *
 * \returns             Cleared force output structure
 */
static ForceOutputs setupForceOutputs(ForceHelperBuffers*                 forceHelperBuffers,
                                      gmx::ArrayRefWithPadding<gmx::RVec> force,
                                      const StepWorkload&                 stepWork,
                                      gmx_wallcycle_t                     wcycle)
{
    wallcycle_sub_start(wcycle, ewcsCLEAR_FORCE_BUFFER);

    /* NOTE: We assume fr->shiftForces is all zeros here */
    gmx::ForceWithShiftForces forceWithShiftForces(
            force, stepWork.computeVirial, forceHelperBuffers->shiftForces());

    if (stepWork.computeForces)
    {
        /* Clear the short- and long-range forces */
        clearRVecs(forceWithShiftForces.force(), true);

        /* Clear the shift forces */
        clearRVecs(forceWithShiftForces.shiftForces(), false);
    }

    /* If we need to compute the virial, we might need a separate
     * force buffer for algorithms for which the virial is calculated
     * directly, such as PME. Otherwise, forceWithVirial uses the
     * the same force (f in legacy calls) buffer as other algorithms.
     */
    const bool useSeparateForceWithVirialBuffer =
            (stepWork.computeForces
             && (stepWork.computeVirial && forceHelperBuffers->haveDirectVirialContributions()));
    /* forceWithVirial uses the local atom range only */
    gmx::ForceWithVirial forceWithVirial(
            useSeparateForceWithVirialBuffer ? forceHelperBuffers->forceBufferForDirectVirialContributions()
                                             : force.unpaddedArrayRef(),
            stepWork.computeVirial);

    if (useSeparateForceWithVirialBuffer)
    {
        /* TODO: update comment
         * We only compute forces on local atoms. Note that vsites can
         * spread to non-local atoms, but that part of the buffer is
         * cleared separately in the vsite spreading code.
         */
        clearRVecs(forceWithVirial.force_, true);
    }

    wallcycle_sub_stop(wcycle, ewcsCLEAR_FORCE_BUFFER);

    return ForceOutputs(
            forceWithShiftForces, forceHelperBuffers->haveDirectVirialContributions(), forceWithVirial);
}


/*! \brief Set up flags that have the lifetime of the domain indicating what type of work is there to compute.
 */
static DomainLifetimeWorkload setupDomainLifetimeWorkload(const t_inputrec&         inputrec,
                                                          const t_forcerec&         fr,
                                                          const pull_t*             pull_work,
                                                          const gmx_edsam*          ed,
                                                          const t_mdatoms&          mdatoms,
                                                          const SimulationWorkload& simulationWork,
                                                          const StepWorkload&       stepWork)
{
    DomainLifetimeWorkload domainWork;
    // Note that haveSpecialForces is constant over the whole run
    domainWork.haveSpecialForces =
            haveSpecialForces(inputrec, *fr.forceProviders, pull_work, stepWork.computeForces, ed);
    domainWork.haveCpuListedForceWork = false;
    domainWork.haveCpuBondedWork      = false;
    for (const auto& listedForces : fr.listedForces)
    {
        if (listedForces.haveCpuListedForces(*fr.fcdata))
        {
            domainWork.haveCpuListedForceWork = true;
        }
        if (listedForces.haveCpuBondeds())
        {
            domainWork.haveCpuBondedWork = true;
        }
    }
    domainWork.haveGpuBondedWork = ((fr.gpuBonded != nullptr) && fr.gpuBonded->haveInteractions());
    // Note that haveFreeEnergyWork is constant over the whole run
    domainWork.haveFreeEnergyWork =
            (fr.efep != FreeEnergyPerturbationType::No && mdatoms.nPerturbed != 0);
    // We assume we have local force work if there are CPU
    // force tasks including PME or nonbondeds.
    domainWork.haveCpuLocalForceWork =
            domainWork.haveSpecialForces || domainWork.haveCpuListedForceWork
            || domainWork.haveFreeEnergyWork || simulationWork.useCpuNonbonded || simulationWork.useCpuPme
            || simulationWork.haveEwaldSurfaceContribution || inputrec.nwall > 0;

    return domainWork;
}

/*! \brief Set up force flag stuct from the force bitmask.
 *
 * \param[in]      legacyFlags          Force bitmask flags used to construct the new flags
 * \param[in]      mtsLevels            The multiple time-stepping levels, either empty or 2 levels
 * \param[in]      step                 The current MD step
 * \param[in]      simulationWork       Simulation workload description.
 * \param[in]      rankHasPmeDuty       If this rank computes PME.
 *
 * \returns New Stepworkload description.
 */
static StepWorkload setupStepWorkload(const int                     legacyFlags,
                                      ArrayRef<const gmx::MtsLevel> mtsLevels,
                                      const int64_t                 step,
                                      const SimulationWorkload&     simulationWork,
                                      const bool                    rankHasPmeDuty)
{
    GMX_ASSERT(mtsLevels.empty() || mtsLevels.size() == 2, "Expect 0 or 2 MTS levels");
    const bool computeSlowForces = (mtsLevels.empty() || step % mtsLevels[1].stepFactor == 0);

    StepWorkload flags;
    flags.stateChanged        = ((legacyFlags & GMX_FORCE_STATECHANGED) != 0);
    flags.haveDynamicBox      = ((legacyFlags & GMX_FORCE_DYNAMICBOX) != 0);
    flags.doNeighborSearch    = ((legacyFlags & GMX_FORCE_NS) != 0);
    flags.computeSlowForces   = computeSlowForces;
    flags.computeVirial       = ((legacyFlags & GMX_FORCE_VIRIAL) != 0);
    flags.computeEnergy       = ((legacyFlags & GMX_FORCE_ENERGY) != 0);
    flags.computeForces       = ((legacyFlags & GMX_FORCE_FORCES) != 0);
    flags.computeListedForces = ((legacyFlags & GMX_FORCE_LISTED) != 0);
    flags.computeNonbondedForces =
            ((legacyFlags & GMX_FORCE_NONBONDED) != 0) && simulationWork.computeNonbonded
            && !(simulationWork.computeNonbondedAtMtsLevel1 && !computeSlowForces);
    flags.computeDhdl = ((legacyFlags & GMX_FORCE_DHDL) != 0);

    if (simulationWork.useGpuBufferOps)
    {
        GMX_ASSERT(simulationWork.useGpuNonbonded,
                   "Can only offload buffer ops if nonbonded computation is also offloaded");
    }
    flags.useGpuXBufferOps = simulationWork.useGpuBufferOps;
    // on virial steps the CPU reduction path is taken
    flags.useGpuFBufferOps = simulationWork.useGpuBufferOps && !flags.computeVirial;
    flags.useGpuPmeFReduction = flags.computeSlowForces && flags.useGpuFBufferOps && simulationWork.useGpuPme
                                && (rankHasPmeDuty || simulationWork.useGpuPmePpCommunication);
    flags.useGpuXHalo = simulationWork.useGpuHaloExchange;
    flags.useGpuFHalo = simulationWork.useGpuHaloExchange && flags.useGpuFBufferOps;

    return flags;
}


/* \brief Launch end-of-step GPU tasks: buffer clearing and rolling pruning.
 *
 * TODO: eliminate \p useGpuPmeOnThisRank when this is
 * incorporated in DomainLifetimeWorkload.
 */
static void launchGpuEndOfStepTasks(nonbonded_verlet_t*               nbv,
                                    gmx::GpuBonded*                   gpuBonded,
                                    gmx_pme_t*                        pmedata,
                                    gmx_enerdata_t*                   enerd,
                                    const gmx::MdrunScheduleWorkload& runScheduleWork,
                                    bool                              useGpuPmeOnThisRank,
                                    int64_t                           step,
                                    gmx_wallcycle_t                   wcycle)
{
    if (runScheduleWork.simulationWork.useGpuNonbonded && runScheduleWork.stepWork.computeNonbondedForces)
    {
        /* Launch pruning before buffer clearing because the API overhead of the
         * clear kernel launches can leave the GPU idle while it could be running
         * the prune kernel.
         */
        if (nbv->isDynamicPruningStepGpu(step))
        {
            nbv->dispatchPruneKernelGpu(step);
        }

        /* now clear the GPU outputs while we finish the step on the CPU */
        wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
        wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
        Nbnxm::gpu_clear_outputs(nbv->gpu_nbv, runScheduleWork.stepWork.computeVirial);
        wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
        wallcycle_stop(wcycle, ewcLAUNCH_GPU);
    }

    if (useGpuPmeOnThisRank)
    {
        pme_gpu_reinit_computation(pmedata, wcycle);
    }

    if (runScheduleWork.domainWork.haveGpuBondedWork && runScheduleWork.stepWork.computeEnergy)
    {
        // in principle this should be included in the DD balancing region,
        // but generally it is infrequent so we'll omit it for the sake of
        // simpler code
        gpuBonded->waitAccumulateEnergyTerms(enerd);

        gpuBonded->clearEnergies();
    }
}

//! \brief Data structure to hold dipole-related data and staging arrays
struct DipoleData
{
    //! Dipole staging for fast summing over MPI
    gmx::DVec muStaging[2] = { { 0.0, 0.0, 0.0 } };
    //! Dipole staging for states A and B (index 0 and 1 resp.)
    gmx::RVec muStateAB[2] = { { 0.0_real, 0.0_real, 0.0_real } };
};


static void reduceAndUpdateMuTot(DipoleData*                   dipoleData,
                                 const t_commrec*              cr,
                                 const bool                    haveFreeEnergy,
                                 gmx::ArrayRef<const real>     lambda,
                                 rvec                          muTotal,
                                 const DDBalanceRegionHandler& ddBalanceRegionHandler)
{
    if (PAR(cr))
    {
        gmx_sumd(2 * DIM, dipoleData->muStaging[0], cr);
        ddBalanceRegionHandler.reopenRegionCpu();
    }
    for (int i = 0; i < 2; i++)
    {
        for (int j = 0; j < DIM; j++)
        {
            dipoleData->muStateAB[i][j] = dipoleData->muStaging[i][j];
        }
    }

    if (!haveFreeEnergy)
    {
        copy_rvec(dipoleData->muStateAB[0], muTotal);
    }
    else
    {
        for (int j = 0; j < DIM; j++)
        {
            muTotal[j] = (1.0 - lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)])
                                 * dipoleData->muStateAB[0][j]
                         + lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)]
                                   * dipoleData->muStateAB[1][j];
        }
    }
}

/*! \brief Combines MTS level0 and level1 force buffes into a full and MTS-combined force buffer.
 *
 * \param[in]     numAtoms        The number of atoms to combine forces for
 * \param[in,out] forceMtsLevel0  Input: F_level0, output: F_level0 + F_level1
 * \param[in,out] forceMts        Input: F_level1, output: F_level0 + mtsFactor * F_level1
 * \param[in]     mtsFactor       The factor between the level0 and level1 time step
 */
static void combineMtsForces(const int      numAtoms,
                             ArrayRef<RVec> forceMtsLevel0,
                             ArrayRef<RVec> forceMts,
                             const real     mtsFactor)
{
    const int gmx_unused numThreads = gmx_omp_nthreads_get(emntDefault);
#pragma omp parallel for num_threads(numThreads) schedule(static)
    for (int i = 0; i < numAtoms; i++)
    {
        const RVec forceMtsLevel0Tmp = forceMtsLevel0[i];
        forceMtsLevel0[i] += forceMts[i];
        forceMts[i] = forceMtsLevel0Tmp + mtsFactor * forceMts[i];
    }
}

/*! \brief Setup for the local and non-local GPU force reductions:
 * reinitialization plus the registration of forces and dependencies.
 *
 * \param [in] runScheduleWork               Schedule workload flag structure
 * \param [in] cr                            Communication record object
 * \param [in] fr                            Force record object
 */
static void setupGpuForceReductions(gmx::MdrunScheduleWorkload* runScheduleWork,
                                    const t_commrec*            cr,
                                    t_forcerec*                 fr)
{

    nonbonded_verlet_t*          nbv      = fr->nbv.get();
    gmx::StatePropagatorDataGpu* stateGpu = fr->stateGpu;

    // (re-)initialize local GPU force reduction
    const bool accumulate =
            runScheduleWork->domainWork.haveCpuLocalForceWork || havePPDomainDecomposition(cr);
    const int atomStart = 0;
    fr->gpuForceReduction[gmx::AtomLocality::Local]->reinit(stateGpu->getForces(),
                                                            nbv->getNumAtoms(AtomLocality::Local),
                                                            nbv->getGridIndices(),
                                                            atomStart,
                                                            accumulate,
                                                            stateGpu->fReducedOnDevice());

    // register forces and add dependencies
    fr->gpuForceReduction[gmx::AtomLocality::Local]->registerNbnxmForce(nbv->getGpuForces());

    if (runScheduleWork->simulationWork.useGpuPme
        && (thisRankHasDuty(cr, DUTY_PME) || runScheduleWork->simulationWork.useGpuPmePpCommunication))
    {
        DeviceBuffer<gmx::RVec> forcePtr =
                thisRankHasDuty(cr, DUTY_PME) ? pme_gpu_get_device_f(fr->pmedata)
                                              :                    // PME force buffer on same GPU
                        fr->pmePpCommGpu->getGpuForceStagingPtr(); // buffer received from other GPU
        fr->gpuForceReduction[gmx::AtomLocality::Local]->registerRvecForce(forcePtr);

        GpuEventSynchronizer* const pmeSynchronizer =
                (thisRankHasDuty(cr, DUTY_PME) ? pme_gpu_get_f_ready_synchronizer(fr->pmedata)
                                               : // PME force buffer on same GPU
                         fr->pmePpCommGpu->getForcesReadySynchronizer()); // buffer received from other GPU
        fr->gpuForceReduction[gmx::AtomLocality::Local]->addDependency(pmeSynchronizer);
    }

    if ((runScheduleWork->domainWork.haveCpuLocalForceWork || havePPDomainDecomposition(cr))
        && !runScheduleWork->simulationWork.useGpuHaloExchange)
    {
        auto forcesReadyLocality = havePPDomainDecomposition(cr) ? AtomLocality::Local : AtomLocality::All;
        const bool useGpuForceBufferOps = true;
        fr->gpuForceReduction[gmx::AtomLocality::Local]->addDependency(
                stateGpu->getForcesReadyOnDeviceEvent(forcesReadyLocality, useGpuForceBufferOps));
    }

    if (runScheduleWork->simulationWork.useGpuHaloExchange)
    {
        fr->gpuForceReduction[gmx::AtomLocality::Local]->addDependency(
                cr->dd->gpuHaloExchange[0][0]->getForcesReadyOnDeviceEvent());
    }

    if (havePPDomainDecomposition(cr))
    {
        // (re-)initialize non-local GPU force reduction
        const bool accumulate = runScheduleWork->domainWork.haveCpuBondedWork
                                || runScheduleWork->domainWork.haveFreeEnergyWork;
        const int atomStart = dd_numHomeAtoms(*cr->dd);
        fr->gpuForceReduction[gmx::AtomLocality::NonLocal]->reinit(stateGpu->getForces(),
                                                                   nbv->getNumAtoms(AtomLocality::NonLocal),
                                                                   nbv->getGridIndices(),
                                                                   atomStart,
                                                                   accumulate);

        // register forces and add dependencies
        fr->gpuForceReduction[gmx::AtomLocality::NonLocal]->registerNbnxmForce(nbv->getGpuForces());
        if (runScheduleWork->domainWork.haveCpuBondedWork || runScheduleWork->domainWork.haveFreeEnergyWork)
        {
            fr->gpuForceReduction[gmx::AtomLocality::NonLocal]->addDependency(
                    stateGpu->getForcesReadyOnDeviceEvent(AtomLocality::NonLocal, true));
        }
    }
}


void do_force(FILE*                               fplog,
              const t_commrec*                    cr,
              const gmx_multisim_t*               ms,
              const t_inputrec&                   inputrec,
              gmx::Awh*                           awh,
              gmx_enfrot*                         enforcedRotation,
              gmx::ImdSession*                    imdSession,
              pull_t*                             pull_work,
              int64_t                             step,
              t_nrnb*                             nrnb,
              gmx_wallcycle_t                     wcycle,
              const gmx_localtop_t*               top,
              const matrix                        box,
              gmx::ArrayRefWithPadding<gmx::RVec> x,
              const history_t*                    hist,
              gmx::ForceBuffersView*              forceView,
              tensor                              vir_force,
              const t_mdatoms*                    mdatoms,
              gmx_enerdata_t*                     enerd,
              gmx::ArrayRef<const real>           lambda,
              t_forcerec*                         fr,
              gmx::MdrunScheduleWorkload*         runScheduleWork,
              gmx::VirtualSitesHandler*           vsite,
              rvec                                muTotal,
              double                              t,
              gmx_edsam*                          ed,
              int                                 legacyFlags,
              const DDBalanceRegionHandler&       ddBalanceRegionHandler)
{
    auto force = forceView->forceWithPadding();
    GMX_ASSERT(force.unpaddedArrayRef().ssize() >= fr->natoms_force_constr,
               "The size of the force buffer should be at least the number of atoms to compute "
               "forces for");

    nonbonded_verlet_t*  nbv = fr->nbv.get();
    interaction_const_t* ic  = fr->ic.get();

    gmx::StatePropagatorDataGpu* stateGpu = fr->stateGpu;

    const SimulationWorkload& simulationWork = runScheduleWork->simulationWork;

    runScheduleWork->stepWork = setupStepWorkload(
            legacyFlags, inputrec.mtsLevels, step, simulationWork, thisRankHasDuty(cr, DUTY_PME));
    const StepWorkload& stepWork = runScheduleWork->stepWork;

    const bool useGpuPmeOnThisRank =
            simulationWork.useGpuPme && thisRankHasDuty(cr, DUTY_PME) && stepWork.computeSlowForces;

    /* At a search step we need to start the first balancing region
     * somewhere early inside the step after communication during domain
     * decomposition (and not during the previous step as usual).
     */
    if (stepWork.doNeighborSearch)
    {
        ddBalanceRegionHandler.openBeforeForceComputationCpu(DdAllowBalanceRegionReopen::yes);
    }

    clear_mat(vir_force);

    if (fr->pbcType != PbcType::No)
    {
        /* Compute shift vectors every step,
         * because of pressure coupling or box deformation!
         */
        if (stepWork.haveDynamicBox && stepWork.stateChanged)
        {
            calc_shifts(box, fr->shift_vec);
        }

        const bool fillGrid = (stepWork.doNeighborSearch && stepWork.stateChanged);
        const bool calcCGCM = (fillGrid && !DOMAINDECOMP(cr));
        if (calcCGCM)
        {
            put_atoms_in_box_omp(fr->pbcType,
                                 box,
                                 x.unpaddedArrayRef().subArray(0, mdatoms->homenr),
                                 gmx_omp_nthreads_get(emntDefault));
            inc_nrnb(nrnb, eNR_SHIFTX, mdatoms->homenr);
        }
    }

    nbnxn_atomdata_copy_shiftvec(stepWork.haveDynamicBox, fr->shift_vec, nbv->nbat.get());

    const bool pmeSendCoordinatesFromGpu =
            GMX_MPI && simulationWork.useGpuPmePpCommunication && !(stepWork.doNeighborSearch);
    const bool reinitGpuPmePpComms =
            GMX_MPI && simulationWork.useGpuPmePpCommunication && (stepWork.doNeighborSearch);

    const auto localXReadyOnDevice = (useGpuPmeOnThisRank || simulationWork.useGpuBufferOps)
                                             ? stateGpu->getCoordinatesReadyOnDeviceEvent(
                                                       AtomLocality::Local, simulationWork, stepWork)
                                             : nullptr;

    // Copy coordinate from the GPU if update is on the GPU and there
    // are forces to be computed on the CPU, or for the computation of
    // virial, or if host-side data will be transferred from this task
    // to a remote task for halo exchange or PME-PP communication. At
    // search steps the current coordinates are already on the host,
    // hence copy is not needed.
    const bool haveHostPmePpComms =
            !thisRankHasDuty(cr, DUTY_PME) && !simulationWork.useGpuPmePpCommunication;

    GMX_ASSERT(simulationWork.useGpuHaloExchange
                       == ((cr->dd != nullptr) && (!cr->dd->gpuHaloExchange[0].empty())),
               "The GPU halo exchange is active, but it has not been constructed.");
    const bool haveHostHaloExchangeComms =
            havePPDomainDecomposition(cr) && !simulationWork.useGpuHaloExchange;

    bool gmx_used_in_debug haveCopiedXFromGpu = false;
    if (simulationWork.useGpuUpdate && !stepWork.doNeighborSearch
        && (runScheduleWork->domainWork.haveCpuLocalForceWork || stepWork.computeVirial
            || haveHostPmePpComms || haveHostHaloExchangeComms))
    {
        stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
        haveCopiedXFromGpu = true;
    }

    // If coordinates are to be sent to PME task from CPU memory, perform that send here.
    // Otherwise the send will occur after H2D coordinate transfer.
    if (GMX_MPI && !thisRankHasDuty(cr, DUTY_PME) && !pmeSendCoordinatesFromGpu && stepWork.computeSlowForces)
    {
        /* Send particle coordinates to the pme nodes */
        if (!stepWork.doNeighborSearch && simulationWork.useGpuUpdate)
        {
            GMX_ASSERT(haveCopiedXFromGpu,
                       "a wait should only be triggered if copy has been scheduled");
            stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
        }

        gmx_pme_send_coordinates(fr,
                                 cr,
                                 box,
                                 as_rvec_array(x.unpaddedArrayRef().data()),
                                 lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
                                 lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)],
                                 (stepWork.computeVirial || stepWork.computeEnergy),
                                 step,
                                 simulationWork.useGpuPmePpCommunication,
                                 reinitGpuPmePpComms,
                                 pmeSendCoordinatesFromGpu,
                                 localXReadyOnDevice,
                                 wcycle);
    }

    // Coordinates on the device are needed if PME or BufferOps are offloaded.
    // The local coordinates can be copied right away.
    // NOTE: Consider moving this copy to right after they are updated and constrained,
    //       if the later is not offloaded.
    if (useGpuPmeOnThisRank || stepWork.useGpuXBufferOps)
    {
        if (stepWork.doNeighborSearch)
        {
            // TODO refactor this to do_md, after partitioning.
            stateGpu->reinit(mdatoms->homenr,
                             cr->dd != nullptr ? dd_numAtomsZones(*cr->dd) : mdatoms->homenr);
            if (useGpuPmeOnThisRank)
            {
                // TODO: This should be moved into PME setup function ( pme_gpu_prepare_computation(...) )
                pme_gpu_set_device_x(fr->pmedata, stateGpu->getCoordinates());
            }
        }
        // We need to copy coordinates when:
        // 1. Update is not offloaded
        // 2. The buffers were reinitialized on search step
        if (!simulationWork.useGpuUpdate || stepWork.doNeighborSearch)
        {
            GMX_ASSERT(stateGpu != nullptr, "stateGpu should not be null");
            stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
        }
    }

    // If coordinates are to be sent to PME task from GPU memory, perform that send here.
    // Otherwise the send will occur before the H2D coordinate transfer.
    if (!thisRankHasDuty(cr, DUTY_PME) && pmeSendCoordinatesFromGpu)
    {
        /* Send particle coordinates to the pme nodes */
        gmx_pme_send_coordinates(fr,
                                 cr,
                                 box,
                                 as_rvec_array(x.unpaddedArrayRef().data()),
                                 lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
                                 lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)],
                                 (stepWork.computeVirial || stepWork.computeEnergy),
                                 step,
                                 simulationWork.useGpuPmePpCommunication,
                                 reinitGpuPmePpComms,
                                 pmeSendCoordinatesFromGpu,
                                 localXReadyOnDevice,
                                 wcycle);
    }

    if (useGpuPmeOnThisRank)
    {
        launchPmeGpuSpread(fr->pmedata,
                           box,
                           stepWork,
                           localXReadyOnDevice,
                           lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
                           wcycle);
    }

    const gmx::DomainLifetimeWorkload& domainWork = runScheduleWork->domainWork;

    /* do gridding for pair search */
    if (stepWork.doNeighborSearch)
    {
        if (fr->wholeMoleculeTransform && stepWork.stateChanged)
        {
            fr->wholeMoleculeTransform->updateForAtomPbcJumps(x.unpaddedArrayRef(), box);
        }

        wallcycle_start(wcycle, ewcNS);
        if (!DOMAINDECOMP(cr))
        {
            const rvec vzero       = { 0.0_real, 0.0_real, 0.0_real };
            const rvec boxDiagonal = { box[XX][XX], box[YY][YY], box[ZZ][ZZ] };
            wallcycle_sub_start(wcycle, ewcsNBS_GRID_LOCAL);
            nbnxn_put_on_grid(nbv,
                              box,
                              0,
                              vzero,
                              boxDiagonal,
                              nullptr,
                              { 0, mdatoms->homenr },
                              -1,
                              fr->cginfo,
                              x.unpaddedArrayRef(),
                              0,
                              nullptr);
            wallcycle_sub_stop(wcycle, ewcsNBS_GRID_LOCAL);
        }
        else
        {
            wallcycle_sub_start(wcycle, ewcsNBS_GRID_NONLOCAL);
            nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
            wallcycle_sub_stop(wcycle, ewcsNBS_GRID_NONLOCAL);
        }

        nbv->setAtomProperties(gmx::constArrayRefFromArray(mdatoms->typeA, mdatoms->nr),
                               gmx::constArrayRefFromArray(mdatoms->chargeA, mdatoms->nr),
                               fr->cginfo);

        wallcycle_stop(wcycle, ewcNS);

        /* initialize the GPU nbnxm atom data and bonded data structures */
        if (simulationWork.useGpuNonbonded)
        {
            // Note: cycle counting only nononbondeds, gpuBonded counts internally
            wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
            wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
            Nbnxm::gpu_init_atomdata(nbv->gpu_nbv, nbv->nbat.get());
            wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
            wallcycle_stop(wcycle, ewcLAUNCH_GPU);

            if (fr->gpuBonded)
            {
                /* Now we put all atoms on the grid, we can assign bonded
                 * interactions to the GPU, where the grid order is
                 * needed. Also the xq, f and fshift device buffers have
                 * been reallocated if needed, so the bonded code can
                 * learn about them. */
                // TODO the xq, f, and fshift buffers are now shared
                // resources, so they should be maintained by a
                // higher-level object than the nb module.
                fr->gpuBonded->updateInteractionListsAndDeviceBuffers(nbv->getGridIndices(),
                                                                      top->idef,
                                                                      Nbnxm::gpu_get_xq(nbv->gpu_nbv),
                                                                      Nbnxm::gpu_get_f(nbv->gpu_nbv),
                                                                      Nbnxm::gpu_get_fshift(nbv->gpu_nbv));
            }
        }

        // Need to run after the GPU-offload bonded interaction lists
        // are set up to be able to determine whether there is bonded work.
        runScheduleWork->domainWork = setupDomainLifetimeWorkload(
                inputrec, *fr, pull_work, ed, *mdatoms, simulationWork, stepWork);

        wallcycle_start_nocount(wcycle, ewcNS);
        wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_LOCAL);
        /* Note that with a GPU the launch overhead of the list transfer is not timed separately */
        nbv->constructPairlist(InteractionLocality::Local, top->excls, step, nrnb);

        nbv->setupGpuShortRangeWork(fr->gpuBonded, InteractionLocality::Local);

        wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_LOCAL);
        wallcycle_stop(wcycle, ewcNS);

        if (stepWork.useGpuXBufferOps)
        {
            nbv->atomdata_init_copy_x_to_nbat_x_gpu();
        }

        if (simulationWork.useGpuBufferOps)
        {
            setupGpuForceReductions(runScheduleWork, cr, fr);
        }
    }
    else if (!EI_TPI(inputrec.eI) && stepWork.computeNonbondedForces)
    {
        if (stepWork.useGpuXBufferOps)
        {
            GMX_ASSERT(stateGpu, "stateGpu should be valid when buffer ops are offloaded");
            nbv->convertCoordinatesGpu(AtomLocality::Local, stateGpu->getCoordinates(), localXReadyOnDevice);
        }
        else
        {
            if (simulationWork.useGpuUpdate)
            {
                GMX_ASSERT(stateGpu, "need a valid stateGpu object");
                GMX_ASSERT(haveCopiedXFromGpu,
                           "a wait should only be triggered if copy has been scheduled");
                stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
            }
            nbv->convertCoordinates(AtomLocality::Local, x.unpaddedArrayRef());
        }
    }

    if (simulationWork.useGpuNonbonded && (stepWork.computeNonbondedForces || domainWork.haveGpuBondedWork))
    {
        ddBalanceRegionHandler.openBeforeForceComputationGpu();

        wallcycle_start(wcycle, ewcLAUNCH_GPU);
        wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
        Nbnxm::gpu_upload_shiftvec(nbv->gpu_nbv, nbv->nbat.get());
        if (stepWork.doNeighborSearch || !stepWork.useGpuXBufferOps)
        {
            Nbnxm::gpu_copy_xq_to_gpu(nbv->gpu_nbv, nbv->nbat.get(), AtomLocality::Local);
        }
        wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
        wallcycle_stop(wcycle, ewcLAUNCH_GPU);
        // with X buffer ops offloaded to the GPU on all but the search steps

        // bonded work not split into separate local and non-local, so with DD
        // we can only launch the kernel after non-local coordinates have been received.
        if (domainWork.haveGpuBondedWork && !havePPDomainDecomposition(cr))
        {
            fr->gpuBonded->setPbcAndlaunchKernel(fr->pbcType, box, fr->bMolPBC, stepWork);
        }

        /* launch local nonbonded work on GPU */
        wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
        wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);
        do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::Local, enbvClearFNo, step, nrnb, wcycle);
        wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
        wallcycle_stop(wcycle, ewcLAUNCH_GPU);
    }

    if (useGpuPmeOnThisRank)
    {
        // In PME GPU and mixed mode we launch FFT / gather after the
        // X copy/transform to allow overlap as well as after the GPU NB
        // launch to avoid FFT launch overhead hijacking the CPU and delaying
        // the nonbonded kernel.
        launchPmeGpuFftAndGather(fr->pmedata,
                                 lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
                                 wcycle,
                                 stepWork);
    }

    /* Communicate coordinates and sum dipole if necessary +
       do non-local pair search */
    if (havePPDomainDecomposition(cr))
    {
        if (stepWork.doNeighborSearch)
        {
            // TODO: fuse this branch with the above large stepWork.doNeighborSearch block
            wallcycle_start_nocount(wcycle, ewcNS);
            wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_NONLOCAL);
            /* Note that with a GPU the launch overhead of the list transfer is not timed separately */
            nbv->constructPairlist(InteractionLocality::NonLocal, top->excls, step, nrnb);

            nbv->setupGpuShortRangeWork(fr->gpuBonded, InteractionLocality::NonLocal);
            wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_NONLOCAL);
            wallcycle_stop(wcycle, ewcNS);
            // TODO refactor this GPU halo exchange re-initialisation
            // to location in do_md where GPU halo exchange is
            // constructed at partitioning, after above stateGpu
            // re-initialization has similarly been refactored
            if (simulationWork.useGpuHaloExchange)
            {
                reinitGpuHaloExchange(*cr, stateGpu->getCoordinates(), stateGpu->getForces());
            }
        }
        else
        {
            if (stepWork.useGpuXHalo)
            {
                // The following must be called after local setCoordinates (which records an event
                // when the coordinate data has been copied to the device).
                communicateGpuHaloCoordinates(*cr, box, localXReadyOnDevice);

                if (domainWork.haveCpuBondedWork || domainWork.haveFreeEnergyWork)
                {
                    // non-local part of coordinate buffer must be copied back to host for CPU work
                    stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
                }
            }
            else
            {
                if (simulationWork.useGpuUpdate)
                {
                    GMX_ASSERT(haveCopiedXFromGpu,
                               "a wait should only be triggered if copy has been scheduled");
                    stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
                }
                dd_move_x(cr->dd, box, x.unpaddedArrayRef(), wcycle);
            }

            if (stepWork.useGpuXBufferOps)
            {
                if (!useGpuPmeOnThisRank && !stepWork.useGpuXHalo)
                {
                    stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
                }
                nbv->convertCoordinatesGpu(AtomLocality::NonLocal,
                                           stateGpu->getCoordinates(),
                                           stateGpu->getCoordinatesReadyOnDeviceEvent(
                                                   AtomLocality::NonLocal, simulationWork, stepWork));
            }
            else
            {
                nbv->convertCoordinates(AtomLocality::NonLocal, x.unpaddedArrayRef());
            }
        }

        if (simulationWork.useGpuNonbonded)
        {

            if (stepWork.doNeighborSearch || !stepWork.useGpuXBufferOps)
            {
                wallcycle_start(wcycle, ewcLAUNCH_GPU);
                wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
                Nbnxm::gpu_copy_xq_to_gpu(nbv->gpu_nbv, nbv->nbat.get(), AtomLocality::NonLocal);
                wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
                wallcycle_stop(wcycle, ewcLAUNCH_GPU);
            }

            if (domainWork.haveGpuBondedWork)
            {
                fr->gpuBonded->setPbcAndlaunchKernel(fr->pbcType, box, fr->bMolPBC, stepWork);
            }

            /* launch non-local nonbonded tasks on GPU */
            wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
            wallcycle_sub_start(wcycle, ewcsLAUNCH_GPU_NONBONDED);
            do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFNo, step, nrnb, wcycle);
            wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);
            wallcycle_stop(wcycle, ewcLAUNCH_GPU);
        }
    }

    if (simulationWork.useGpuNonbonded && stepWork.computeNonbondedForces)
    {
        /* launch D2H copy-back F */
        wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU);
        wallcycle_sub_start_nocount(wcycle, ewcsLAUNCH_GPU_NONBONDED);

        if (havePPDomainDecomposition(cr))
        {
            Nbnxm::gpu_launch_cpyback(nbv->gpu_nbv, nbv->nbat.get(), stepWork, AtomLocality::NonLocal);
        }
        Nbnxm::gpu_launch_cpyback(nbv->gpu_nbv, nbv->nbat.get(), stepWork, AtomLocality::Local);
        wallcycle_sub_stop(wcycle, ewcsLAUNCH_GPU_NONBONDED);

        if (domainWork.haveGpuBondedWork && stepWork.computeEnergy)
        {
            fr->gpuBonded->launchEnergyTransfer();
        }
        wallcycle_stop(wcycle, ewcLAUNCH_GPU);
    }

    gmx::ArrayRef<const gmx::RVec> xWholeMolecules;
    if (fr->wholeMoleculeTransform)
    {
        xWholeMolecules = fr->wholeMoleculeTransform->wholeMoleculeCoordinates(x.unpaddedArrayRef(), box);
    }

    DipoleData dipoleData;

    if (simulationWork.computeMuTot)
    {
        const int start = 0;

        /* Calculate total (local) dipole moment in a temporary common array.
         * This makes it possible to sum them over nodes faster.
         */
        gmx::ArrayRef<const gmx::RVec> xRef =
                (xWholeMolecules.empty() ? x.unpaddedArrayRef() : xWholeMolecules);
        calc_mu(start,
                mdatoms->homenr,
                xRef,
                gmx::arrayRefFromArray(mdatoms->chargeA, mdatoms->nr),
                gmx::arrayRefFromArray(mdatoms->chargeB, mdatoms->nr),
                mdatoms->nChargePerturbed != 0,
                dipoleData.muStaging[0],
                dipoleData.muStaging[1]);

        reduceAndUpdateMuTot(
                &dipoleData, cr, (fr->efep != FreeEnergyPerturbationType::No), lambda, muTotal, ddBalanceRegionHandler);
    }

    /* Reset energies */
    reset_enerdata(enerd);

    if (DOMAINDECOMP(cr) && !thisRankHasDuty(cr, DUTY_PME))
    {
        wallcycle_start(wcycle, ewcPPDURINGPME);
        dd_force_flop_start(cr->dd, nrnb);
    }

    // For the rest of the CPU tasks that depend on GPU-update produced coordinates,
    // this wait ensures that the D2H transfer is complete.
    if (simulationWork.useGpuUpdate && !stepWork.doNeighborSearch
        && (runScheduleWork->domainWork.haveCpuLocalForceWork || stepWork.computeVirial))
    {
        GMX_ASSERT(haveCopiedXFromGpu, "a wait should only be triggered if copy has been scheduled");
        stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
    }

    if (inputrec.bRot)
    {
        wallcycle_start(wcycle, ewcROT);
        do_rotation(cr, enforcedRotation, box, as_rvec_array(x.unpaddedArrayRef().data()), t, step, stepWork.doNeighborSearch);
        wallcycle_stop(wcycle, ewcROT);
    }

    /* Start the force cycle counter.
     * Note that a different counter is used for dynamic load balancing.
     */
    wallcycle_start(wcycle, ewcFORCE);

    /* Set up and clear force outputs:
     * forceOutMtsLevel0:  everything except what is in the other two outputs
     * forceOutMtsLevel1:  PME-mesh and listed-forces group 1
     * forceOutNonbonded: non-bonded forces
     * Without multiple time stepping all point to the same object.
     * With multiple time-stepping the use is different for MTS fast (level0 only) and slow steps.
     */
    ForceOutputs forceOutMtsLevel0 =
            setupForceOutputs(&fr->forceHelperBuffers[0], force, stepWork, wcycle);

    // Force output for MTS combined forces, only set at level1 MTS steps
    std::optional<ForceOutputs> forceOutMts =
            (fr->useMts && stepWork.computeSlowForces)
                    ? std::optional(setupForceOutputs(&fr->forceHelperBuffers[1],
                                                      forceView->forceMtsCombinedWithPadding(),
                                                      stepWork,
                                                      wcycle))
                    : std::nullopt;

    ForceOutputs* forceOutMtsLevel1 =
            fr->useMts ? (stepWork.computeSlowForces ? &forceOutMts.value() : nullptr) : &forceOutMtsLevel0;

    const bool nonbondedAtMtsLevel1 = runScheduleWork->simulationWork.computeNonbondedAtMtsLevel1;

    ForceOutputs* forceOutNonbonded = nonbondedAtMtsLevel1 ? forceOutMtsLevel1 : &forceOutMtsLevel0;

    if (inputrec.bPull && pull_have_constraint(*pull_work))
    {
        clear_pull_forces(pull_work);
    }

    /* We calculate the non-bonded forces, when done on the CPU, here.
     * We do this before calling do_force_lowlevel, because in that
     * function, the listed forces are calculated before PME, which
     * does communication.  With this order, non-bonded and listed
     * force calculation imbalance can be balanced out by the domain
     * decomposition load balancing.
     */

    const bool useOrEmulateGpuNb = simulationWork.useGpuNonbonded || fr->nbv->emulateGpu();

    if (!useOrEmulateGpuNb)
    {
        do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::Local, enbvClearFYes, step, nrnb, wcycle);
    }

    if (fr->efep != FreeEnergyPerturbationType::No && stepWork.computeNonbondedForces)
    {
        /* Calculate the local and non-local free energy interactions here.
         * Happens here on the CPU both with and without GPU.
         */
        nbv->dispatchFreeEnergyKernel(InteractionLocality::Local,
                                      fr,
                                      as_rvec_array(x.unpaddedArrayRef().data()),
                                      &forceOutNonbonded->forceWithShiftForces(),
                                      *mdatoms,
                                      inputrec.fepvals.get(),
                                      lambda,
                                      enerd,
                                      stepWork,
                                      nrnb);

        if (havePPDomainDecomposition(cr))
        {
            nbv->dispatchFreeEnergyKernel(InteractionLocality::NonLocal,
                                          fr,
                                          as_rvec_array(x.unpaddedArrayRef().data()),
                                          &forceOutNonbonded->forceWithShiftForces(),
                                          *mdatoms,
                                          inputrec.fepvals.get(),
                                          lambda,
                                          enerd,
                                          stepWork,
                                          nrnb);
        }
    }

    if (stepWork.computeNonbondedForces && !useOrEmulateGpuNb)
    {
        if (havePPDomainDecomposition(cr))
        {
            do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFNo, step, nrnb, wcycle);
        }

        if (stepWork.computeForces)
        {
            /* Add all the non-bonded force to the normal force array.
             * This can be split into a local and a non-local part when overlapping
             * communication with calculation with domain decomposition.
             */
            wallcycle_stop(wcycle, ewcFORCE);
            nbv->atomdata_add_nbat_f_to_f(AtomLocality::All,
                                          forceOutNonbonded->forceWithShiftForces().force());
            wallcycle_start_nocount(wcycle, ewcFORCE);
        }

        /* If there are multiple fshift output buffers we need to reduce them */
        if (stepWork.computeVirial)
        {
            /* This is not in a subcounter because it takes a
               negligible and constant-sized amount of time */
            nbnxn_atomdata_add_nbat_fshift_to_fshift(
                    *nbv->nbat, forceOutNonbonded->forceWithShiftForces().shiftForces());
        }
    }

    // TODO Force flags should include haveFreeEnergyWork for this domain
    if (stepWork.useGpuXHalo && (domainWork.haveCpuBondedWork || domainWork.haveFreeEnergyWork))
    {
        wallcycle_stop(wcycle, ewcFORCE);
        /* Wait for non-local coordinate data to be copied from device */
        stateGpu->waitCoordinatesReadyOnHost(AtomLocality::NonLocal);
        wallcycle_start_nocount(wcycle, ewcFORCE);
    }

    // Compute wall interactions, when present.
    // Note: should be moved to special forces.
    if (inputrec.nwall && stepWork.computeNonbondedForces)
    {
        /* foreign lambda component for walls */
        real dvdl_walls = do_walls(inputrec,
                                   *fr,
                                   box,
                                   *mdatoms,
                                   x.unpaddedConstArrayRef(),
                                   &forceOutMtsLevel0.forceWithVirial(),
                                   lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)],
                                   enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR].data(),
                                   nrnb);
        enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Vdw] += dvdl_walls;
    }

    if (stepWork.computeListedForces)
    {
        /* Check whether we need to take into account PBC in listed interactions */
        bool needMolPbc = false;
        for (const auto& listedForces : fr->listedForces)
        {
            if (listedForces.haveCpuListedForces(*fr->fcdata))
            {
                needMolPbc = fr->bMolPBC;
            }
        }

        t_pbc pbc;

        if (needMolPbc)
        {
            /* Since all atoms are in the rectangular or triclinic unit-cell,
             * only single box vector shifts (2 in x) are required.
             */
            set_pbc_dd(&pbc, fr->pbcType, DOMAINDECOMP(cr) ? cr->dd->numCells : nullptr, TRUE, box);
        }

        for (int mtsIndex = 0; mtsIndex < (fr->useMts && stepWork.computeSlowForces ? 2 : 1); mtsIndex++)
        {
            ListedForces& listedForces = fr->listedForces[mtsIndex];
            ForceOutputs& forceOut     = (mtsIndex == 0 ? forceOutMtsLevel0 : *forceOutMtsLevel1);
            listedForces.calculate(wcycle,
                                   box,
                                   inputrec.fepvals.get(),
                                   cr,
                                   ms,
                                   x,
                                   xWholeMolecules,
                                   fr->fcdata.get(),
                                   hist,
                                   &forceOut,
                                   fr,
                                   &pbc,
                                   enerd,
                                   nrnb,
                                   lambda,
                                   mdatoms,
                                   DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr,
                                   stepWork);
        }
    }

    if (stepWork.computeSlowForces)
    {
        calculateLongRangeNonbondeds(fr,
                                     inputrec,
                                     cr,
                                     nrnb,
                                     wcycle,
                                     mdatoms,
                                     x.unpaddedConstArrayRef(),
                                     &forceOutMtsLevel1->forceWithVirial(),
                                     enerd,
                                     box,
                                     lambda,
                                     dipoleData.muStateAB,
                                     stepWork,
                                     ddBalanceRegionHandler);
    }

    wallcycle_stop(wcycle, ewcFORCE);

    // VdW dispersion correction, only computed on master rank to avoid double counting
    if ((stepWork.computeEnergy || stepWork.computeVirial) && fr->dispersionCorrection && MASTER(cr))
    {
        // Calculate long range corrections to pressure and energy
        const DispersionCorrection::Correction correction = fr->dispersionCorrection->calculate(
                box, lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)]);

        if (stepWork.computeEnergy)
        {
            enerd->term[F_DISPCORR] = correction.energy;
            enerd->term[F_DVDL_VDW] += correction.dvdl;
            enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Vdw] += correction.dvdl;
        }
        if (stepWork.computeVirial)
        {
            correction.correctVirial(vir_force);
            enerd->term[F_PDISPCORR] = correction.pressure;
        }
    }

    computeSpecialForces(fplog,
                         cr,
                         inputrec,
                         awh,
                         enforcedRotation,
                         imdSession,
                         pull_work,
                         step,
                         t,
                         wcycle,
                         fr->forceProviders,
                         box,
                         x.unpaddedArrayRef(),
                         mdatoms,
                         lambda,
                         stepWork,
                         &forceOutMtsLevel0.forceWithVirial(),
                         forceOutMtsLevel1 ? &forceOutMtsLevel1->forceWithVirial() : nullptr,
                         enerd,
                         ed,
                         stepWork.doNeighborSearch);

    if (havePPDomainDecomposition(cr) && stepWork.computeForces && stepWork.useGpuFHalo
        && domainWork.haveCpuLocalForceWork)
    {
        stateGpu->copyForcesToGpu(forceOutMtsLevel0.forceWithShiftForces().force(), AtomLocality::Local);
    }

    GMX_ASSERT(!(nonbondedAtMtsLevel1 && stepWork.useGpuFBufferOps),
               "The schedule below does not allow for nonbonded MTS with GPU buffer ops");
    GMX_ASSERT(!(nonbondedAtMtsLevel1 && stepWork.useGpuFHalo),
               "The schedule below does not allow for nonbonded MTS with GPU halo exchange");
    // Will store the amount of cycles spent waiting for the GPU that
    // will be later used in the DLB accounting.
    float cycles_wait_gpu = 0;
    if (useOrEmulateGpuNb && stepWork.computeNonbondedForces)
    {
        auto& forceWithShiftForces = forceOutNonbonded->forceWithShiftForces();

        /* wait for non-local forces (or calculate in emulation mode) */
        if (havePPDomainDecomposition(cr))
        {
            if (simulationWork.useGpuNonbonded)
            {
                cycles_wait_gpu += Nbnxm::gpu_wait_finish_task(
                        nbv->gpu_nbv,
                        stepWork,
                        AtomLocality::NonLocal,
                        enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR].data(),
                        enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR].data(),
                        forceWithShiftForces.shiftForces(),
                        wcycle);
            }
            else
            {
                wallcycle_start_nocount(wcycle, ewcFORCE);
                do_nb_verlet(
                        fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFYes, step, nrnb, wcycle);
                wallcycle_stop(wcycle, ewcFORCE);
            }

            if (stepWork.useGpuFBufferOps)
            {
                // TODO: move this into DomainLifetimeWorkload, including the second part of the
                // condition The bonded and free energy CPU tasks can have non-local force
                // contributions which are a dependency for the GPU force reduction.
                bool haveNonLocalForceContribInCpuBuffer =
                        domainWork.haveCpuBondedWork || domainWork.haveFreeEnergyWork;

                if (haveNonLocalForceContribInCpuBuffer)
                {
                    stateGpu->copyForcesToGpu(forceOutMtsLevel0.forceWithShiftForces().force(),
                                              AtomLocality::NonLocal);
                }


                fr->gpuForceReduction[gmx::AtomLocality::NonLocal]->execute();

                if (!stepWork.useGpuFHalo)
                {
                    // copy from GPU input for dd_move_f()
                    stateGpu->copyForcesFromGpu(forceOutMtsLevel0.forceWithShiftForces().force(),
                                                AtomLocality::NonLocal);
                }
            }
            else
            {
                nbv->atomdata_add_nbat_f_to_f(AtomLocality::NonLocal, forceWithShiftForces.force());
            }

            if (fr->nbv->emulateGpu() && stepWork.computeVirial)
            {
                nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat, forceWithShiftForces.shiftForces());
            }
        }
    }

    /* Combining the forces for multiple time stepping before the halo exchange, when possible,
     * avoids an extra halo exchange (when DD is used) and post-processing step.
     */
    const bool combineMtsForcesBeforeHaloExchange =
            (stepWork.computeForces && fr->useMts && stepWork.computeSlowForces
             && (legacyFlags & GMX_FORCE_DO_NOT_NEED_NORMAL_FORCE) != 0
             && !(stepWork.computeVirial || simulationWork.useGpuNonbonded || useGpuPmeOnThisRank));
    if (combineMtsForcesBeforeHaloExchange)
    {
        const int numAtoms = havePPDomainDecomposition(cr) ? dd_numAtomsZones(*cr->dd) : mdatoms->homenr;
        combineMtsForces(numAtoms,
                         force.unpaddedArrayRef(),
                         forceView->forceMtsCombined(),
                         inputrec.mtsLevels[1].stepFactor);
    }

    if (havePPDomainDecomposition(cr))
    {
        /* We are done with the CPU compute.
         * We will now communicate the non-local forces.
         * If we use a GPU this will overlap with GPU work, so in that case
         * we do not close the DD force balancing region here.
         */
        ddBalanceRegionHandler.closeAfterForceComputationCpu();

        if (stepWork.computeForces)
        {

            if (stepWork.useGpuFHalo)
            {
                // If there exist CPU forces, data from halo exchange should accumulate into these
                bool accumulateForces = domainWork.haveCpuLocalForceWork;
                if (!accumulateForces)
                {
                    // Force halo exchange will set a subset of local atoms with remote non-local data
                    // First clear local portion of force array, so that untouched atoms are zero
                    stateGpu->clearForcesOnGpu(AtomLocality::Local);
                }
                communicateGpuHaloForces(*cr, accumulateForces);
            }
            else
            {
                if (stepWork.useGpuFBufferOps)
                {
                    stateGpu->waitForcesReadyOnHost(AtomLocality::NonLocal);
                }

                // Without MTS or with MTS at slow steps with uncombined forces we need to
                // communicate the fast forces
                if (!fr->useMts || !combineMtsForcesBeforeHaloExchange)
                {
                    dd_move_f(cr->dd, &forceOutMtsLevel0.forceWithShiftForces(), wcycle);
                }
                // With MTS we need to communicate the slow or combined (in forceOutMtsLevel1) forces
                if (fr->useMts && stepWork.computeSlowForces)
                {
                    dd_move_f(cr->dd, &forceOutMtsLevel1->forceWithShiftForces(), wcycle);
                }
            }
        }
    }

    // With both nonbonded and PME offloaded a GPU on the same rank, we use
    // an alternating wait/reduction scheme.
    bool alternateGpuWait = (!c_disableAlternatingWait && useGpuPmeOnThisRank && simulationWork.useGpuNonbonded
                             && !DOMAINDECOMP(cr) && !stepWork.useGpuFBufferOps);
    if (alternateGpuWait)
    {
        alternatePmeNbGpuWaitReduce(fr->nbv.get(),
                                    fr->pmedata,
                                    forceOutNonbonded,
                                    forceOutMtsLevel1,
                                    enerd,
                                    lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
                                    stepWork,
                                    wcycle);
    }

    if (!alternateGpuWait && useGpuPmeOnThisRank)
    {
        pme_gpu_wait_and_reduce(fr->pmedata,
                                stepWork,
                                wcycle,
                                &forceOutMtsLevel1->forceWithVirial(),
                                enerd,
                                lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)]);
    }

    /* Wait for local GPU NB outputs on the non-alternating wait path */
    if (!alternateGpuWait && stepWork.computeNonbondedForces && simulationWork.useGpuNonbonded)
    {
        /* Measured overhead on CUDA and OpenCL with(out) GPU sharing
         * is between 0.5 and 1.5 Mcycles. So 2 MCycles is an overestimate,
         * but even with a step of 0.1 ms the difference is less than 1%
         * of the step time.
         */
        const float gpuWaitApiOverheadMargin = 2e6F; /* cycles */
        const float waitCycles               = Nbnxm::gpu_wait_finish_task(
                nbv->gpu_nbv,
                stepWork,
                AtomLocality::Local,
                enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR].data(),
                enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR].data(),
                forceOutNonbonded->forceWithShiftForces().shiftForces(),
                wcycle);

        if (ddBalanceRegionHandler.useBalancingRegion())
        {
            DdBalanceRegionWaitedForGpu waitedForGpu = DdBalanceRegionWaitedForGpu::yes;
            if (stepWork.computeForces && waitCycles <= gpuWaitApiOverheadMargin)
            {
                /* We measured few cycles, it could be that the kernel
                 * and transfer finished earlier and there was no actual
                 * wait time, only API call overhead.
                 * Then the actual time could be anywhere between 0 and
                 * cycles_wait_est. We will use half of cycles_wait_est.
                 */
                waitedForGpu = DdBalanceRegionWaitedForGpu::no;
            }
            ddBalanceRegionHandler.closeAfterForceComputationGpu(cycles_wait_gpu, waitedForGpu);
        }
    }

    if (fr->nbv->emulateGpu())
    {
        // NOTE: emulation kernel is not included in the balancing region,
        // but emulation mode does not target performance anyway
        wallcycle_start_nocount(wcycle, ewcFORCE);
        do_nb_verlet(fr,
                     ic,
                     enerd,
                     stepWork,
                     InteractionLocality::Local,
                     DOMAINDECOMP(cr) ? enbvClearFNo : enbvClearFYes,
                     step,
                     nrnb,
                     wcycle);
        wallcycle_stop(wcycle, ewcFORCE);
    }

    // If on GPU PME-PP comms path, receive forces from PME before GPU buffer ops
    // TODO refactor this and unify with below default-path call to the same function
    if (PAR(cr) && !thisRankHasDuty(cr, DUTY_PME) && stepWork.computeSlowForces
        && simulationWork.useGpuPmePpCommunication)
    {
        /* In case of node-splitting, the PP nodes receive the long-range
         * forces, virial and energy from the PME nodes here.
         */
        pme_receive_force_ener(fr,
                               cr,
                               &forceOutMtsLevel1->forceWithVirial(),
                               enerd,
                               simulationWork.useGpuPmePpCommunication,
                               stepWork.useGpuPmeFReduction,
                               wcycle);
    }


    /* Do the nonbonded GPU (or emulation) force buffer reduction
     * on the non-alternating path. */
    GMX_ASSERT(!(nonbondedAtMtsLevel1 && stepWork.useGpuFBufferOps),
               "The schedule below does not allow for nonbonded MTS with GPU buffer ops");
    if (useOrEmulateGpuNb && !alternateGpuWait)
    {
        if (stepWork.useGpuFBufferOps)
        {
            ArrayRef<gmx::RVec> forceWithShift = forceOutNonbonded->forceWithShiftForces().force();

            // Flag to specify whether the CPU force buffer has contributions to
            // local atoms. This depends on whether there are CPU-based force tasks
            // or when DD is active the halo exchange has resulted in contributions
            // from the non-local part.
            const bool haveLocalForceContribInCpuBuffer =
                    (domainWork.haveCpuLocalForceWork || havePPDomainDecomposition(cr));

            // TODO: move these steps as early as possible:
            // - CPU f H2D should be as soon as all CPU-side forces are done
            // - wait for force reduction does not need to block host (at least not here, it's sufficient to wait
            //   before the next CPU task that consumes the forces: vsite spread or update)
            // - copy is not perfomed if GPU force halo exchange is active, because it would overwrite the result
            //   of the halo exchange. In that case the copy is instead performed above, before the exchange.
            //   These should be unified.
            if (haveLocalForceContribInCpuBuffer && !stepWork.useGpuFHalo)
            {
                // Note: AtomLocality::All is used for the non-DD case because, as in this
                // case copyForcesToGpu() uses a separate stream, it allows overlap of
                // CPU force H2D with GPU force tasks on all streams including those in the
                // local stream which would otherwise be implicit dependencies for the
                // transfer and would not overlap.
                auto locality = havePPDomainDecomposition(cr) ? AtomLocality::Local : AtomLocality::All;

                stateGpu->copyForcesToGpu(forceWithShift, locality);
            }

            if (stepWork.computeNonbondedForces)
            {
                fr->gpuForceReduction[gmx::AtomLocality::Local]->execute();
            }

            // Copy forces to host if they are needed for update or if virtual sites are enabled.
            // If there are vsites, we need to copy forces every step to spread vsite forces on host.
            // TODO: When the output flags will be included in step workload, this copy can be combined with the
            //       copy call done in sim_utils(...) for the output.
            // NOTE: If there are virtual sites, the forces are modified on host after this D2H copy. Hence,
            //       they should not be copied in do_md(...) for the output.
            if (!simulationWork.useGpuUpdate
                || (simulationWork.useGpuUpdate && DOMAINDECOMP(cr) && haveHostPmePpComms) || vsite)
            {
                stateGpu->copyForcesFromGpu(forceWithShift, AtomLocality::Local);
                stateGpu->waitForcesReadyOnHost(AtomLocality::Local);
            }
        }
        else if (stepWork.computeNonbondedForces)
        {
            ArrayRef<gmx::RVec> forceWithShift = forceOutNonbonded->forceWithShiftForces().force();
            nbv->atomdata_add_nbat_f_to_f(AtomLocality::Local, forceWithShift);
        }
    }

    launchGpuEndOfStepTasks(
            nbv, fr->gpuBonded, fr->pmedata, enerd, *runScheduleWork, useGpuPmeOnThisRank, step, wcycle);

    if (DOMAINDECOMP(cr))
    {
        dd_force_flop_stop(cr->dd, nrnb);
    }

    const bool haveCombinedMtsForces = (stepWork.computeForces && fr->useMts && stepWork.computeSlowForces
                                        && combineMtsForcesBeforeHaloExchange);
    if (stepWork.computeForces)
    {
        postProcessForceWithShiftForces(
                nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutMtsLevel0, vir_force, *mdatoms, *fr, vsite, stepWork);

        if (fr->useMts && stepWork.computeSlowForces && !haveCombinedMtsForces)
        {
            postProcessForceWithShiftForces(
                    nrnb, wcycle, box, x.unpaddedArrayRef(), forceOutMtsLevel1, vir_force, *mdatoms, *fr, vsite, stepWork);
        }
    }

    // TODO refactor this and unify with above GPU PME-PP / GPU update path call to the same function
    if (PAR(cr) && !thisRankHasDuty(cr, DUTY_PME) && !simulationWork.useGpuPmePpCommunication
        && stepWork.computeSlowForces)
    {
        /* In case of node-splitting, the PP nodes receive the long-range
         * forces, virial and energy from the PME nodes here.
         */
        pme_receive_force_ener(fr,
                               cr,
                               &forceOutMtsLevel1->forceWithVirial(),
                               enerd,
                               simulationWork.useGpuPmePpCommunication,
                               false,
                               wcycle);
    }

    if (stepWork.computeForces)
    {
        /* If we don't use MTS or if we already combined the MTS forces before, we only
         * need to post-process one ForceOutputs object here, called forceOutCombined,
         * otherwise we have to post-process two outputs and then combine them.
         */
        ForceOutputs& forceOutCombined = (haveCombinedMtsForces ? forceOutMts.value() : forceOutMtsLevel0);
        postProcessForces(
                cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutCombined, vir_force, mdatoms, fr, vsite, stepWork);

        if (fr->useMts && stepWork.computeSlowForces && !haveCombinedMtsForces)
        {
            postProcessForces(
                    cr, step, nrnb, wcycle, box, x.unpaddedArrayRef(), forceOutMtsLevel1, vir_force, mdatoms, fr, vsite, stepWork);

            combineMtsForces(mdatoms->homenr,
                             force.unpaddedArrayRef(),
                             forceView->forceMtsCombined(),
                             inputrec.mtsLevels[1].stepFactor);
        }
    }

    if (stepWork.computeEnergy)
    {
        /* Compute the final potential energy terms */
        accumulatePotentialEnergies(enerd, lambda, inputrec.fepvals.get());

        if (!EI_TPI(inputrec.eI))
        {
            checkPotentialEnergyValidity(step, *enerd, inputrec);
        }
    }

    /* In case we don't have constraints and are using GPUs, the next balancing
     * region starts here.
     * Some "special" work at the end of do_force_cuts?, such as vsite spread,
     * virial calculation and COM pulling, is not thus not included in
     * the balance timing, which is ok as most tasks do communication.
     */
    ddBalanceRegionHandler.openBeforeForceComputationCpu(DdAllowBalanceRegionReopen::no);
}