hillclimber 0.1.6__cp314-cp314t-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl

plumed/_lib/lib/plumed/patches/gromacs-2022.5.diff/src/gromacs/mdrun/rerun.cpp

@@ -0,0 +1,997 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright 2018- 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.
+ */
+/*! \internal \file
+ *
+ * \brief Implements the loop for simulation reruns
+ *
+ * \author Pascal Merz <pascal.merz@colorado.edu>
+ * \ingroup module_mdrun
+ */
+#include "gmxpre.h"
+
+#include <cinttypes>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+
+#include <algorithm>
+#include <memory>
+
+#include "gromacs/applied_forces/awh/awh.h"
+#include "gromacs/commandline/filenm.h"
+#include "gromacs/domdec/collect.h"
+#include "gromacs/domdec/dlbtiming.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_network.h"
+#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/domdec/localtopologychecker.h"
+#include "gromacs/domdec/mdsetup.h"
+#include "gromacs/domdec/partition.h"
+#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/ewald/pme_load_balancing.h"
+#include "gromacs/ewald/pme_pp.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/gpu_utils/gpu_utils.h"
+#include "gromacs/math/units.h"
+#include "gromacs/listed_forces/listed_forces.h"
+#include "gromacs/math/functions.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdlib/checkpointhandler.h"
+#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/ebin.h"
+#include "gromacs/mdlib/enerdata_utils.h"
+#include "gromacs/mdlib/energyoutput.h"
+#include "gromacs/mdlib/expanded.h"
+#include "gromacs/mdlib/force.h"
+#include "gromacs/mdlib/force_flags.h"
+#include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/freeenergyparameters.h"
+#include "gromacs/mdlib/md_support.h"
+#include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/mdoutf.h"
+#include "gromacs/mdlib/membed.h"
+#include "gromacs/mdlib/resethandler.h"
+#include "gromacs/mdlib/sighandler.h"
+#include "gromacs/mdlib/simulationsignal.h"
+#include "gromacs/mdlib/stat.h"
+#include "gromacs/mdlib/stophandler.h"
+#include "gromacs/mdlib/tgroup.h"
+#include "gromacs/mdlib/trajectory_writing.h"
+#include "gromacs/mdlib/update.h"
+#include "gromacs/mdlib/vcm.h"
+#include "gromacs/mdlib/vsite.h"
+#include "gromacs/mdrunutility/handlerestart.h"
+#include "gromacs/mdrunutility/multisim.h"
+#include "gromacs/mdrunutility/printtime.h"
+#include "gromacs/mdtypes/awh_history.h"
+#include "gromacs/mdtypes/awh_params.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/df_history.h"
+#include "gromacs/mdtypes/energyhistory.h"
+#include "gromacs/mdtypes/forcebuffers.h"
+#include "gromacs/mdtypes/forcerec.h"
+#include "gromacs/mdtypes/group.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/interaction_const.h"
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/mdrunoptions.h"
+#include "gromacs/mdtypes/observableshistory.h"
+#include "gromacs/mdtypes/observablesreducer.h"
+#include "gromacs/mdtypes/simulation_workload.h"
+#include "gromacs/mdtypes/state.h"
+#include "gromacs/mimic/utilities.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/output.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/swap/swapcoords.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/trajectory/trajectoryframe.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/logger.h"
+#include "gromacs/utility/real.h"
+
+#include "legacysimulator.h"
+#include "replicaexchange.h"
+#include "shellfc.h"
+
+/* PLUMED */
+#include "../../../Plumed.h"
+extern int    plumedswitch;
+extern plumed plumedmain;
+/* END PLUMED */
+
+using gmx::SimulationSignaller;
+using gmx::VirtualSitesHandler;
+
+/*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
+ *
+ * \param[in]     rerunFrame      The trajectory frame to compute energy/forces for
+ * \param[in,out] globalState     The global state container
+ * \param[in]     constructVsites When true, vsite coordinates are constructed
+ * \param[in]     vsite           Vsite setup, can be nullptr when \p constructVsites = false
+ */
+static void prepareRerunState(const t_trxframe&          rerunFrame,
+                              t_state*                   globalState,
+                              bool                       constructVsites,
+                              const VirtualSitesHandler* vsite)
+{
+    auto x      = makeArrayRef(globalState->x);
+    auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec*>(rerunFrame.x), globalState->natoms);
+    std::copy(rerunX.begin(), rerunX.end(), x.begin());
+    copy_mat(rerunFrame.box, globalState->box);
+
+    if (constructVsites)
+    {
+        GMX_ASSERT(vsite, "Need valid vsite for constructing vsites");
+
+        vsite->construct(globalState->x, globalState->v, globalState->box, gmx::VSiteOperation::PositionsAndVelocities);
+    }
+}
+
+void gmx::LegacySimulator::do_rerun()
+{
+    // TODO Historically, the EM and MD "integrators" used different
+    // names for the t_inputrec *parameter, but these must have the
+    // same name, now that it's a member of a struct. We use this ir
+    // alias to avoid a large ripple of nearly useless changes.
+    // t_inputrec is being replaced by IMdpOptionsProvider, so this
+    // will go away eventually.
+    const t_inputrec* ir = inputrec;
+    double            t;
+    bool              isLastStep               = false;
+    bool              doFreeEnergyPerturbation = false;
+    unsigned int      force_flags;
+    tensor            force_vir, shake_vir, total_vir, pres;
+    t_trxstatus*      status = nullptr;
+    rvec              mu_tot;
+    t_trxframe        rerun_fr;
+    ForceBuffers      f;
+    gmx_global_stat_t gstat;
+    gmx_shellfc_t*    shellfc;
+
+    double cycles;
+
+    SimulationSignals signals;
+    /* PLUMED */
+    int plumedNeedsEnergy=0;
+    int plumedWantsToStop=0;
+    matrix plumed_vir;
+    real lambdaForce=0;
+    real realFepState=0;
+    /* END PLUMED */
+
+    // Most global communnication stages don't propagate mdrun
+    // signals, and will use this object to achieve that.
+    SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
+
+    GMX_LOG(mdlog.info)
+            .asParagraph()
+            .appendText(
+                    "Note that it is planned that the command gmx mdrun -rerun will "
+                    "be available in a different form in a future version of GROMACS, "
+                    "e.g. gmx rerun -f.");
+
+    if (ir->efep != FreeEnergyPerturbationType::No
+        && (mdAtoms->mdatoms()->nMassPerturbed > 0 || (constr && constr->havePerturbedConstraints())))
+    {
+        gmx_fatal(FARGS,
+                  "Perturbed masses or constraints are not supported by rerun. "
+                  "Either make a .tpr without mass and constraint perturbation, "
+                  "or use GROMACS 2018.4, 2018.5 or later 2018 version.");
+    }
+    if (ir->bExpanded)
+    {
+        gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
+    }
+    if (ir->bSimTemp)
+    {
+        gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
+    }
+    if (ir->bDoAwh)
+    {
+        gmx_fatal(FARGS, "AWH not supported by rerun.");
+    }
+    if (replExParams.exchangeInterval > 0)
+    {
+        gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
+    }
+    if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
+    {
+        gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
+    }
+    if (ir->bIMD)
+    {
+        gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
+    }
+    if (isMultiSim(ms))
+    {
+        gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
+    }
+    if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](SimulatedAnnealing i) {
+            return i != SimulatedAnnealing::No;
+        }))
+    {
+        gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
+    }
+
+    /* Rerun can't work if an output file name is the same as the input file name.
+     * If this is the case, the user will get an error telling them what the issue is.
+     */
+    if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0
+        || strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
+    {
+        gmx_fatal(FARGS,
+                  "When using mdrun -rerun, the name of the input trajectory file "
+                  "%s cannot be identical to the name of an output file (whether "
+                  "given explicitly with -o or -x, or by default)",
+                  opt2fn("-rerun", nfile, fnm));
+    }
+
+    /* Settings for rerun */
+    {
+        // TODO: Avoid changing inputrec (#3854)
+        auto* nonConstInputrec               = const_cast<t_inputrec*>(inputrec);
+        nonConstInputrec->nstlist            = 1;
+        nonConstInputrec->nstcalcenergy      = 1;
+        nonConstInputrec->nstxout_compressed = 0;
+    }
+    int        nstglobalcomm = 1;
+    const bool bNS           = true;
+
+    ObservablesReducer observablesReducer = observablesReducerBuilder->build();
+
+    const SimulationGroups* groups = &top_global.groups;
+    if (ir->eI == IntegrationAlgorithm::Mimic)
+    {
+        auto* nonConstGlobalTopology                         = const_cast<gmx_mtop_t*>(&top_global);
+        nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
+    }
+    int*                fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
+    gmx::ArrayRef<real> lambda    = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
+    initialize_lambdas(fplog,
+                       ir->efep,
+                       ir->bSimTemp,
+                       *ir->fepvals,
+                       ir->simtempvals->temperatures,
+                       gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
+                       MASTER(cr),
+                       fep_state,
+                       lambda);
+    const bool        simulationsShareState = false;
+    gmx_mdoutf*       outf                  = init_mdoutf(fplog,
+                                   nfile,
+                                   fnm,
+                                   mdrunOptions,
+                                   cr,
+                                   outputProvider,
+                                   mdModulesNotifiers,
+                                   ir,
+                                   top_global,
+                                   oenv,
+                                   wcycle,
+                                   StartingBehavior::NewSimulation,
+                                   simulationsShareState,
+                                   ms);
+    gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
+                                   top_global,
+                                   *ir,
+                                   pull_work,
+                                   mdoutf_get_fp_dhdl(outf),
+                                   true,
+                                   StartingBehavior::NewSimulation,
+                                   simulationsShareState,
+                                   mdModulesNotifiers);
+
+    gstat = global_stat_init(ir);
+
+    /* Check for polarizable models and flexible constraints */
+    shellfc = init_shell_flexcon(fplog,
+                                 top_global,
+                                 constr ? constr->numFlexibleConstraints() : 0,
+                                 ir->nstcalcenergy,
+                                 haveDDAtomOrdering(*cr),
+                                 runScheduleWork->simulationWork.useGpuPme);
+
+    if (haveDDAtomOrdering(*cr))
+    {
+        // Local state only becomes valid now.
+        dd_init_local_state(*cr->dd, state_global, state);
+
+        /* Distribute the charge groups over the nodes from the master node */
+        dd_partition_system(fplog,
+                            mdlog,
+                            ir->init_step,
+                            cr,
+                            TRUE,
+                            1,
+                            state_global,
+                            top_global,
+                            *ir,
+                            imdSession,
+                            pull_work,
+                            state,
+                            &f,
+                            mdAtoms,
+                            top,
+                            fr,
+                            vsite,
+                            constr,
+                            nrnb,
+                            nullptr,
+                            FALSE);
+    }
+    else
+    {
+        state_change_natoms(state_global, state_global->natoms);
+        /* Copy the pointer to the global state */
+        state = state_global;
+
+        mdAlgorithmsSetupAtomData(cr, *ir, top_global, top, fr, &f, mdAtoms, constr, vsite, shellfc);
+    }
+
+    auto* mdatoms = mdAtoms->mdatoms();
+    fr->longRangeNonbondeds->updateAfterPartition(*mdatoms);
+
+    // NOTE: The global state is no longer used at this point.
+    // But state_global is still used as temporary storage space for writing
+    // the global state to file and potentially for replica exchange.
+    // (Global topology should persist.)
+
+    update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
+
+    if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
+    {
+        doFreeEnergyPerturbation = true;
+    }
+
+    int64_t step     = ir->init_step;
+    int64_t step_rel = 0;
+
+    {
+        int    cglo_flags   = CGLO_GSTAT;
+        bool   bSumEkinhOld = false;
+        t_vcm* vcm          = nullptr;
+        compute_globals(gstat,
+                        cr,
+                        ir,
+                        fr,
+                        ekind,
+                        makeConstArrayRef(state->x),
+                        makeConstArrayRef(state->v),
+                        state->box,
+                        mdatoms,
+                        nrnb,
+                        vcm,
+                        nullptr,
+                        enerd,
+                        force_vir,
+                        shake_vir,
+                        total_vir,
+                        pres,
+                        &nullSignaller,
+                        state->box,
+                        &bSumEkinhOld,
+                        cglo_flags,
+                        step,
+                        &observablesReducer);
+        // Clean up after pre-step use of compute_globals()
+        observablesReducer.markAsReadyToReduce();
+    }
+
+    if (MASTER(cr))
+    {
+        fprintf(stderr,
+                "starting md rerun '%s', reading coordinates from"
+                " input trajectory '%s'\n\n",
+                *(top_global.name),
+                opt2fn("-rerun", nfile, fnm));
+        if (mdrunOptions.verbose)
+        {
+            fprintf(stderr,
+                    "Calculated time to finish depends on nsteps from "
+                    "run input file,\nwhich may not correspond to the time "
+                    "needed to process input trajectory.\n\n");
+        }
+        fprintf(fplog, "\n");
+    }
+
+    /* PLUMED */
+    if(plumedswitch){
+      /* detect plumed API version */
+      int pversion=0;
+      plumed_cmd(plumedmain,"getApiVersion",&pversion);
+      /* setting kbT is only implemented with api>1) */
+      real kbT=ir->opts.ref_t[0]*gmx::c_boltz;
+      if(pversion>1) plumed_cmd(plumedmain,"setKbT",&kbT);
+      if(pversion>2){
+        int res=1;
+        if( (startingBehavior != StartingBehavior::NewSimulation) ) plumed_cmd(plumedmain,"setRestart",&res);
+      }
+
+      if(PAR(cr)){
+        if(haveDDAtomOrdering(*cr)) {
+          plumed_cmd(plumedmain,"setMPIComm",&cr->dd->mpi_comm_all);
+        }
+      }
+      plumed_cmd(plumedmain,"setNatoms",top_global.natoms);
+      plumed_cmd(plumedmain,"setMDEngine","gromacs");
+      plumed_cmd(plumedmain,"setLog",fplog);
+      real real_delta_t=ir->delta_t;
+      plumed_cmd(plumedmain,"setTimestep",&real_delta_t);
+      plumed_cmd(plumedmain,"init",nullptr);
+
+      if(haveDDAtomOrdering(*cr)) {
+        int nat_home = dd_numHomeAtoms(*cr->dd);
+        plumed_cmd(plumedmain,"setAtomsNlocal",&nat_home);
+        plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data());
+      }
+      realFepState = state->fep_state;
+      plumed_cmd(plumedmain, "setExtraCV lambda", &realFepState);
+      plumed_cmd(plumedmain, "setExtraCVForce lambda", &lambdaForce);
+    }
+    /* END PLUMED */
+
+    walltime_accounting_start_time(walltime_accounting);
+    wallcycle_start(wcycle, WallCycleCounter::Run);
+    print_start(fplog, cr, walltime_accounting, "mdrun");
+
+    /***********************************************************
+     *
+     *             Loop over MD steps
+     *
+     ************************************************************/
+
+    if (constr)
+    {
+        GMX_LOG(mdlog.info)
+                .asParagraph()
+                .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
+    }
+
+    rerun_fr.natoms = 0;
+    if (MASTER(cr))
+    {
+        isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
+        if (rerun_fr.natoms != top_global.natoms)
+        {
+            gmx_fatal(FARGS,
+                      "Number of atoms in trajectory (%d) does not match the "
+                      "run input file (%d)\n",
+                      rerun_fr.natoms,
+                      top_global.natoms);
+        }
+
+        if (ir->pbcType != PbcType::No)
+        {
+            if (!rerun_fr.bBox)
+            {
+                gmx_fatal(FARGS,
+                          "Rerun trajectory frame step %" PRId64
+                          " time %f "
+                          "does not contain a box, while pbc is used",
+                          rerun_fr.step,
+                          rerun_fr.time);
+            }
+            if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
+            {
+                gmx_fatal(FARGS,
+                          "Rerun trajectory frame step %" PRId64
+                          " time %f "
+                          "has too small box dimensions",
+                          rerun_fr.step,
+                          rerun_fr.time);
+            }
+        }
+    }
+
+    GMX_LOG(mdlog.info)
+            .asParagraph()
+            .appendText(
+                    "Rerun does not report kinetic energy, total energy, temperature, virial and "
+                    "pressure.");
+
+    if (PAR(cr))
+    {
+        rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
+    }
+
+    if (ir->pbcType != PbcType::No)
+    {
+        /* Set the shift vectors.
+         * Necessary here when have a static box different from the tpr box.
+         */
+        calc_shifts(rerun_fr.box, fr->shift_vec);
+    }
+
+    auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
+            compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
+            false,
+            MASTER(cr),
+            ir->nstlist,
+            mdrunOptions.reproducible,
+            nstglobalcomm,
+            mdrunOptions.maximumHoursToRun,
+            ir->nstlist == 0,
+            fplog,
+            step,
+            bNS,
+            walltime_accounting);
+
+    // we don't do counter resetting in rerun - finish will always be valid
+    walltime_accounting_set_valid_finish(walltime_accounting);
+
+    const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
+
+    /* and stop now if we should */
+    isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
+    while (!isLastStep)
+    {
+        wallcycle_start(wcycle, WallCycleCounter::Step);
+
+        if (rerun_fr.bStep)
+        {
+            step     = rerun_fr.step;
+            step_rel = step - ir->init_step;
+        }
+        if (rerun_fr.bTime)
+        {
+            t = rerun_fr.time;
+        }
+        else
+        {
+            t = step;
+        }
+
+        if (ir->efep != FreeEnergyPerturbationType::No && MASTER(cr))
+        {
+            if (rerun_fr.bLambda)
+            {
+                ir->fepvals->init_lambda = rerun_fr.lambda;
+            }
+            else
+            {
+                if (rerun_fr.bFepState)
+                {
+                    state->fep_state = rerun_fr.fep_state;
+                }
+            }
+
+            state_global->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
+        }
+
+        if (MASTER(cr))
+        {
+            const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
+            if (constructVsites && haveDDAtomOrdering(*cr))
+            {
+                gmx_fatal(FARGS,
+                          "Vsite recalculation with -rerun is not implemented with domain "
+                          "decomposition, "
+                          "use a single rank");
+            }
+            prepareRerunState(rerun_fr, state_global, constructVsites, vsite);
+        }
+
+        isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
+
+        if (haveDDAtomOrdering(*cr))
+        {
+            /* Repartition the domain decomposition */
+            const bool bMasterState = true;
+            dd_partition_system(fplog,
+                                mdlog,
+                                step,
+                                cr,
+                                bMasterState,
+                                nstglobalcomm,
+                                state_global,
+                                top_global,
+                                *ir,
+                                imdSession,
+                                pull_work,
+                                state,
+                                &f,
+                                mdAtoms,
+                                top,
+                                fr,
+                                vsite,
+                                constr,
+                                nrnb,
+                                wcycle,
+                                mdrunOptions.verbose);
+                /* PLUMED */
+                if(plumedswitch){
+                  int nat_home = dd_numHomeAtoms(*cr->dd);
+                  plumed_cmd(plumedmain,"setAtomsNlocal",&nat_home);
+                  plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->globalAtomIndices.data());
+                }
+                /* END PLUMED */
+        }
+
+        if (MASTER(cr))
+        {
+            EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
+        }
+
+        if (ir->efep != FreeEnergyPerturbationType::No)
+        {
+            update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
+        }
+
+        fr->longRangeNonbondeds->updateAfterPartition(*mdatoms);
+
+        force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
+                       | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
+                       GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
+
+        if (shellfc)
+        {
+            /* Now is the time to relax the shells */
+            relax_shell_flexcon(fplog,
+                                cr,
+                                ms,
+                                mdrunOptions.verbose,
+                                enforcedRotation,
+                                step,
+                                ir,
+                                imdSession,
+                                pull_work,
+                                bNS,
+                                force_flags,
+                                top,
+                                constr,
+                                enerd,
+                                state->natoms,
+                                state->x.arrayRefWithPadding(),
+                                state->v.arrayRefWithPadding(),
+                                state->box,
+                                state->lambda,
+                                &state->hist,
+                                &f.view(),
+                                force_vir,
+                                *mdatoms,
+                                fr->longRangeNonbondeds.get(),
+                                nrnb,
+                                wcycle,
+                                shellfc,
+                                fr,
+                                runScheduleWork,
+                                t,
+                                mu_tot,
+                                vsite,
+                                ddBalanceRegionHandler);
+        }
+        else
+        {
+            /* The coordinates (x) are shifted (to get whole molecules)
+             * in do_force.
+             * This is parallellized as well, and does communication too.
+             * Check comments in sim_util.c
+             */
+            Awh*       awh = nullptr;
+            gmx_edsam* ed  = nullptr;
+             /* PLUMED */
+            plumedNeedsEnergy=0;
+            if(plumedswitch){
+              int pversion=0;
+              plumed_cmd(plumedmain,"getApiVersion",&pversion);
+              long int lstep=step; plumed_cmd(plumedmain,"setStepLong",&lstep);
+              plumed_cmd(plumedmain,"setPositions",&state->x[0][0]);
+              plumed_cmd(plumedmain,"setMasses",&mdatoms->massT[0]);
+              plumed_cmd(plumedmain,"setCharges",&mdatoms->chargeA[0]);
+              plumed_cmd(plumedmain,"setBox",&state->box[0][0]);
+              plumed_cmd(plumedmain,"prepareCalc",nullptr);
+              plumed_cmd(plumedmain,"setStopFlag",&plumedWantsToStop);
+              plumed_cmd(plumedmain,"setForces",&f.view().force()[0][0]);
+              plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
+              if(plumedNeedsEnergy) force_flags |= GMX_FORCE_ENERGY | GMX_FORCE_VIRIAL;
+              clear_mat(plumed_vir);
+              plumed_cmd(plumedmain,"setVirial",&plumed_vir[0][0]);
+            }
+            /* END PLUMED */
+            try
+            {
+                do_force(fplog,
+                         cr,
+                         ms,
+                         *ir,
+                         awh,
+                         enforcedRotation,
+                         imdSession,
+                         pull_work,
+                         step,
+                         nrnb,
+                         wcycle,
+                         top,
+                         state->box,
+                         state->x.arrayRefWithPadding(),
+                         &state->hist,
+                         &f.view(),
+                         force_vir,
+                         mdatoms,
+                         enerd,
+                         state->lambda,
+                         fr,
+                         runScheduleWork,
+                         vsite,
+                         mu_tot,
+                         t,
+                         ed,
+                         fr->longRangeNonbondeds.get(),
+                         GMX_FORCE_NS | force_flags,
+                         ddBalanceRegionHandler);
+            }
+            catch (const gmx::InternalError&)
+            {
+                GMX_LOG(mdlog.warning)
+                        .asParagraph()
+                        .appendText(
+                                "Continuing with next frame after catching invalid force in "
+                                "previous frame");
+            };
+            /* PLUMED */
+            if(plumedswitch){
+              if(plumedNeedsEnergy){
+                msmul(force_vir,2.0,plumed_vir);
+                plumed_cmd(plumedmain,"setEnergy",&enerd->term[F_EPOT]);
+                plumed_cmd(plumedmain,"performCalc",nullptr);
+                msmul(plumed_vir,0.5,force_vir);
+              } else {
+                msmul(plumed_vir,0.5,plumed_vir);
+                m_add(force_vir,plumed_vir,force_vir);
+              }
+              if(plumedWantsToStop) isLastStep = true;
+            }
+            /* END PLUMED */
+        }
+
+        /* Now we have the energies and forces corresponding to the
+         * coordinates at time t.
+         */
+        {
+            const bool isCheckpointingStep = false;
+            const bool doRerun             = true;
+            do_md_trajectory_writing(fplog,
+                                     cr,
+                                     nfile,
+                                     fnm,
+                                     step,
+                                     step_rel,
+                                     t,
+                                     ir,
+                                     state,
+                                     state_global,
+                                     observablesHistory,
+                                     top_global,
+                                     fr,
+                                     outf,
+                                     energyOutput,
+                                     ekind,
+                                     f.view().force(),
+                                     isCheckpointingStep,
+                                     doRerun,
+                                     isLastStep,
+                                     mdrunOptions.writeConfout,
+                                     EkindataState::NotUsed);
+        }
+
+        stopHandler->setSignal();
+
+        {
+            const bool          doInterSimSignal = false;
+            const bool          doIntraSimSignal = true;
+            bool                bSumEkinhOld     = false;
+            t_vcm*              vcm              = nullptr;
+            SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
+
+            int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
+            compute_globals(gstat,
+                            cr,
+                            ir,
+                            fr,
+                            ekind,
+                            makeConstArrayRef(state->x),
+                            makeConstArrayRef(state->v),
+                            state->box,
+                            mdatoms,
+                            nrnb,
+                            vcm,
+                            wcycle,
+                            enerd,
+                            force_vir,
+                            shake_vir,
+                            total_vir,
+                            pres,
+                            &signaller,
+                            state->box,
+                            &bSumEkinhOld,
+                            cglo_flags,
+                            step,
+                            &observablesReducer);
+            // Clean up after pre-step use of compute_globals()
+            observablesReducer.markAsReadyToReduce();
+        }
+
+        /* Note: this is OK, but there are some numerical precision issues with using the convergence of
+           the virial that should probably be addressed eventually. state->veta has better properies,
+           but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
+           generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
+
+        /* Output stuff */
+        if (MASTER(cr))
+        {
+            const bool bCalcEnerStep = true;
+            energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
+                                             bCalcEnerStep,
+                                             t,
+                                             mdatoms->tmass,
+                                             enerd,
+                                             ir->fepvals.get(),
+                                             state->box,
+                                             PTCouplingArrays({ state->boxv,
+                                                                state->nosehoover_xi,
+                                                                state->nosehoover_vxi,
+                                                                state->nhpres_xi,
+                                                                state->nhpres_vxi }),
+                                             state->fep_state,
+                                             total_vir,
+                                             pres,
+                                             ekind,
+                                             mu_tot,
+                                             constr);
+
+            const bool do_ene = true;
+            const bool do_log = true;
+            Awh*       awh    = nullptr;
+            const bool do_dr  = ir->nstdisreout != 0;
+            const bool do_or  = ir->nstorireout != 0;
+
+            EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
+            energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+                                               do_ene,
+                                               do_dr,
+                                               do_or,
+                                               do_log ? fplog : nullptr,
+                                               step,
+                                               t,
+                                               fr->fcdata.get(),
+                                               awh);
+
+            if (ir->bPull)
+            {
+                pull_print_output(pull_work, step, t);
+            }
+
+            if (do_per_step(step, ir->nstlog))
+            {
+                if (fflush(fplog) != 0)
+                {
+                    gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
+                }
+            }
+        }
+
+        /* Print the remaining wall clock time for the run */
+        if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
+        {
+            if (shellfc)
+            {
+                fprintf(stderr, "\n");
+            }
+            print_time(stderr, walltime_accounting, step, ir, cr);
+        }
+
+        /* Ion/water position swapping.
+         * Not done in last step since trajectory writing happens before this call
+         * in the MD loop and exchanges would be lost anyway. */
+        if ((ir->eSwapCoords != SwapType::No) && (step > 0) && !isLastStep
+            && do_per_step(step, ir->swap->nstswap))
+        {
+            const bool doRerun = true;
+            do_swapcoords(cr,
+                          step,
+                          t,
+                          ir,
+                          swap,
+                          wcycle,
+                          rerun_fr.x,
+                          rerun_fr.box,
+                          MASTER(cr) && mdrunOptions.verbose,
+                          doRerun);
+        }
+
+        if (MASTER(cr))
+        {
+            /* read next frame from input trajectory */
+            isLastStep = !read_next_frame(oenv, status, &rerun_fr);
+        }
+
+        if (PAR(cr))
+        {
+            rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
+        }
+
+        cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
+        if (haveDDAtomOrdering(*cr) && wcycle)
+        {
+            dd_cycles_add(cr->dd, cycles, ddCyclStep);
+        }
+
+        if (!rerun_fr.bStep)
+        {
+            /* increase the MD step number */
+            step++;
+            step_rel++;
+        }
+        observablesReducer.markAsReadyToReduce();
+    }
+    /* End of main MD loop */
+
+    /* Closing TNG files can include compressing data. Therefore it is good to do that
+     * before stopping the time measurements. */
+    mdoutf_tng_close(outf);
+
+    /* Stop measuring walltime */
+    walltime_accounting_end_time(walltime_accounting);
+
+    if (MASTER(cr))
+    {
+        close_trx(status);
+    }
+
+    if (!thisRankHasDuty(cr, DUTY_PME))
+    {
+        /* Tell the PME only node to finish */
+        gmx_pme_send_finish(cr);
+    }
+
+    done_mdoutf(outf);
+
+    done_shellfc(fplog, shellfc, step_rel);
+
+    walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
+}