hillclimber 0.1.6__cp313-cp313-macosx_15_0_x86_64.whl

plumed/_lib/lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdlib/sim_util.cpp

@@ -0,0 +1,2564 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright 1991- The GROMACS Authors
+ * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
+ * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * https://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at https://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out https://www.gromacs.org.
+ */
+#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_coordinate_receiver_gpu.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/listed_forces.h"
+#include "gromacs/listed_forces/listed_forces_gpu.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/mdrunutility/mdmodulesnotifiers.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/stringutil.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;
+
+/* PLUMED */
+#include "../../../Plumed.h"
+extern int    plumedswitch;
+extern plumed plumedmain;
+/* END PLUMED */
+
+// 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(ModuleMultiThread::Default);
+#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());
+    const rvec* shiftVecPointer = as_rvec_array(fr->shift_vec.data());
+    calc_vir(gmx::c_numShiftVectors, shiftVecPointer, fshift, vir_part, pbcType == PbcType::Screw, box);
+    inc_nrnb(nrnb, eNR_VIRIAL, gmx::c_numShiftVectors);
+
+    /* 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,
+                                   const t_mdatoms*               mdatoms,
+                                   gmx_enerdata_t*                enerd,
+                                   pull_t*                        pull_work,
+                                   const real*                    lambda,
+                                   double                         t,
+                                   gmx_wallcycle*                 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, WallCycleCounter::PullPot);
+    set_pbc(&pbc, ir.pbcType, box);
+    dvdl = 0;
+    enerd->term[F_COM_PULL] +=
+            pull_potential(pull_work,
+                           mdatoms->massT,
+                           pbc,
+                           cr,
+                           t,
+                           lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Restraint)],
+                           x,
+                           &dvdl);
+    enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Restraint] += dvdl;
+    wallcycle_stop(wcycle, WallCycleCounter::PullPot);
+}
+
+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*        wcycle)
+{
+    real  e_q, e_lj, dvdl_q, dvdl_lj;
+    float cycles_ppdpme, cycles_seppme;
+
+    cycles_ppdpme = wallcycle_stop(wcycle, WallCycleCounter::PpDuringPme);
+    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, WallCycleCounter::PpPmeWaitRecvF);
+    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, WallCycleCounter::PpPmeWaitRecvF);
+}
+
+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*            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*            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*             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, WallCycleSubCounter::NonbondedPruning);
+            nbv->dispatchPruneKernelCpu(ilocality, fr->shift_vec);
+            wallcycle_sub_stop(wcycle, WallCycleSubCounter::NonbondedPruning);
+        }
+    }
+
+    nbv->dispatchNonbondedKernel(
+            ilocality,
+            *ic,
+            stepWork,
+            clearF,
+            fr->shift_vec,
+            enerd->grpp.energyGroupPairTerms[fr->haveBuckingham ? NonBondedEnergyTerms::BuckinghamSR
+                                                                : NonBondedEnergyTerms::LJSR],
+            enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR],
+            nrnb);
+}
+
+static inline void clearRVecs(ArrayRef<RVec> v, const bool useOpenmpThreading)
+{
+    int nth = gmx_omp_nthreads_get_simple_rvec_task(ModuleMultiThread::Default, 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
+ *                      \c 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_THROW(gmx::InternalError(gmx::formatString(
+                "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 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*                 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::makeArrayRef(mdatoms->chargeA).subArray(0, mdatoms->homenr),
+                gmx::makeArrayRef(mdatoms->massT).subArray(0, mdatoms->homenr),
+                t,
+                step,
+                box,
+                *cr);
+        gmx::ForceProviderOutput forceProviderOutput(forceWithVirialMtsLevel0, enerd);
+
+        /* Collect forces from modules */
+        forceProviders->calculateForces(forceProviderInput, &forceProviderOutput);
+    }
+
+    const int  pullMtsLevel = forceGroupMtsLevel(inputrec.mtsLevels, gmx::MtsForceGroups::Pull);
+    const bool doPulling    = (inputrec.bPull && pull_have_potential(*pull_work)
+                            && (pullMtsLevel == 0 || stepWork.computeSlowForces));
+
+    /* pull_potential_wrapper(), awh->applyBiasForcesAndUpdateBias(), pull_apply_forces()
+     * have to be called in this order
+     */
+    if (doPulling)
+    {
+        pull_potential_wrapper(cr, inputrec, box, x, mdatoms, enerd, pull_work, lambda.data(), t, wcycle);
+    }
+    if (awh && (pullMtsLevel == 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);
+        }
+
+        enerd->term[F_COM_PULL] += awh->applyBiasForcesAndUpdateBias(
+                inputrec.pbcType, foreignLambdaDeltaH, foreignLambdaDhDl, box, t, step, wcycle, fplog);
+    }
+    if (doPulling)
+    {
+        wallcycle_start_nocount(wcycle, WallCycleCounter::PullPot);
+        auto& forceWithVirial = (pullMtsLevel == 0) ? forceWithVirialMtsLevel0 : forceWithVirialMtsLevel1;
+        pull_apply_forces(pull_work, mdatoms->massT, cr, forceWithVirial);
+        wallcycle_stop(wcycle, WallCycleCounter::PullPot);
+    }
+
+    /* Add the forces from enforced rotation potentials (if any) */
+    if (inputrec.bRot)
+    {
+        wallcycle_start(wcycle, WallCycleCounter::RotAdd);
+        enerd->term[F_COM_PULL] +=
+                add_rot_forces(enforcedRotation, forceWithVirialMtsLevel0->force_, cr, step, t);
+        wallcycle_stop(wcycle, WallCycleCounter::RotAdd);
+    }
+
+    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, x, forceWithVirialMtsLevel0->force_, ed, box, step, didNeighborSearch);
+    }
+
+    /* Add forces from interactive molecular dynamics (IMD), if any */
+    if (inputrec.bIMD && stepWork.computeForces)
+    {
+        imdSession->applyForces(forceWithVirialMtsLevel0->force_);
+    }
+}
+
+/*! \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]  useMdGpuGraph        Whether MD GPU Graph is in use.
+ * \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,
+                                      bool                  useMdGpuGraph,
+                                      gmx_wallcycle*        wcycle)
+{
+    wallcycle_start(wcycle, WallCycleCounter::PmeGpuMesh);
+    pme_gpu_prepare_computation(pmedata, box, wcycle, stepWork);
+    bool                           useGpuDirectComm         = false;
+    gmx::PmeCoordinateReceiverGpu* pmeCoordinateReceiverGpu = nullptr;
+    pme_gpu_launch_spread(
+            pmedata, xReadyOnDevice, wcycle, lambdaQ, useGpuDirectComm, pmeCoordinateReceiverGpu, useMdGpuGraph);
+    wallcycle_stop(wcycle, WallCycleCounter::PmeGpuMesh);
+}
+
+/*! \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*           wcycle,
+                                     const gmx::StepWorkload& stepWork)
+{
+    wallcycle_start_nocount(wcycle, WallCycleCounter::PmeGpuMesh);
+    pme_gpu_launch_complex_transforms(pmedata, wcycle, stepWork);
+    pme_gpu_launch_gather(pmedata, wcycle, lambdaQ, stepWork.computeVirial);
+    wallcycle_stop(wcycle, WallCycleCounter::PmeGpuMesh);
+}
+
+/*! \brief
+ * Blocks until PME GPU tasks are completed, and gets the output forces and virial/energy
+ * (if they were to be computed).
+ *
+ * \param[in]  pme             The PME data structure.
+ * \param[in]  stepWork        The required work for this simulation step
+ * \param[in]  wcycle          The wallclock counter.
+ * \param[out] forceWithVirial The output force and virial
+ * \param[out] enerd           The output energies
+ * \param[in]  lambdaQ         The Coulomb lambda to use when calculating the results.
+ */
+static void pmeGpuWaitAndReduce(gmx_pme_t*               pme,
+                                const gmx::StepWorkload& stepWork,
+                                gmx_wallcycle*           wcycle,
+                                gmx::ForceWithVirial*    forceWithVirial,
+                                gmx_enerdata_t*          enerd,
+                                const real               lambdaQ)
+{
+    wallcycle_start_nocount(wcycle, WallCycleCounter::PmeGpuMesh);
+
+    pme_gpu_wait_and_reduce(pme, stepWork, wcycle, forceWithVirial, enerd, lambdaQ);
+
+    wallcycle_stop(wcycle, WallCycleCounter::PmeGpuMesh);
+}
+
+/*! \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*      wcycle)
+{
+    bool isPmeGpuDone = false;
+    bool isNbGpuDone  = false;
+
+    gmx::ArrayRef<const gmx::RVec> pmeGpuForces;
+
+    while (!isPmeGpuDone || !isNbGpuDone)
+    {
+        if (!isPmeGpuDone)
+        {
+            wallcycle_start_nocount(wcycle, WallCycleCounter::PmeGpuMesh);
+            GpuTaskCompletion completionType =
+                    (isNbGpuDone) ? GpuTaskCompletion::Wait : GpuTaskCompletion::Check;
+            isPmeGpuDone = pme_gpu_try_finish_task(
+                    pmedata, stepWork, wcycle, &forceOutputsPme->forceWithVirial(), enerd, lambdaQ, completionType);
+            wallcycle_stop(wcycle, WallCycleCounter::PmeGpuMesh);
+        }
+
+        if (!isNbGpuDone)
+        {
+            auto&             forceBuffersNonbonded = forceOutputsNonbonded->forceWithShiftForces();
+            GpuTaskCompletion completionType =
+                    (isPmeGpuDone) ? GpuTaskCompletion::Wait : GpuTaskCompletion::Check;
+            // To get the wcycle call count right, when in GpuTaskCompletion::Check mode,
+            // we start without counting and only when the task finished we issue a
+            // start/stop to increment.
+            // GpuTaskCompletion::Wait mode the timing is expected to be done in the caller.
+            wallcycle_start_nocount(wcycle, WallCycleCounter::WaitGpuNbL);
+            isNbGpuDone = Nbnxm::gpu_try_finish_task(
+                    nbv->gpuNbv(),
+                    stepWork,
+                    AtomLocality::Local,
+                    enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR].data(),
+                    enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR].data(),
+                    forceBuffersNonbonded.shiftForces(),
+                    completionType);
+            wallcycle_stop(wcycle, WallCycleCounter::WaitGpuNbL);
+
+            if (isNbGpuDone)
+            {
+                wallcycle_increment_event_count(wcycle, WallCycleCounter::WaitGpuNbL);
+                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] domainWork                Domain lifetime workload flags
+ * \param[in] stepWork                  Step schedule flags
+ * \param[in] havePpDomainDecomposition Whether we have a PP domain decomposition
+ * \param[out] wcycle                   wallcycle recording structure
+ *
+ * \returns                             Cleared force output structure
+ */
+static ForceOutputs setupForceOutputs(ForceHelperBuffers*                 forceHelperBuffers,
+                                      gmx::ArrayRefWithPadding<gmx::RVec> force,
+                                      const DomainLifetimeWorkload&       domainWork,
+                                      const StepWorkload&                 stepWork,
+                                      const bool                          havePpDomainDecomposition,
+                                      gmx_wallcycle*                      wcycle)
+{
+    /* NOTE: We assume fr->shiftForces is all zeros here */
+    gmx::ForceWithShiftForces forceWithShiftForces(
+            force, stepWork.computeVirial, forceHelperBuffers->shiftForces());
+
+    if (stepWork.computeForces
+        && (domainWork.haveCpuLocalForceWork || !stepWork.useGpuFBufferOps
+            || (havePpDomainDecomposition && !stepWork.useGpuFHalo)))
+    {
+        wallcycle_sub_start(wcycle, WallCycleSubCounter::ClearForceBuffer);
+        /* Clear the short- and long-range forces */
+        clearRVecs(forceWithShiftForces.force(), true);
+
+        /* Clear the shift forces */
+        clearRVecs(forceWithShiftForces.shiftForces(), false);
+        wallcycle_sub_stop(wcycle, WallCycleSubCounter::ClearForceBuffer);
+    }
+
+    /* 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)
+    {
+        wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::ClearForceBuffer);
+        /* 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, WallCycleSubCounter::ClearForceBuffer);
+    }
+
+
+    return ForceOutputs(
+            forceWithShiftForces, forceHelperBuffers->haveDirectVirialContributions(), forceWithVirial);
+}
+
+/* \brief Launch end-of-step GPU tasks: buffer clearing and rolling pruning.
+ *
+ */
+static void launchGpuEndOfStepTasks(nonbonded_verlet_t*               nbv,
+                                    gmx::ListedForcesGpu*             listedForcesGpu,
+                                    gmx_pme_t*                        pmedata,
+                                    gmx_enerdata_t*                   enerd,
+                                    const gmx::MdrunScheduleWorkload& runScheduleWork,
+                                    int64_t                           step,
+                                    gmx_wallcycle*                    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, WallCycleCounter::LaunchGpuPp);
+        wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+        Nbnxm::gpu_clear_outputs(nbv->gpuNbv(), runScheduleWork.stepWork.computeVirial);
+        wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+        wallcycle_stop(wcycle, WallCycleCounter::LaunchGpuPp);
+    }
+
+    if (runScheduleWork.stepWork.haveGpuPmeOnThisRank)
+    {
+        wallcycle_start_nocount(wcycle, WallCycleCounter::PmeGpuMesh);
+        bool gpuGraphWithSeparatePmeRank = false;
+        pme_gpu_reinit_computation(pmedata, gpuGraphWithSeparatePmeRank, wcycle);
+        wallcycle_stop(wcycle, WallCycleCounter::PmeGpuMesh);
+    }
+
+    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
+        listedForcesGpu->waitAccumulateEnergyTerms(enerd);
+
+        listedForcesGpu->clearEnergies();
+    }
+}
+
+/*! \brief Compute the number of times the "local coordinates ready on device" GPU event will be used as a synchronization point.
+ *
+ * When some work is offloaded to GPU, force calculation should wait for the atom coordinates to
+ * be ready on the device. The coordinates can come either from H2D copy at the beginning of the step,
+ * or from the GPU integration at the end of the previous step.
+ *
+ * In GROMACS, we usually follow the "mark once - wait once" approach. But this event is "consumed"
+ * (that is, waited upon either on host or on the device) multiple times, since many tasks
+ * in different streams depend on the coordinates.
+ *
+ * This function return the number of times the event will be consumed based on this step's workload.
+ *
+ * \param simulationWork Simulation workload flags.
+ * \param stepWork Step workload flags.
+ * \param pmeSendCoordinatesFromGpu Whether peer-to-peer communication is used for PME coordinates.
+ * \return
+ */
+static int getExpectedLocalXReadyOnDeviceConsumptionCount(gmx_used_in_debug const SimulationWorkload& simulationWork,
+                                                          const StepWorkload& stepWork,
+                                                          bool pmeSendCoordinatesFromGpu)
+{
+    int result = 0;
+    if (stepWork.computeSlowForces)
+    {
+        if (pmeSendCoordinatesFromGpu)
+        {
+            GMX_ASSERT(simulationWork.haveSeparatePmeRank,
+                       "GPU PME PP communications require having a separate PME rank");
+            // Event is consumed by gmx_pme_send_coordinates for GPU PME PP Communications
+            result++;
+        }
+        if (stepWork.haveGpuPmeOnThisRank)
+        {
+            // Event is consumed by launchPmeGpuSpread
+            result++;
+        }
+        if (stepWork.computeNonbondedForces && stepWork.useGpuXBufferOps)
+        {
+            // Event is consumed by convertCoordinatesGpu
+            result++;
+        }
+    }
+    if (stepWork.useGpuXHalo)
+    {
+        // Event is consumed by communicateGpuHaloCoordinates
+        result++;
+        if (GMX_THREAD_MPI) // Issue #4262
+        {
+            result++;
+        }
+    }
+    if (stepWork.clearGpuFBufferEarly && simulationWork.useGpuUpdate)
+    {
+        // Event is consumed by force clearing which waits for the update to complete
+        result++;
+    }
+    return result;
+}
+
+/*! \brief Compute the number of times the "local forces ready on device" GPU event will be used as a synchronization point.
+ *
+ * In GROMACS, we usually follow the "mark once - wait once" approach. But this event is "consumed"
+ * (that is, waited upon either on host or on the device) multiple times, since many tasks
+ * in different streams depend on the local forces.
+ *
+ * \param simulationWork Simulation workload flags.
+ * \param domainWork Domain workload flags.
+ * \param stepWork Step workload flags.
+ * \param useOrEmulateGpuNb Whether GPU non-bonded calculations are used or emulated.
+ * \param alternateGpuWait Whether alternating wait/reduce scheme is used.
+ * \return The number of times the event will be consumed based on this step's workload.
+ */
+static int getExpectedLocalFReadyOnDeviceConsumptionCount(const SimulationWorkload& simulationWork,
+                                                          const DomainLifetimeWorkload& domainWork,
+                                                          const StepWorkload&           stepWork,
+                                                          bool useOrEmulateGpuNb,
+                                                          bool alternateGpuWait)
+{
+    int  counter = 0;
+    bool eventUsedInGpuForceReduction =
+            (domainWork.haveCpuLocalForceWork
+             || (simulationWork.havePpDomainDecomposition && !simulationWork.useGpuHaloExchange));
+    bool gpuForceReductionUsed = useOrEmulateGpuNb && !alternateGpuWait && stepWork.useGpuFBufferOps
+                                 && stepWork.computeNonbondedForces;
+    if (gpuForceReductionUsed && eventUsedInGpuForceReduction)
+    {
+        counter++;
+    }
+    bool gpuForceHaloUsed = simulationWork.havePpDomainDecomposition && stepWork.computeForces
+                            && stepWork.useGpuFHalo;
+    if (gpuForceHaloUsed)
+    {
+        counter++;
+    }
+    return counter;
+}
+
+//! \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 buffers 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(ModuleMultiThread::Default);
+#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 GPU force reduction:
+ * reinitialization plus the registration of forces and dependencies.
+ *
+ * \param [in] runScheduleWork     Schedule workload flag structure
+ * \param [in] nbv                 Non-bonded Verlet object
+ * \param [in] stateGpu            GPU state propagator object
+ * \param [in] gpuForceReduction   GPU force reduction object
+ * \param [in] pmePpCommGpu        PME-PP GPU communication object
+ * \param [in] pmedata             PME data object
+ * \param [in] dd                  Domain decomposition object
+ */
+static void setupLocalGpuForceReduction(const gmx::MdrunScheduleWorkload& runScheduleWork,
+                                        nonbonded_verlet_t*               nbv,
+                                        gmx::StatePropagatorDataGpu*      stateGpu,
+                                        gmx::GpuForceReduction*           gpuForceReduction,
+                                        gmx::PmePpCommGpu*                pmePpCommGpu,
+                                        const gmx_pme_t*                  pmedata,
+                                        const gmx_domdec_t*               dd)
+{
+    GMX_ASSERT(!runScheduleWork.simulationWork.useMts,
+               "GPU force reduction is not compatible with MTS");
+
+    // (re-)initialize local GPU force reduction
+    const bool accumulate = runScheduleWork.domainWork.haveCpuLocalForceWork
+                            || runScheduleWork.simulationWork.havePpDomainDecomposition;
+    const int atomStart = 0;
+    gpuForceReduction->reinit(stateGpu->getForces(),
+                              nbv->getNumAtoms(AtomLocality::Local),
+                              nbv->getGridIndices(),
+                              atomStart,
+                              accumulate,
+                              stateGpu->fReducedOnDevice(AtomLocality::Local));
+
+    // register forces and add dependencies
+    gpuForceReduction->registerNbnxmForce(Nbnxm::gpu_get_f(nbv->gpuNbv()));
+
+    DeviceBuffer<gmx::RVec> pmeForcePtr;
+    GpuEventSynchronizer*   pmeSynchronizer     = nullptr;
+    bool                    havePmeContribution = false;
+
+    if (runScheduleWork.simulationWork.haveGpuPmeOnPpRank())
+    {
+        pmeForcePtr = pme_gpu_get_device_f(pmedata);
+        if (pmeForcePtr)
+        {
+            pmeSynchronizer     = pme_gpu_get_f_ready_synchronizer(pmedata);
+            havePmeContribution = true;
+        }
+    }
+    else if (runScheduleWork.simulationWork.useGpuPmePpCommunication)
+    {
+        pmeForcePtr = pmePpCommGpu->getGpuForceStagingPtr();
+        GMX_ASSERT(pmeForcePtr, "PME force for reduction has no data");
+        if (GMX_THREAD_MPI)
+        {
+            pmeSynchronizer = pmePpCommGpu->getForcesReadySynchronizer();
+        }
+        havePmeContribution = true;
+    }
+
+    if (havePmeContribution)
+    {
+        gpuForceReduction->registerRvecForce(pmeForcePtr);
+        if (runScheduleWork.simulationWork.useNvshmem)
+        {
+            DeviceBuffer<uint64_t> forcesReadyNvshmemFlags = pmePpCommGpu->getGpuForcesSyncObj();
+            gpuForceReduction->registerForcesReadyNvshmemFlags(forcesReadyNvshmemFlags);
+        }
+
+        if (!runScheduleWork.simulationWork.useGpuPmePpCommunication || GMX_THREAD_MPI)
+        {
+            GMX_ASSERT(pmeSynchronizer != nullptr, "PME force ready cuda event should not be NULL");
+            gpuForceReduction->addDependency(pmeSynchronizer);
+        }
+    }
+
+    if (runScheduleWork.domainWork.haveCpuLocalForceWork
+        || (runScheduleWork.simulationWork.havePpDomainDecomposition
+            && !runScheduleWork.simulationWork.useGpuHaloExchange))
+    {
+        gpuForceReduction->addDependency(stateGpu->fReadyOnDevice(AtomLocality::Local));
+    }
+
+    if (runScheduleWork.simulationWork.useGpuHaloExchange)
+    {
+        gpuForceReduction->addDependency(dd->gpuHaloExchange[0][0]->getForcesReadyOnDeviceEvent());
+    }
+}
+
+/*! \brief Setup for the non-local GPU force reduction:
+ * reinitialization plus the registration of forces and dependencies.
+ *
+ * \param [in] runScheduleWork     Schedule workload flag structure
+ * \param [in] nbv                 Non-bonded Verlet object
+ * \param [in] stateGpu            GPU state propagator object
+ * \param [in] gpuForceReduction   GPU force reduction object
+ * \param [in] dd                  Domain decomposition object
+ */
+static void setupNonLocalGpuForceReduction(const gmx::MdrunScheduleWorkload& runScheduleWork,
+                                           nonbonded_verlet_t*               nbv,
+                                           gmx::StatePropagatorDataGpu*      stateGpu,
+                                           gmx::GpuForceReduction*           gpuForceReduction,
+                                           const gmx_domdec_t*               dd)
+{
+    // (re-)initialize non-local GPU force reduction
+    const bool accumulate = runScheduleWork.domainWork.haveCpuNonLocalForceWork;
+    const int  atomStart  = dd_numHomeAtoms(*dd);
+    gpuForceReduction->reinit(stateGpu->getForces(),
+                              nbv->getNumAtoms(AtomLocality::NonLocal),
+                              nbv->getGridIndices(),
+                              atomStart,
+                              accumulate,
+                              stateGpu->fReducedOnDevice(AtomLocality::NonLocal));
+
+    // register forces and add dependencies
+    gpuForceReduction->registerNbnxmForce(Nbnxm::gpu_get_f(nbv->gpuNbv()));
+
+    if (runScheduleWork.domainWork.haveCpuNonLocalForceWork)
+    {
+        gpuForceReduction->addDependency(stateGpu->fReadyOnDevice(AtomLocality::NonLocal));
+    }
+}
+
+
+/*! \brief Return the number of local atoms.
+ */
+static int getLocalAtomCount(const gmx_domdec_t* dd, const t_mdatoms& mdatoms, bool havePPDomainDecomposition)
+{
+    GMX_ASSERT(!(havePPDomainDecomposition && (dd == nullptr)),
+               "Can't have PP decomposition with dd uninitialized!");
+    return havePPDomainDecomposition ? dd_numAtomsZones(*dd) : mdatoms.homenr;
+}
+
+/*! \brief Does pair search and closely related activities required on search steps.
+ */
+static void doPairSearch(const t_commrec*                    cr,
+                         const t_inputrec&                   inputrec,
+                         const gmx::MDModulesNotifiers&      mdModulesNotifiers,
+                         int64_t                             step,
+                         t_nrnb*                             nrnb,
+                         gmx_wallcycle*                      wcycle,
+                         const gmx_localtop_t&               top,
+                         const matrix                        box,
+                         gmx::ArrayRefWithPadding<gmx::RVec> x,
+                         gmx::ArrayRef<gmx::RVec>            v,
+                         const t_mdatoms&                    mdatoms,
+                         t_forcerec*                         fr,
+                         const gmx::MdrunScheduleWorkload&   runScheduleWork)
+{
+    nonbonded_verlet_t* nbv = fr->nbv.get();
+
+    gmx::StatePropagatorDataGpu* stateGpu = fr->stateGpu;
+
+    const SimulationWorkload& simulationWork = runScheduleWork.simulationWork;
+    const StepWorkload&       stepWork       = runScheduleWork.stepWork;
+
+    if (gmx::needStateGpu(simulationWork))
+    {
+        // TODO refactor this to do_md, after partitioning.
+        stateGpu->reinit(mdatoms.homenr,
+                         getLocalAtomCount(cr->dd, mdatoms, simulationWork.havePpDomainDecomposition));
+    }
+
+    if (simulationWork.haveGpuPmeOnPpRank())
+    {
+        GMX_ASSERT(gmx::needStateGpu(simulationWork), "StatePropagatorDataGpu is needed");
+        // TODO: This should be moved into PME setup function ( pme_gpu_prepare_computation(...) )
+        pme_gpu_set_device_x(fr->pmedata, stateGpu->getCoordinates());
+    }
+
+    if (fr->pbcType != PbcType::No)
+    {
+        const bool calcCGCM = (stepWork.stateChanged && !haveDDAtomOrdering(*cr));
+        if (calcCGCM)
+        {
+            put_atoms_in_box_omp(fr->pbcType,
+                                 box,
+                                 fr->haveBoxDeformation,
+                                 inputrec.deform,
+                                 x.unpaddedArrayRef().subArray(0, mdatoms.homenr),
+                                 v.empty() ? ArrayRef<RVec>() : v.subArray(0, mdatoms.homenr),
+                                 gmx_omp_nthreads_get(ModuleMultiThread::Default));
+            inc_nrnb(nrnb, eNR_SHIFTX, mdatoms.homenr);
+        }
+
+        if (!haveDDAtomOrdering(*cr))
+        {
+            // Atoms might have changed periodic image, signal MDModules
+            gmx::MDModulesAtomsRedistributedSignal mdModulesAtomsRedistributedSignal(
+                    box, x.unpaddedArrayRef().subArray(0, mdatoms.homenr));
+            mdModulesNotifiers.simulationSetupNotifier_.notify(mdModulesAtomsRedistributedSignal);
+        }
+    }
+
+    if (fr->wholeMoleculeTransform && stepWork.stateChanged)
+    {
+        fr->wholeMoleculeTransform->updateForAtomPbcJumps(x.unpaddedArrayRef(), box);
+    }
+
+    wallcycle_start(wcycle, WallCycleCounter::NS);
+    if (!haveDDAtomOrdering(*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, WallCycleSubCounter::NBSGridLocal);
+        nbv->putAtomsOnGrid(
+                box, 0, vzero, boxDiagonal, nullptr, { 0, mdatoms.homenr }, -1, fr->atomInfo, x.unpaddedArrayRef(), 0, nullptr);
+        wallcycle_sub_stop(wcycle, WallCycleSubCounter::NBSGridLocal);
+    }
+    else
+    {
+        wallcycle_sub_start(wcycle, WallCycleSubCounter::NBSGridNonLocal);
+        nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->atomInfo, x.unpaddedArrayRef());
+        wallcycle_sub_stop(wcycle, WallCycleSubCounter::NBSGridNonLocal);
+    }
+
+    nbv->setAtomProperties(mdatoms.typeA, mdatoms.chargeA, fr->atomInfo);
+
+    wallcycle_stop(wcycle, WallCycleCounter::NS);
+
+    /* initialize the GPU nbnxm atom data and bonded data structures */
+    if (simulationWork.useGpuNonbonded)
+    {
+        // Note: cycle counting only nononbondeds, GPU listed forces counts internally
+        wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpuPp);
+        wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+        Nbnxm::gpu_init_atomdata(nbv->gpuNbv(), &nbv->nbat());
+        wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+        wallcycle_stop(wcycle, WallCycleCounter::LaunchGpuPp);
+
+        if (fr->listedForcesGpu)
+        {
+            /* 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->listedForcesGpu->updateInteractionListsAndDeviceBuffers(
+                    nbv->getGridIndices(), top.idef, Nbnxm::gpuGetNBAtomData(nbv->gpuNbv()));
+        }
+    }
+
+    wallcycle_start_nocount(wcycle, WallCycleCounter::NS);
+    wallcycle_sub_start(wcycle, WallCycleSubCounter::NBSSearchLocal);
+    /* 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->listedForcesGpu.get(), InteractionLocality::Local);
+
+    wallcycle_sub_stop(wcycle, WallCycleSubCounter::NBSSearchLocal);
+    wallcycle_stop(wcycle, WallCycleCounter::NS);
+
+    if (simulationWork.useGpuXBufferOpsWhenAllowed)
+    {
+        nbv->atomdata_init_copy_x_to_nbat_x_gpu();
+    }
+
+    if (simulationWork.useGpuFBufferOpsWhenAllowed)
+    {
+        // with MPI, direct GPU communication, and separate PME ranks we need
+        // gmx_pme_send_coordinates() to be called before we can set up force reduction
+        bool delaySetupLocalGpuForceReduction = GMX_MPI && simulationWork.useGpuPmePpCommunication;
+        if (!delaySetupLocalGpuForceReduction)
+        {
+            setupLocalGpuForceReduction(runScheduleWork,
+                                        nbv,
+                                        stateGpu,
+                                        fr->gpuForceReduction[gmx::AtomLocality::Local].get(),
+                                        fr->pmePpCommGpu.get(),
+                                        fr->pmedata,
+                                        cr->dd);
+        }
+
+        if (simulationWork.havePpDomainDecomposition)
+        {
+            setupNonLocalGpuForceReduction(runScheduleWork,
+                                           nbv,
+                                           stateGpu,
+                                           fr->gpuForceReduction[gmx::AtomLocality::NonLocal].get(),
+                                           cr->dd);
+        }
+    }
+
+    /* do non-local pair search */
+    if (simulationWork.havePpDomainDecomposition)
+    {
+        wallcycle_start_nocount(wcycle, WallCycleCounter::NS);
+        wallcycle_sub_start(wcycle, WallCycleSubCounter::NBSSearchNonLocal);
+        /* 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->listedForcesGpu.get(), InteractionLocality::NonLocal);
+        wallcycle_sub_stop(wcycle, WallCycleSubCounter::NBSSearchNonLocal);
+        wallcycle_stop(wcycle, WallCycleCounter::NS);
+        // 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());
+        }
+    }
+
+    // With FEP we set up the reduction over threads for local+non-local simultaneously,
+    // so we need to do that here after the local and non-local pairlist construction.
+    if (fr->efep != FreeEnergyPerturbationType::No)
+    {
+        wallcycle_sub_start(wcycle, WallCycleSubCounter::NonbondedFep);
+        nbv->setupFepThreadedForceBuffer(fr->natoms_force_constr);
+        wallcycle_sub_stop(wcycle, WallCycleSubCounter::NonbondedFep);
+    }
+}
+
+void do_force(FILE*                               fplog,
+              const t_commrec*                    cr,
+              const gmx_multisim_t*               ms,
+              const t_inputrec&                   inputrec,
+              const gmx::MDModulesNotifiers&      mdModulesNotifiers,
+              gmx::Awh*                           awh,
+              gmx_enfrot*                         enforcedRotation,
+              gmx::ImdSession*                    imdSession,
+              pull_t*                             pull_work,
+              int64_t                             step,
+              t_nrnb*                             nrnb,
+              gmx_wallcycle*                      wcycle,
+              const gmx_localtop_t*               top,
+              const matrix                        box,
+              gmx::ArrayRefWithPadding<gmx::RVec> x,
+              gmx::ArrayRef<gmx::RVec>            v,
+              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,
+              const gmx::MdrunScheduleWorkload&   runScheduleWork,
+              gmx::VirtualSitesHandler*           vsite,
+              rvec                                muTotal,
+              double                              t,
+              gmx_edsam*                          ed,
+              CpuPpLongRangeNonbondeds*           longRangeNonbondeds,
+              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;
+
+    const gmx::DomainLifetimeWorkload& domainWork = runScheduleWork.domainWork;
+
+    const StepWorkload& stepWork = runScheduleWork.stepWork;
+
+    if (stepWork.doNeighborSearch)
+    {
+        doPairSearch(cr, inputrec, mdModulesNotifiers, step, nrnb, wcycle, *top, box, x, v, *mdatoms, fr, runScheduleWork);
+
+        /* 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).
+         */
+        ddBalanceRegionHandler.openBeforeForceComputationCpu(DdAllowBalanceRegionReopen::yes);
+    }
+
+    const bool pmeSendCoordinatesFromGpu =
+            simulationWork.useGpuPmePpCommunication && !stepWork.doNeighborSearch;
+    auto* localXReadyOnDevice = (stepWork.haveGpuPmeOnThisRank || stepWork.useGpuXBufferOps
+                                 || simulationWork.useGpuUpdate || pmeSendCoordinatesFromGpu)
+                                        ? stateGpu->getCoordinatesReadyOnDeviceEvent(
+                                                AtomLocality::Local, simulationWork, stepWork)
+                                        : nullptr;
+
+    if (stepWork.clearGpuFBufferEarly)
+    {
+        // GPU 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.
+        // The dependency for this is that forces from previous timestep have been consumed,
+        // which is satisfied when localXReadyOnDevice has been marked for GPU update case.
+        // For CPU update, the forces are consumed by the beginning of the step, so no extra sync needed.
+        GpuEventSynchronizer* dependency = simulationWork.useGpuUpdate ? localXReadyOnDevice : nullptr;
+        stateGpu->clearForcesOnGpu(AtomLocality::Local, dependency);
+    }
+
+    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);
+        }
+    }
+    nbnxn_atomdata_copy_shiftvec(stepWork.haveDynamicBox, fr->shift_vec, &nbv->nbat());
+
+
+    GMX_ASSERT(simulationWork.useGpuHaloExchange
+                       == ((cr->dd != nullptr) && (!cr->dd->gpuHaloExchange[0].empty())),
+               "The GPU halo exchange is active, but it has not been constructed.");
+
+    bool gmx_used_in_debug haveCopiedXFromGpu = false;
+    // 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.
+    if (simulationWork.useGpuUpdate && !stepWork.doNeighborSearch
+        && (runScheduleWork.domainWork.haveCpuLocalForceWork || stepWork.computeVirial
+            || simulationWork.useCpuPmePpCommunication || simulationWork.useCpuHaloExchange
+            || simulationWork.computeMuTot))
+    {
+        stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
+        haveCopiedXFromGpu = true;
+    }
+
+    // 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 (stepWork.haveGpuPmeOnThisRank || stepWork.useGpuXBufferOps || pmeSendCoordinatesFromGpu)
+    {
+        GMX_ASSERT(stateGpu != nullptr, "stateGpu should not be null");
+        const int expectedLocalXReadyOnDeviceConsumptionCount =
+                getExpectedLocalXReadyOnDeviceConsumptionCount(
+                        simulationWork, stepWork, pmeSendCoordinatesFromGpu);
+
+        // We need to copy coordinates when:
+        // 1. Update is not offloaded
+        // 2. The buffers were reinitialized on search step
+        if (!simulationWork.useGpuUpdate || stepWork.doNeighborSearch)
+        {
+            stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(),
+                                           AtomLocality::Local,
+                                           expectedLocalXReadyOnDeviceConsumptionCount);
+        }
+        else if (simulationWork.useGpuUpdate)
+        {
+            stateGpu->setXUpdatedOnDeviceEventExpectedConsumptionCount(
+                    expectedLocalXReadyOnDeviceConsumptionCount);
+        }
+    }
+
+    if (stepWork.computePmeOnSeparateRank)
+    {
+        /* Send particle coordinates to the pme nodes */
+        if (!pmeSendCoordinatesFromGpu && !stepWork.doNeighborSearch && simulationWork.useGpuUpdate)
+        {
+            GMX_ASSERT(haveCopiedXFromGpu,
+                       "a wait should only be triggered if copy has been scheduled");
+            stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
+        }
+
+        const bool reinitGpuPmePpComms =
+                simulationWork.useGpuPmePpCommunication && stepWork.doNeighborSearch;
+        gmx_pme_send_coordinates(fr,
+                                 cr,
+                                 box,
+                                 x.unpaddedArrayRef(),
+                                 lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+                                 lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)],
+                                 (stepWork.computeVirial || stepWork.computeEnergy),
+                                 step,
+                                 simulationWork.useGpuPmePpCommunication,
+                                 reinitGpuPmePpComms,
+                                 pmeSendCoordinatesFromGpu,
+                                 stepWork.useGpuPmeFReduction,
+                                 pmeSendCoordinatesFromGpu ? localXReadyOnDevice : nullptr,
+                                 simulationWork.useMdGpuGraph,
+                                 wcycle);
+    }
+
+    if (simulationWork.useGpuFBufferOpsWhenAllowed && stepWork.doNeighborSearch)
+    {
+        // with MPI, direct GPU communication, and separate PME ranks we need
+        // gmx_pme_send_coordinates() to be called before we can set up force reduction
+        bool doSetupLocalGpuForceReduction = GMX_MPI && simulationWork.useGpuPmePpCommunication;
+        if (doSetupLocalGpuForceReduction)
+        {
+            setupLocalGpuForceReduction(runScheduleWork,
+                                        fr->nbv.get(),
+                                        stateGpu,
+                                        fr->gpuForceReduction[gmx::AtomLocality::Local].get(),
+                                        fr->pmePpCommGpu.get(),
+                                        fr->pmedata,
+                                        cr->dd);
+        }
+    }
+
+    if (stepWork.haveGpuPmeOnThisRank)
+    {
+        launchPmeGpuSpread(fr->pmedata,
+                           box,
+                           stepWork,
+                           localXReadyOnDevice,
+                           lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+                           simulationWork.useMdGpuGraph,
+                           wcycle);
+    }
+
+
+    if (!stepWork.doNeighborSearch && !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, WallCycleCounter::LaunchGpuPp);
+        wallcycle_sub_start(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+        Nbnxm::gpu_upload_shiftvec(nbv->gpuNbv(), &nbv->nbat());
+        if (!stepWork.useGpuXBufferOps)
+        {
+            Nbnxm::gpu_copy_xq_to_gpu(nbv->gpuNbv(), &nbv->nbat(), AtomLocality::Local);
+        }
+        wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+        wallcycle_stop(wcycle, WallCycleCounter::LaunchGpuPp);
+        // 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 && !simulationWork.havePpDomainDecomposition)
+        {
+            fr->listedForcesGpu->setPbcAndlaunchKernel(fr->pbcType, box, fr->bMolPBC, stepWork);
+        }
+
+        /* launch local nonbonded work on GPU */
+        wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpuPp);
+        wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+        do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::Local, enbvClearFNo, step, nrnb, wcycle);
+        wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+        wallcycle_stop(wcycle, WallCycleCounter::LaunchGpuPp);
+    }
+
+    if (stepWork.haveGpuPmeOnThisRank)
+    {
+        // 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 */
+    if (simulationWork.havePpDomainDecomposition)
+    {
+        if (!stepWork.doNeighborSearch)
+        {
+            GpuEventSynchronizer* gpuCoordinateHaloLaunched = nullptr;
+            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).
+                gpuCoordinateHaloLaunched = communicateGpuHaloCoordinates(*cr, box, localXReadyOnDevice);
+
+                if (domainWork.haveCpuNonLocalForceWork)
+                {
+                    // non-local part of coordinate buffer must be copied back to host for CPU work
+                    stateGpu->copyCoordinatesFromGpu(
+                            x.unpaddedArrayRef(), AtomLocality::NonLocal, gpuCoordinateHaloLaunched);
+                }
+            }
+            else
+            {
+                if (simulationWork.useGpuUpdate)
+                {
+                    GMX_ASSERT(haveCopiedXFromGpu,
+                               "a wait should only be triggered if copy has been scheduled");
+                    const bool haveAlreadyWaited =
+                            (stepWork.computePmeOnSeparateRank && !pmeSendCoordinatesFromGpu);
+                    if (!haveAlreadyWaited)
+                    {
+                        stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
+                    }
+                }
+                dd_move_x(cr->dd, box, x.unpaddedArrayRef(), wcycle);
+            }
+
+            if (stepWork.useGpuXBufferOps)
+            {
+                if (!stepWork.useGpuXHalo)
+                {
+                    stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
+                }
+                GpuEventSynchronizer* xReadyOnDeviceEvent = stateGpu->getCoordinatesReadyOnDeviceEvent(
+                        AtomLocality::NonLocal, simulationWork, stepWork, gpuCoordinateHaloLaunched);
+                if (stepWork.useGpuXHalo && domainWork.haveCpuNonLocalForceWork)
+                {
+                    /* We already enqueued an event for Gpu Halo exchange completion into the
+                     * NonLocal stream when D2H copying the coordinates. */
+                    xReadyOnDeviceEvent = nullptr;
+                }
+                nbv->convertCoordinatesGpu(
+                        AtomLocality::NonLocal, stateGpu->getCoordinates(), xReadyOnDeviceEvent);
+            }
+            else
+            {
+                nbv->convertCoordinates(AtomLocality::NonLocal, x.unpaddedArrayRef());
+            }
+        }
+
+        if (simulationWork.useGpuNonbonded)
+        {
+
+            if (!stepWork.useGpuXBufferOps)
+            {
+                wallcycle_start(wcycle, WallCycleCounter::LaunchGpuPp);
+                wallcycle_sub_start(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+                Nbnxm::gpu_copy_xq_to_gpu(nbv->gpuNbv(), &nbv->nbat(), AtomLocality::NonLocal);
+                wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+                wallcycle_stop(wcycle, WallCycleCounter::LaunchGpuPp);
+            }
+
+            if (domainWork.haveGpuBondedWork)
+            {
+                fr->listedForcesGpu->setPbcAndlaunchKernel(fr->pbcType, box, fr->bMolPBC, stepWork);
+            }
+
+            /* launch non-local nonbonded tasks on GPU */
+            wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpuPp);
+            wallcycle_sub_start(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+            do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFNo, step, nrnb, wcycle);
+            wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+            wallcycle_stop(wcycle, WallCycleCounter::LaunchGpuPp);
+        }
+    }
+
+    if (simulationWork.useGpuNonbonded && stepWork.computeNonbondedForces)
+    {
+        /* launch D2H copy-back F */
+        wallcycle_start_nocount(wcycle, WallCycleCounter::LaunchGpuPp);
+        wallcycle_sub_start_nocount(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+
+        if (simulationWork.havePpDomainDecomposition)
+        {
+            Nbnxm::gpu_launch_cpyback(nbv->gpuNbv(), &nbv->nbat(), stepWork, AtomLocality::NonLocal);
+        }
+        Nbnxm::gpu_launch_cpyback(nbv->gpuNbv(), &nbv->nbat(), stepWork, AtomLocality::Local);
+        wallcycle_sub_stop(wcycle, WallCycleSubCounter::LaunchGpuNonBonded);
+
+        if (domainWork.haveGpuBondedWork && stepWork.computeEnergy)
+        {
+            fr->listedForcesGpu->launchEnergyTransfer();
+        }
+        wallcycle_stop(wcycle, WallCycleCounter::LaunchGpuPp);
+    }
+
+    gmx::ArrayRef<const gmx::RVec> xWholeMolecules;
+    if (fr->wholeMoleculeTransform)
+    {
+        xWholeMolecules = fr->wholeMoleculeTransform->wholeMoleculeCoordinates(x.unpaddedArrayRef(), box);
+    }
+
+    // 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)
+    {
+        const bool needCoordsOnHost = (runScheduleWork.domainWork.haveCpuLocalForceWork
+                                       || stepWork.computeVirial || simulationWork.computeMuTot);
+        const bool haveAlreadyWaited =
+                simulationWork.useCpuHaloExchange
+                || (stepWork.computePmeOnSeparateRank && !pmeSendCoordinatesFromGpu);
+        if (needCoordsOnHost && !haveAlreadyWaited)
+        {
+            GMX_ASSERT(haveCopiedXFromGpu,
+                       "a wait should only be triggered if copy has been scheduled");
+            stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
+        }
+    }
+
+    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,
+                mdatoms->chargeA,
+                mdatoms->chargeB,
+                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 (haveDDAtomOrdering(*cr) && simulationWork.haveSeparatePmeRank)
+    {
+        wallcycle_start(wcycle, WallCycleCounter::PpDuringPme);
+        dd_force_flop_start(cr->dd, nrnb);
+    }
+
+    if (inputrec.bRot)
+    {
+        wallcycle_start(wcycle, WallCycleCounter::Rot);
+        do_rotation(cr, enforcedRotation, box, x.unpaddedConstArrayRef(), t, step, stepWork.doNeighborSearch);
+        wallcycle_stop(wcycle, WallCycleCounter::Rot);
+    }
+
+    /* Start the force cycle counter.
+     * Note that a different counter is used for dynamic load balancing.
+     */
+    wallcycle_start(wcycle, WallCycleCounter::Force);
+
+    /* 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.
+     *
+     * Note that CPU force buffer clearing needs to happen after the completion of the
+     * previous step's CPU force H2D transfer (prior to force reduction).
+     * In the current code this is ensured by the earlier waitCoordinatesReadyOnHost()
+     * which is sufficient, but it is suboptimal as it prevents overlap of the force clearing
+     * with independent GPU work (integration/constraints, x D2H copy).
+     */
+    ForceOutputs forceOutMtsLevel0 = setupForceOutputs(
+            &fr->forceHelperBuffers[0], force, domainWork, stepWork, simulationWork.havePpDomainDecomposition, wcycle);
+
+    // Force output for MTS combined forces, only set at level1 MTS steps
+    std::optional<ForceOutputs> forceOutMts =
+            (simulationWork.useMts && stepWork.computeSlowForces)
+                    ? std::optional(setupForceOutputs(&fr->forceHelperBuffers[1],
+                                                      forceView->forceMtsCombinedWithPadding(),
+                                                      domainWork,
+                                                      stepWork,
+                                                      simulationWork.havePpDomainDecomposition,
+                                                      wcycle))
+                    : std::nullopt;
+
+    ForceOutputs* forceOutMtsLevel1 =
+            simulationWork.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);
+    }
+
+    wallcycle_stop(wcycle, WallCycleCounter::Force);
+
+    /* 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)
+    {
+        wallcycle_start_nocount(wcycle, WallCycleCounter::Force);
+        do_nb_verlet(fr, ic, enerd, stepWork, InteractionLocality::Local, enbvClearFYes, step, nrnb, wcycle);
+        wallcycle_stop(wcycle, WallCycleCounter::Force);
+    }
+
+    if (stepWork.useGpuXHalo && domainWork.haveCpuNonLocalForceWork)
+    {
+        /* Wait for non-local coordinate data to be copied from device */
+        stateGpu->waitCoordinatesReadyOnHost(AtomLocality::NonLocal);
+    }
+
+    wallcycle_start_nocount(wcycle, WallCycleCounter::Force);
+    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->dispatchFreeEnergyKernels(x,
+                                       &forceOutNonbonded->forceWithShiftForces(),
+                                       fr->use_simd_kernels,
+                                       fr->ntype,
+                                       *fr->ic,
+                                       fr->shift_vec,
+                                       fr->nbfp,
+                                       fr->ljpme_c6grid,
+                                       mdatoms->chargeA,
+                                       mdatoms->chargeB,
+                                       mdatoms->typeA,
+                                       mdatoms->typeB,
+                                       lambda,
+                                       enerd,
+                                       stepWork,
+                                       nrnb);
+    }
+
+    if (stepWork.computeNonbondedForces && !useOrEmulateGpuNb)
+    {
+        if (simulationWork.havePpDomainDecomposition)
+        {
+            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, WallCycleCounter::Force);
+            nbv->atomdata_add_nbat_f_to_f(AtomLocality::All,
+                                          forceOutNonbonded->forceWithShiftForces().force());
+            wallcycle_start_nocount(wcycle, WallCycleCounter::Force);
+        }
+
+        /* 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());
+        }
+    }
+
+    // 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->typeA,
+                                   mdatoms->typeB,
+                                   mdatoms->cENER,
+                                   mdatoms->homenr,
+                                   mdatoms->nPerturbed,
+                                   x.unpaddedConstArrayRef(),
+                                   &forceOutMtsLevel0.forceWithVirial(),
+                                   lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)],
+                                   enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR],
+                                   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, haveDDAtomOrdering(*cr) ? cr->dd->numCells : nullptr, TRUE, box);
+        }
+
+        for (int mtsIndex = 0; mtsIndex < (simulationWork.useMts && stepWork.computeSlowForces ? 2 : 1);
+             mtsIndex++)
+        {
+            ListedForces& listedForces = fr->listedForces[mtsIndex];
+            ForceOutputs& forceOut     = (mtsIndex == 0 ? forceOutMtsLevel0 : *forceOutMtsLevel1);
+            listedForces.calculate(wcycle,
+                                   box,
+                                   cr,
+                                   ms,
+                                   x,
+                                   xWholeMolecules,
+                                   fr->fcdata.get(),
+                                   hist,
+                                   &forceOut,
+                                   fr,
+                                   &pbc,
+                                   enerd,
+                                   nrnb,
+                                   lambda,
+                                   mdatoms->chargeA,
+                                   mdatoms->chargeB,
+                                   makeConstArrayRef(mdatoms->bPerturbed),
+                                   mdatoms->cENER,
+                                   mdatoms->nPerturbed,
+                                   haveDDAtomOrdering(*cr) ? cr->dd->globalAtomIndices.data() : nullptr,
+                                   stepWork);
+        }
+    }
+
+    if (stepWork.computeSlowForces)
+    {
+        longRangeNonbondeds->calculate(fr->pmedata,
+                                       cr,
+                                       x.unpaddedConstArrayRef(),
+                                       &forceOutMtsLevel1->forceWithVirial(),
+                                       enerd,
+                                       box,
+                                       lambda,
+                                       dipoleData.muStateAB,
+                                       stepWork,
+                                       ddBalanceRegionHandler);
+    }
+
+    /* PLUMED */
+    if(plumedswitch){
+      int plumedNeedsEnergy;
+      plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
+      if(!plumedNeedsEnergy) plumed_cmd(plumedmain,"performCalc",nullptr);
+    }
+    /* END PLUMED */ 
+
+    wallcycle_stop(wcycle, WallCycleCounter::Force);
+
+    // VdW dispersion correction, only computed on main rank to avoid double counting
+    if ((stepWork.computeEnergy || stepWork.computeVirial) && fr->dispersionCorrection && MAIN(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;
+        }
+    }
+
+    const bool needToReceivePmeResultsFromSeparateRank = (PAR(cr) && stepWork.computePmeOnSeparateRank);
+    const bool needToReceivePmeResults =
+            (stepWork.haveGpuPmeOnThisRank || needToReceivePmeResultsFromSeparateRank);
+
+    /* When running free energy perturbations steered by AWH and doing PME calculations on the
+     * GPU we must wait for the PME calculation (dhdl) results to finish before sampling the
+     * FEP dimension with AWH. */
+    const bool needEarlyPmeResults = (awh != nullptr && awh->hasFepLambdaDimension() && needToReceivePmeResults
+                                      && stepWork.computeEnergy && stepWork.computeSlowForces);
+    if (needEarlyPmeResults)
+    {
+        if (stepWork.haveGpuPmeOnThisRank)
+        {
+            pmeGpuWaitAndReduce(fr->pmedata,
+                                stepWork,
+                                wcycle,
+                                &forceOutMtsLevel1->forceWithVirial(),
+                                enerd,
+                                lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)]);
+        }
+        else if (needToReceivePmeResultsFromSeparateRank)
+        {
+            /* 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);
+        }
+    }
+
+    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 (simulationWork.havePpDomainDecomposition && 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 (simulationWork.havePpDomainDecomposition)
+        {
+            if (simulationWork.useGpuNonbonded)
+            {
+                cycles_wait_gpu += Nbnxm::gpu_wait_finish_task(
+                        nbv->gpuNbv(),
+                        stepWork,
+                        AtomLocality::NonLocal,
+                        enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::LJSR].data(),
+                        enerd->grpp.energyGroupPairTerms[NonBondedEnergyTerms::CoulombSR].data(),
+                        forceWithShiftForces.shiftForces(),
+                        wcycle);
+            }
+            else
+            {
+                wallcycle_start_nocount(wcycle, WallCycleCounter::Force);
+                do_nb_verlet(
+                        fr, ic, enerd, stepWork, InteractionLocality::NonLocal, enbvClearFYes, step, nrnb, wcycle);
+                wallcycle_stop(wcycle, WallCycleCounter::Force);
+            }
+
+            if (stepWork.useGpuFBufferOps)
+            {
+                if (domainWork.haveCpuNonLocalForceWork)
+                {
+                    stateGpu->copyForcesToGpu(forceOutMtsLevel0.forceWithShiftForces().force(),
+                                              AtomLocality::NonLocal);
+                }
+
+
+                fr->gpuForceReduction[gmx::AtomLocality::NonLocal]->execute();
+
+                if (!stepWork.useGpuFHalo)
+                {
+                    /* We don't explicitly wait for the forces to be reduced on device,
+                     * but wait for them to finish copying to CPU instead.
+                     * So, we manually consume the event, see Issue #3988. */
+                    stateGpu->consumeForcesReducedOnDeviceEvent(AtomLocality::NonLocal);
+                    // 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.
+     */
+    if (stepWork.combineMtsForcesBeforeHaloExchange)
+    {
+        wallcycle_start_nocount(wcycle, WallCycleCounter::Force);
+        combineMtsForces(getLocalAtomCount(cr->dd, *mdatoms, simulationWork.havePpDomainDecomposition),
+                         force.unpaddedArrayRef(),
+                         forceView->forceMtsCombined(),
+                         inputrec.mtsLevels[1].stepFactor);
+        wallcycle_stop(wcycle, WallCycleCounter::Force);
+    }
+
+    // With both nonbonded and PME offloaded a GPU on the same rank, we use
+    // an alternating wait/reduction scheme.
+    // When running free energy perturbations steered by AWH and calculating PME on GPU,
+    // i.e. if needEarlyPmeResults == true, the PME results have already been reduced above.
+    const bool alternateGpuWait = (!c_disableAlternatingWait && stepWork.haveGpuPmeOnThisRank
+                                   && simulationWork.useGpuNonbonded && !simulationWork.havePpDomainDecomposition
+                                   && !stepWork.useGpuFBufferOps && !needEarlyPmeResults);
+
+
+    const int expectedLocalFReadyOnDeviceConsumptionCount = getExpectedLocalFReadyOnDeviceConsumptionCount(
+            simulationWork, domainWork, stepWork, useOrEmulateGpuNb, alternateGpuWait);
+    // If expectedLocalFReadyOnDeviceConsumptionCount == 0, stateGpu can be uninitialized
+    if (expectedLocalFReadyOnDeviceConsumptionCount > 0)
+    {
+        stateGpu->setFReadyOnDeviceEventExpectedConsumptionCount(
+                AtomLocality::Local, expectedLocalFReadyOnDeviceConsumptionCount);
+    }
+
+    if (simulationWork.havePpDomainDecomposition)
+    {
+        /* 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;
+                gmx::FixedCapacityVector<GpuEventSynchronizer*, 2> gpuForceHaloDependencies;
+                // completion of both H2D copy and clearing is signaled by fReadyOnDevice
+                if (domainWork.haveCpuLocalForceWork || stepWork.clearGpuFBufferEarly)
+                {
+                    gpuForceHaloDependencies.push_back(stateGpu->fReadyOnDevice(AtomLocality::Local));
+                }
+                gpuForceHaloDependencies.push_back(stateGpu->fReducedOnDevice(AtomLocality::NonLocal));
+
+                communicateGpuHaloForces(*cr, accumulateForces, &gpuForceHaloDependencies);
+            }
+            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 (!simulationWork.useMts || !stepWork.combineMtsForcesBeforeHaloExchange)
+                {
+                    dd_move_f(cr->dd, &forceOutMtsLevel0.forceWithShiftForces(), wcycle);
+                }
+                // With MTS we need to communicate the slow or combined (in forceOutMtsLevel1) forces
+                if (simulationWork.useMts && stepWork.computeSlowForces)
+                {
+                    dd_move_f(cr->dd, &forceOutMtsLevel1->forceWithShiftForces(), wcycle);
+                }
+            }
+        }
+    }
+
+    if (alternateGpuWait)
+    {
+        alternatePmeNbGpuWaitReduce(fr->nbv.get(),
+                                    fr->pmedata,
+                                    forceOutNonbonded,
+                                    forceOutMtsLevel1,
+                                    enerd,
+                                    lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
+                                    stepWork,
+                                    wcycle);
+    }
+
+    if (!alternateGpuWait && stepWork.haveGpuPmeOnThisRank && !needEarlyPmeResults)
+    {
+        pmeGpuWaitAndReduce(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->gpuNbv(),
+                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, WallCycleCounter::Force);
+        do_nb_verlet(fr,
+                     ic,
+                     enerd,
+                     stepWork,
+                     InteractionLocality::Local,
+                     haveDDAtomOrdering(*cr) ? enbvClearFNo : enbvClearFYes,
+                     step,
+                     nrnb,
+                     wcycle);
+        wallcycle_stop(wcycle, WallCycleCounter::Force);
+    }
+
+    // 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
+    // When running free energy perturbations steered by AWH and calculating PME on GPU,
+    // i.e. if needEarlyPmeResults == true, the PME results have already been reduced above.
+    if (needToReceivePmeResultsFromSeparateRank && simulationWork.useGpuPmePpCommunication && !needEarlyPmeResults)
+    {
+        /* 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();
+
+            // 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 (domainWork.haveLocalForceContribInCpuBuffer && !stepWork.useGpuFHalo)
+            {
+                stateGpu->copyForcesToGpu(forceWithShift, AtomLocality::Local);
+            }
+
+            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 && haveDDAtomOrdering(*cr) && simulationWork.useCpuPmePpCommunication)
+                || vsite)
+            {
+                if (stepWork.computeNonbondedForces)
+                {
+                    /* We have previously issued force reduction on the GPU, but we will
+                     * not use this event, instead relying on the stream being in-order.
+                     * Issue #3988. */
+                    stateGpu->consumeForcesReducedOnDeviceEvent(AtomLocality::Local);
+                }
+                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);
+        }
+    }
+
+    if (expectedLocalFReadyOnDeviceConsumptionCount > 0)
+    {
+        /* The same fReadyOnDevice device synchronizer is later used to track buffer clearing,
+         * so we reset the expected consumption value back to the default (1). */
+        stateGpu->setFReadyOnDeviceEventExpectedConsumptionCount(AtomLocality::Local, 1);
+    }
+
+    launchGpuEndOfStepTasks(
+            nbv, fr->listedForcesGpu.get(), fr->pmedata, enerd, runScheduleWork, step, wcycle);
+
+    if (haveDDAtomOrdering(*cr))
+    {
+        dd_force_flop_stop(cr->dd, nrnb);
+    }
+
+    const bool haveCombinedMtsForces = (stepWork.computeForces && simulationWork.useMts && stepWork.computeSlowForces
+                                        && stepWork.combineMtsForcesBeforeHaloExchange);
+    if (stepWork.computeForces)
+    {
+        postProcessForceWithShiftForces(
+                nrnb, wcycle, box, x.unpaddedArrayRef(), &forceOutMtsLevel0, vir_force, *mdatoms, *fr, vsite, stepWork);
+
+        if (simulationWork.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
+    // When running free energy perturbations steered by AWH and calculating PME on GPU,
+    // i.e. if needEarlyPmeResults == true, the PME results have already been reduced above.
+    if (needToReceivePmeResultsFromSeparateRank && simulationWork.useCpuPmePpCommunication && !needEarlyPmeResults)
+    {
+        /* 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 (simulationWork.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);
+}