hillclimber 0.1.5__cp313-cp313-musllinux_1_2_aarch64.whl

plumed/_lib/lib/plumed/patches/gromacs-2024.3.diff/src/gromacs/mdrun/minimize.cpp.preplumed

@@ -0,0 +1,3514 @@
+/*
+ * 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.
+ */
+/*! \internal \file
+ *
+ * \brief This file defines integrators for energy minimization
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author Erik Lindahl <erik@kth.se>
+ * \ingroup module_mdrun
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <cmath>
+#include <cstring>
+#include <ctime>
+
+#include <algorithm>
+#include <limits>
+#include <vector>
+
+#include "gromacs/commandline/filenm.h"
+#include "gromacs/domdec/collect.h"
+#include "gromacs/domdec/dlbtiming.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/domdec/mdsetup.h"
+#include "gromacs/domdec/partition.h"
+#include "gromacs/ewald/pme_pp.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/mtxio.h"
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/listed_forces/listed_forces.h"
+#include "gromacs/listed_forces/listed_forces_gpu.h"
+#include "gromacs/math/functions.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/coupling.h"
+#include "gromacs/mdlib/ebin.h"
+#include "gromacs/mdlib/enerdata_utils.h"
+#include "gromacs/mdlib/energyoutput.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/md_support.h"
+#include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/stat.h"
+#include "gromacs/mdlib/tgroup.h"
+#include "gromacs/mdlib/trajectory_writing.h"
+#include "gromacs/mdlib/update.h"
+#include "gromacs/mdlib/vsite.h"
+#include "gromacs/mdrunutility/handlerestart.h"
+#include "gromacs/mdrunutility/printtime.h"
+#include "gromacs/mdtypes/checkpointdata.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/forcebuffers.h"
+#include "gromacs/mdtypes/forcerec.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/multipletimestepping.h"
+#include "gromacs/mdtypes/observablesreducer.h"
+#include "gromacs/mdtypes/state.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/taskassignment/include/gromacs/taskassignment/decidesimulationworkload.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/logger.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "legacysimulator.h"
+#include "shellfc.h"
+
+using gmx::ArrayRef;
+using gmx::MDModulesNotifiers;
+using gmx::MdrunScheduleWorkload;
+using gmx::RVec;
+using gmx::VirtualSitesHandler;
+
+//! Utility structure for manipulating states during EM
+typedef struct em_state
+{
+    //! Copy of the global state
+    t_state s;
+    //! Force array
+    gmx::ForceBuffers f;
+    //! Potential energy
+    real epot;
+    //! Norm of the force
+    real fnorm;
+    //! Maximum force
+    real fmax;
+    //! Direction
+    int a_fmax;
+} em_state_t;
+
+//! Print the EM starting conditions
+static void print_em_start(FILE*                     fplog,
+                           const t_commrec*          cr,
+                           gmx_walltime_accounting_t walltime_accounting,
+                           gmx_wallcycle*            wcycle,
+                           const char*               name)
+{
+    walltime_accounting_start_time(walltime_accounting);
+    wallcycle_start(wcycle, WallCycleCounter::Run);
+    print_start(fplog, cr, walltime_accounting, name);
+}
+
+//! Stop counting time for EM
+static void em_time_end(gmx_walltime_accounting_t walltime_accounting, gmx_wallcycle* wcycle)
+{
+    wallcycle_stop(wcycle, WallCycleCounter::Run);
+
+    walltime_accounting_end_time(walltime_accounting);
+}
+
+//! Printing a log file and console header
+static void sp_header(FILE* out, const char* minimizer, real ftol, int nsteps)
+{
+    fprintf(out, "\n");
+    fprintf(out, "%s:\n", minimizer);
+    fprintf(out, "   Tolerance (Fmax)   = %12.5e\n", ftol);
+    fprintf(out, "   Number of steps    = %12d\n", nsteps);
+}
+
+//! Print warning message
+static void warn_step(FILE* fp, real ftol, real fmax, gmx_bool bLastStep, gmx_bool bConstrain)
+{
+    constexpr bool realIsDouble = GMX_DOUBLE;
+    char           buffer[2048];
+
+    if (!std::isfinite(fmax))
+    {
+        sprintf(buffer,
+                "\nEnergy minimization has stopped because the force "
+                "on at least one atom is not finite. This usually means "
+                "atoms are overlapping. Modify the input coordinates to "
+                "remove atom overlap or use soft-core potentials with "
+                "the free energy code to avoid infinite forces.\n%s",
+                !realIsDouble ? "You could also be lucky that switching to double precision "
+                                "is sufficient to obtain finite forces.\n"
+                              : "");
+    }
+    else if (bLastStep)
+    {
+        sprintf(buffer,
+                "\nEnergy minimization reached the maximum number "
+                "of steps before the forces reached the requested "
+                "precision Fmax < %g.\n",
+                ftol);
+    }
+    else
+    {
+        sprintf(buffer,
+                "\nEnergy minimization has stopped, but the forces have "
+                "not converged to the requested precision Fmax < %g (which "
+                "may not be possible for your system). It stopped "
+                "because the algorithm tried to make a new step whose size "
+                "was too small, or there was no change in the energy since "
+                "last step. Either way, we regard the minimization as "
+                "converged to within the available machine precision, "
+                "given your starting configuration and EM parameters.\n%s%s",
+                ftol,
+                !realIsDouble ? "\nDouble precision normally gives you higher accuracy, but "
+                                "this is often not needed for preparing to run molecular "
+                                "dynamics.\n"
+                              : "",
+                bConstrain ? "You might need to increase your constraint accuracy, or turn\n"
+                             "off constraints altogether (set constraints = none in mdp file)\n"
+                           : "");
+    }
+
+    fputs(wrap_lines(buffer, 78, 0, FALSE), stderr);
+    fputs(wrap_lines(buffer, 78, 0, FALSE), fp);
+}
+
+//! Print message about convergence of the EM
+static void print_converged(FILE*             fp,
+                            const char*       alg,
+                            real              ftol,
+                            int64_t           count,
+                            gmx_bool          bDone,
+                            int64_t           nsteps,
+                            const em_state_t* ems,
+                            double            sqrtNumAtoms)
+{
+    char buf[STEPSTRSIZE];
+
+    if (bDone)
+    {
+        fprintf(fp, "\n%s converged to Fmax < %g in %s steps\n", alg, ftol, gmx_step_str(count, buf));
+    }
+    else if (count < nsteps)
+    {
+        fprintf(fp,
+                "\n%s converged to machine precision in %s steps,\n"
+                "but did not reach the requested Fmax < %g.\n",
+                alg,
+                gmx_step_str(count, buf),
+                ftol);
+    }
+    else
+    {
+        fprintf(fp, "\n%s did not converge to Fmax < %g in %s steps.\n", alg, ftol, gmx_step_str(count, buf));
+    }
+
+#if GMX_DOUBLE
+    fprintf(fp, "Potential Energy  = %21.14e\n", ems->epot);
+    fprintf(fp, "Maximum force     = %21.14e on atom %d\n", ems->fmax, ems->a_fmax + 1);
+    fprintf(fp, "Norm of force     = %21.14e\n", ems->fnorm / sqrtNumAtoms);
+#else
+    fprintf(fp, "Potential Energy  = %14.7e\n", ems->epot);
+    fprintf(fp, "Maximum force     = %14.7e on atom %d\n", ems->fmax, ems->a_fmax + 1);
+    fprintf(fp, "Norm of force     = %14.7e\n", ems->fnorm / sqrtNumAtoms);
+#endif
+}
+
+//! Compute the norm and max of the force array in parallel
+static void get_f_norm_max(const t_commrec*               cr,
+                           const t_grpopts*               opts,
+                           t_mdatoms*                     mdatoms,
+                           gmx::ArrayRef<const gmx::RVec> f,
+                           real*                          fnorm,
+                           real*                          fmax,
+                           int*                           a_fmax)
+{
+    double fnorm2, *sum;
+    real   fmax2, fam;
+    int    la_max, a_max, start, end, i, m, gf;
+
+    /* This routine finds the largest force and returns it.
+     * On parallel machines the global max is taken.
+     */
+    fnorm2 = 0;
+    fmax2  = 0;
+    la_max = -1;
+    start  = 0;
+    end    = mdatoms->homenr;
+    if (!mdatoms->cFREEZE.empty())
+    {
+        for (i = start; i < end; i++)
+        {
+            gf  = mdatoms->cFREEZE[i];
+            fam = 0;
+            for (m = 0; m < DIM; m++)
+            {
+                if (!opts->nFreeze[gf][m])
+                {
+                    fam += gmx::square(f[i][m]);
+                }
+            }
+            fnorm2 += fam;
+            if (fam > fmax2)
+            {
+                fmax2  = fam;
+                la_max = i;
+            }
+        }
+    }
+    else
+    {
+        for (i = start; i < end; i++)
+        {
+            fam = norm2(f[i]);
+            fnorm2 += fam;
+            if (fam > fmax2)
+            {
+                fmax2  = fam;
+                la_max = i;
+            }
+        }
+    }
+
+    if (la_max >= 0 && haveDDAtomOrdering(*cr))
+    {
+        a_max = cr->dd->globalAtomIndices[la_max];
+    }
+    else
+    {
+        a_max = la_max;
+    }
+    if (PAR(cr))
+    {
+        snew(sum, 2 * cr->nnodes + 1);
+        sum[2 * cr->nodeid]     = fmax2;
+        sum[2 * cr->nodeid + 1] = a_max;
+        sum[2 * cr->nnodes]     = fnorm2;
+        gmx_sumd(2 * cr->nnodes + 1, sum, cr);
+        fnorm2 = sum[2 * cr->nnodes];
+        /* Determine the global maximum */
+        for (i = 0; i < cr->nnodes; i++)
+        {
+            if (sum[2 * i] > fmax2)
+            {
+                fmax2 = sum[2 * i];
+                a_max = gmx::roundToInt(sum[2 * i + 1]);
+            }
+        }
+        sfree(sum);
+    }
+
+    if (fnorm)
+    {
+        *fnorm = sqrt(fnorm2);
+    }
+    if (fmax)
+    {
+        *fmax = sqrt(fmax2);
+    }
+    if (a_fmax)
+    {
+        *a_fmax = a_max;
+    }
+}
+
+//! Compute the norm of the force
+static void get_state_f_norm_max(const t_commrec* cr, const t_grpopts* opts, t_mdatoms* mdatoms, em_state_t* ems)
+{
+    get_f_norm_max(cr, opts, mdatoms, ems->f.view().force(), &ems->fnorm, &ems->fmax, &ems->a_fmax);
+}
+
+//! Initialize the energy minimization
+static void init_em(FILE*                     fplog,
+                    const gmx::MDLogger&      mdlog,
+                    const char*               title,
+                    const t_commrec*          cr,
+                    const t_inputrec*         ir,
+                    const MDModulesNotifiers& mdModulesNotifiers,
+                    gmx::ImdSession*          imdSession,
+                    pull_t*                   pull_work,
+                    t_state*                  state_global,
+                    const gmx_mtop_t&         top_global,
+                    em_state_t*               ems,
+                    gmx_localtop_t*           top,
+                    t_nrnb*                   nrnb,
+                    t_forcerec*               fr,
+                    gmx::MDAtoms*             mdAtoms,
+                    gmx_global_stat_t*        gstat,
+                    VirtualSitesHandler*      vsite,
+                    gmx::Constraints*         constr,
+                    gmx_shellfc_t**           shellfc)
+{
+    real dvdl_constr;
+
+    if (fplog)
+    {
+        fprintf(fplog, "Initiating %s\n", title);
+    }
+
+    if (MAIN(cr))
+    {
+        state_global->ngtc = 0;
+    }
+    int*                fep_state = MAIN(cr) ? &state_global->fep_state : nullptr;
+    gmx::ArrayRef<real> lambda    = MAIN(cr) ? state_global->lambda : gmx::ArrayRef<real>();
+    initialize_lambdas(
+            fplog, ir->efep, ir->bSimTemp, *ir->fepvals, ir->simtempvals->temperatures, nullptr, MAIN(cr), fep_state, lambda);
+
+    if (ir->eI == IntegrationAlgorithm::NM)
+    {
+        GMX_ASSERT(shellfc != nullptr, "With NM we always support shells");
+
+        *shellfc = init_shell_flexcon(stdout,
+                                      top_global,
+                                      constr ? constr->numFlexibleConstraints() : 0,
+                                      ir->nstcalcenergy,
+                                      haveDDAtomOrdering(*cr),
+                                      thisRankHasDuty(cr, DUTY_PME));
+    }
+    else
+    {
+        GMX_ASSERT(EI_ENERGY_MINIMIZATION(ir->eI),
+                   "This else currently only handles energy minimizers, consider if your algorithm "
+                   "needs shell/flexible-constraint support");
+
+        /* With energy minimization, shells and flexible constraints are
+         * automatically minimized when treated like normal DOFS.
+         */
+        if (shellfc != nullptr)
+        {
+            *shellfc = nullptr;
+        }
+    }
+
+    if (haveDDAtomOrdering(*cr))
+    {
+        // Local state only becomes valid now.
+        dd_init_local_state(*cr->dd, state_global, &ems->s);
+
+        /* Distribute the charge groups over the nodes from the main node */
+        dd_partition_system(fplog,
+                            mdlog,
+                            ir->init_step,
+                            cr,
+                            TRUE,
+                            state_global,
+                            top_global,
+                            *ir,
+                            mdModulesNotifiers,
+                            imdSession,
+                            pull_work,
+                            &ems->s,
+                            &ems->f,
+                            mdAtoms,
+                            top,
+                            fr,
+                            vsite,
+                            constr,
+                            nrnb,
+                            nullptr,
+                            FALSE);
+        dd_store_state(*cr->dd, &ems->s);
+    }
+    else
+    {
+        /* Just copy the state */
+        ems->s = *state_global;
+
+        mdAlgorithmsSetupAtomData(
+                cr, *ir, top_global, top, fr, &ems->f, mdAtoms, constr, vsite, shellfc ? *shellfc : nullptr);
+    }
+
+    update_mdatoms(mdAtoms->mdatoms(), ems->s.lambda[FreeEnergyPerturbationCouplingType::Mass]);
+
+    if (constr)
+    {
+        // TODO how should this cross-module support dependency be managed?
+        if (ir->eConstrAlg == ConstraintAlgorithm::Shake && gmx_mtop_ftype_count(top_global, F_CONSTR) > 0)
+        {
+            gmx_fatal(FARGS,
+                      "Can not do energy minimization with %s, use %s\n",
+                      enumValueToString(ConstraintAlgorithm::Shake),
+                      enumValueToString(ConstraintAlgorithm::Lincs));
+        }
+
+        if (!ir->bContinuation)
+        {
+            /* Constrain the starting coordinates */
+            bool needsLogging  = true;
+            bool computeEnergy = true;
+            bool computeVirial = false;
+            dvdl_constr        = 0;
+            constr->apply(needsLogging,
+                          computeEnergy,
+                          -1,
+                          0,
+                          1.0,
+                          ems->s.x.arrayRefWithPadding(),
+                          ems->s.x.arrayRefWithPadding(),
+                          ArrayRef<RVec>(),
+                          ems->s.box,
+                          ems->s.lambda[FreeEnergyPerturbationCouplingType::Fep],
+                          &dvdl_constr,
+                          gmx::ArrayRefWithPadding<RVec>(),
+                          computeVirial,
+                          nullptr,
+                          gmx::ConstraintVariable::Positions);
+        }
+    }
+
+    if (PAR(cr))
+    {
+        *gstat = global_stat_init(ir);
+    }
+    else
+    {
+        *gstat = nullptr;
+    }
+
+    calc_shifts(ems->s.box, fr->shift_vec);
+}
+
+//! Finalize the minimization
+static void finish_em(const t_commrec*          cr,
+                      gmx_mdoutf_t              outf,
+                      gmx_walltime_accounting_t walltime_accounting,
+                      gmx_wallcycle*            wcycle)
+{
+    if (!thisRankHasDuty(cr, DUTY_PME))
+    {
+        /* Tell the PME only node to finish */
+        gmx_pme_send_finish(cr);
+    }
+
+    done_mdoutf(outf);
+
+    em_time_end(walltime_accounting, wcycle);
+}
+
+//! Swap two different EM states during minimization
+static void swap_em_state(em_state_t** ems1, em_state_t** ems2)
+{
+    em_state_t* tmp;
+
+    tmp   = *ems1;
+    *ems1 = *ems2;
+    *ems2 = tmp;
+}
+
+//! Save the EM trajectory
+static void write_em_traj(FILE*               fplog,
+                          const t_commrec*    cr,
+                          gmx_mdoutf_t        outf,
+                          gmx_bool            bX,
+                          gmx_bool            bF,
+                          const char*         confout,
+                          const gmx_mtop_t&   top_global,
+                          const t_inputrec*   ir,
+                          int64_t             step,
+                          em_state_t*         state,
+                          t_state*            state_global,
+                          ObservablesHistory* observablesHistory)
+{
+    int mdof_flags = 0;
+
+    if (bX)
+    {
+        mdof_flags |= MDOF_X;
+    }
+    if (bF)
+    {
+        mdof_flags |= MDOF_F;
+    }
+
+    /* If we want IMD output, set appropriate MDOF flag */
+    if (ir->bIMD)
+    {
+        mdof_flags |= MDOF_IMD;
+    }
+
+    gmx::WriteCheckpointDataHolder checkpointDataHolder;
+    mdoutf_write_to_trajectory_files(fplog,
+                                     cr,
+                                     outf,
+                                     mdof_flags,
+                                     top_global.natoms,
+                                     step,
+                                     static_cast<double>(step),
+                                     &state->s,
+                                     state_global,
+                                     observablesHistory,
+                                     state->f.view().force(),
+                                     &checkpointDataHolder);
+
+    if (confout != nullptr)
+    {
+        if (haveDDAtomOrdering(*cr))
+        {
+            /* If bX=true, x was collected to state_global in the call above */
+            if (!bX)
+            {
+                auto globalXRef = MAIN(cr) ? state_global->x : gmx::ArrayRef<gmx::RVec>();
+                dd_collect_vec(
+                        cr->dd, state->s.ddp_count, state->s.ddp_count_cg_gl, state->s.cg_gl, state->s.x, globalXRef);
+            }
+        }
+        else
+        {
+            /* Copy the local state pointer */
+            state_global = &state->s;
+        }
+
+        if (MAIN(cr))
+        {
+            if (ir->pbcType != PbcType::No && !ir->bPeriodicMols && haveDDAtomOrdering(*cr))
+            {
+                /* Make molecules whole only for confout writing */
+                do_pbc_mtop(ir->pbcType, state->s.box, &top_global, state_global->x.rvec_array());
+            }
+
+            write_sto_conf_mtop(confout,
+                                *top_global.name,
+                                top_global,
+                                state_global->x.rvec_array(),
+                                nullptr,
+                                ir->pbcType,
+                                state->s.box);
+        }
+    }
+}
+
+//! \brief Do one minimization step
+//
+// \returns true when the step succeeded, false when a constraint error occurred
+static bool do_em_step(const t_commrec*                          cr,
+                       const t_inputrec*                         ir,
+                       t_mdatoms*                                md,
+                       em_state_t*                               ems1,
+                       real                                      a,
+                       gmx::ArrayRefWithPadding<const gmx::RVec> force,
+                       em_state_t*                               ems2,
+                       gmx::Constraints*                         constr,
+                       int64_t                                   count)
+
+{
+    t_state *    s1, *s2;
+    int          start, end;
+    real         dvdl_constr;
+    int nthreads gmx_unused;
+
+    bool validStep = true;
+
+    s1 = &ems1->s;
+    s2 = &ems2->s;
+
+    if (haveDDAtomOrdering(*cr) && s1->ddp_count != cr->dd->ddp_count)
+    {
+        gmx_incons("state mismatch in do_em_step");
+    }
+
+    s2->setFlags(s1->flags());
+
+    if (s2->numAtoms() != s1->numAtoms())
+    {
+        s2->changeNumAtoms(s1->numAtoms());
+        ems2->f.resize(s2->numAtoms());
+    }
+    if (haveDDAtomOrdering(*cr) && s2->cg_gl.size() != s1->cg_gl.size())
+    {
+        s2->cg_gl.resize(s1->cg_gl.size());
+    }
+
+    copy_mat(s1->box, s2->box);
+    /* Copy free energy state */
+    s2->lambda = s1->lambda;
+    copy_mat(s1->box, s2->box);
+
+    start = 0;
+    end   = md->homenr;
+
+    nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Update);
+#pragma omp parallel num_threads(nthreads)
+    {
+        const rvec* x1 = s1->x.rvec_array();
+        rvec*       x2 = s2->x.rvec_array();
+        const rvec* f  = as_rvec_array(force.unpaddedArrayRef().data());
+
+        int gf = 0;
+#pragma omp for schedule(static) nowait
+        for (int i = start; i < end; i++)
+        {
+            try
+            {
+                if (!md->cFREEZE.empty())
+                {
+                    gf = md->cFREEZE[i];
+                }
+                for (int m = 0; m < DIM; m++)
+                {
+                    if (ir->opts.nFreeze[gf][m])
+                    {
+                        x2[i][m] = x1[i][m];
+                    }
+                    else
+                    {
+                        x2[i][m] = x1[i][m] + a * f[i][m];
+                    }
+                }
+            }
+            GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
+        }
+
+        if (s2->hasEntry(StateEntry::Cgp))
+        {
+            /* Copy the CG p vector */
+            const rvec* p1 = s1->cg_p.rvec_array();
+            rvec*       p2 = s2->cg_p.rvec_array();
+#pragma omp for schedule(static) nowait
+            for (int i = start; i < end; i++)
+            {
+                // Trivial OpenMP block that does not throw
+                copy_rvec(p1[i], p2[i]);
+            }
+        }
+
+        if (haveDDAtomOrdering(*cr))
+        {
+            /* OpenMP does not supported unsigned loop variables */
+#pragma omp for schedule(static) nowait
+            for (gmx::Index i = 0; i < gmx::ssize(s2->cg_gl); i++)
+            {
+                s2->cg_gl[i] = s1->cg_gl[i];
+            }
+        }
+    }
+
+    // Copy the DD or pair search counters
+    s2->ddp_count       = s1->ddp_count;
+    s2->ddp_count_cg_gl = s1->ddp_count_cg_gl;
+
+    if (constr)
+    {
+        dvdl_constr = 0;
+        validStep   = constr->apply(TRUE,
+                                  TRUE,
+                                  count,
+                                  0,
+                                  1.0,
+                                  s1->x.arrayRefWithPadding(),
+                                  s2->x.arrayRefWithPadding(),
+                                  ArrayRef<RVec>(),
+                                  s2->box,
+                                  s2->lambda[FreeEnergyPerturbationCouplingType::Bonded],
+                                  &dvdl_constr,
+                                  gmx::ArrayRefWithPadding<RVec>(),
+                                  false,
+                                  nullptr,
+                                  gmx::ConstraintVariable::Positions);
+
+        if (cr->nnodes > 1)
+        {
+            /* This global reduction will affect performance at high
+             * parallelization, but we can not really avoid it.
+             * But usually EM is not run at high parallelization.
+             */
+            int reductionBuffer = static_cast<int>(!validStep);
+            gmx_sumi(1, &reductionBuffer, cr);
+            validStep = (reductionBuffer == 0);
+        }
+
+        // We should move this check to the different minimizers
+        if (!validStep && ir->eI != IntegrationAlgorithm::Steep)
+        {
+            gmx_fatal(FARGS,
+                      "The coordinates could not be constrained. Minimizer '%s' can not handle "
+                      "constraint failures, use minimizer '%s' before using '%s'.",
+                      enumValueToString(ir->eI),
+                      enumValueToString(IntegrationAlgorithm::Steep),
+                      enumValueToString(ir->eI));
+        }
+    }
+
+    return validStep;
+}
+
+//! Prepare EM for using domain decomposition parallellization
+static void em_dd_partition_system(FILE*                     fplog,
+                                   const gmx::MDLogger&      mdlog,
+                                   int                       step,
+                                   const t_commrec*          cr,
+                                   const gmx_mtop_t&         top_global,
+                                   const t_inputrec*         ir,
+                                   const MDModulesNotifiers& mdModulesNotifiers,
+
+                                   gmx::ImdSession*     imdSession,
+                                   pull_t*              pull_work,
+                                   em_state_t*          ems,
+                                   gmx_localtop_t*      top,
+                                   gmx::MDAtoms*        mdAtoms,
+                                   t_forcerec*          fr,
+                                   VirtualSitesHandler* vsite,
+                                   gmx::Constraints*    constr,
+                                   t_nrnb*              nrnb,
+                                   gmx_wallcycle*       wcycle)
+{
+    /* Repartition the domain decomposition */
+    dd_partition_system(fplog,
+                        mdlog,
+                        step,
+                        cr,
+                        FALSE,
+                        nullptr,
+                        top_global,
+                        *ir,
+                        mdModulesNotifiers,
+                        imdSession,
+                        pull_work,
+                        &ems->s,
+                        &ems->f,
+                        mdAtoms,
+                        top,
+                        fr,
+                        vsite,
+                        constr,
+                        nrnb,
+                        wcycle,
+                        FALSE);
+    dd_store_state(*cr->dd, &ems->s);
+}
+
+namespace
+{
+
+//! Copy coordinates, OpenMP parallelized, from \p refCoords to coords
+void setCoordinates(std::vector<RVec>* coords, ArrayRef<const RVec> refCoords)
+{
+    coords->resize(refCoords.size());
+
+    const int gmx_unused nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Update);
+#pragma omp parallel for num_threads(nthreads) schedule(static)
+    for (int i = 0; i < ssize(refCoords); i++)
+    {
+        (*coords)[i] = refCoords[i];
+    }
+}
+
+//! Returns the maximum difference an atom moved between two coordinate sets, over all ranks
+real maxCoordinateDifference(ArrayRef<const RVec> coords1, ArrayRef<const RVec> coords2, MPI_Comm mpiCommMyGroup)
+{
+    GMX_RELEASE_ASSERT(coords1.size() == coords2.size(), "Coordinate counts should match");
+
+    real maxDiffSquared = 0;
+
+#ifndef _MSC_VER // Visual Studio has no support for reduction(max)
+    const int gmx_unused nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Update);
+#    pragma omp parallel for reduction(max : maxDiffSquared) num_threads(nthreads) schedule(static)
+#endif
+    for (int i = 0; i < ssize(coords1); i++)
+    {
+        maxDiffSquared = std::max(maxDiffSquared, gmx::norm2(coords1[i] - coords2[i]));
+    }
+
+#if GMX_MPI
+    int numRanks = 1;
+    if (mpiCommMyGroup != MPI_COMM_NULL)
+    {
+        MPI_Comm_size(mpiCommMyGroup, &numRanks);
+    }
+    if (numRanks > 1)
+    {
+        real maxDiffSquaredReduced;
+        MPI_Allreduce(
+                &maxDiffSquared, &maxDiffSquaredReduced, 1, GMX_DOUBLE ? MPI_DOUBLE : MPI_FLOAT, MPI_MAX, mpiCommMyGroup);
+        maxDiffSquared = maxDiffSquaredReduced;
+    }
+#else
+    GMX_UNUSED_VALUE(mpiCommMyGroup);
+#endif
+
+    return std::sqrt(maxDiffSquared);
+}
+
+/*! \brief Class to handle the work of setting and doing an energy evaluation.
+ *
+ * This class is a mere aggregate of parameters to pass to evaluate an
+ * energy, so that future changes to names and types of them consume
+ * less time when refactoring other code.
+ *
+ * Aggregate initialization is used, for which the chief risk is that
+ * if a member is added at the end and not all initializer lists are
+ * updated, then the member will be value initialized, which will
+ * typically mean initialization to zero.
+ *
+ * Use a braced initializer list to construct one of these. */
+class EnergyEvaluator
+{
+public:
+    /*! \brief Evaluates an energy on the state in \c ems.
+     *
+     * \todo In practice, the same objects mu_tot, vir, and pres
+     * are always passed to this function, so we would rather have
+     * them as data members. However, their C-array types are
+     * unsuited for aggregate initialization. When the types
+     * improve, the call signature of this method can be reduced.
+     */
+    void run(em_state_t* ems, rvec mu_tot, tensor vir, tensor pres, int64_t count, gmx_bool bFirst, int64_t step);
+    //! Handles logging (deprecated).
+    FILE* fplog;
+    //! Handles logging.
+    const gmx::MDLogger& mdlog;
+    //! Handles communication.
+    const t_commrec* cr;
+    //! Coordinates multi-simulations.
+    const gmx_multisim_t* ms;
+    //! Holds the simulation topology.
+    const gmx_mtop_t& top_global;
+    //! Holds the domain topology.
+    gmx_localtop_t* top;
+    //! User input options.
+    const t_inputrec* inputrec;
+    // Handles notifications for MDModules
+    const MDModulesNotifiers& mdModulesNotifiers;
+    //! The Interactive Molecular Dynamics session.
+    gmx::ImdSession* imdSession;
+    //! The pull work object.
+    pull_t* pull_work;
+    //! Data for rotational pulling.
+    gmx_enfrot* enforcedRotation;
+    //! Manages flop accounting.
+    t_nrnb* nrnb;
+    //! Manages wall cycle accounting.
+    gmx_wallcycle* wcycle;
+    //! Legacy coordinator of global reduction.
+    gmx_global_stat_t gstat;
+    //! Coordinates reduction for observables
+    gmx::ObservablesReducer* observablesReducer;
+    //! Handles virtual sites.
+    VirtualSitesHandler* vsite;
+    //! Handles constraints.
+    gmx::Constraints* constr;
+    //! Per-atom data for this domain.
+    gmx::MDAtoms* mdAtoms;
+    //! Handles how to calculate the forces.
+    t_forcerec* fr;
+    //! Schedule of force-calculation work each step for this task.
+    MdrunScheduleWorkload* runScheduleWork;
+    //! Stores the computed energies.
+    gmx_enerdata_t* enerd;
+    //! The DD partitioning count at which the pair list was generated
+    int ddpCountPairSearch;
+    //! The local coordinates that were used for pair searching, stored for computing displacements
+    std::vector<RVec> pairSearchCoordinates;
+};
+
+void EnergyEvaluator::run(em_state_t* ems, rvec mu_tot, tensor vir, tensor pres, int64_t count, gmx_bool bFirst, int64_t step)
+{
+    real     t;
+    gmx_bool bNS;
+    tensor   force_vir, shake_vir, ekin;
+    real     dvdl_constr;
+    real     terminate = 0;
+
+    /* Set the time to the initial time, the time does not change during EM */
+    t = inputrec->init_t;
+
+    if (vsite)
+    {
+        vsite->construct(ems->s.x, {}, ems->s.box, gmx::VSiteOperation::Positions);
+    }
+
+    // Compute the buffer size of the pair list
+    const real bufferSize = inputrec->rlist - std::max(inputrec->rcoulomb, inputrec->rvdw);
+
+    if (bFirst || bufferSize <= 0 || ems->s.ddp_count != ddpCountPairSearch)
+    {
+        /* This is the first state or an old state used before the last ns */
+        bNS = TRUE;
+    }
+    else
+    {
+        // We need to generate a new pairlist when one atom moved more than half the buffer size
+        ArrayRef<const RVec> localCoordinates =
+                ArrayRef<const RVec>(ems->s.x).subArray(0, mdAtoms->mdatoms()->homenr);
+        bNS = 2 * maxCoordinateDifference(pairSearchCoordinates, localCoordinates, cr->mpi_comm_mygroup)
+              > bufferSize;
+    }
+
+    if (bNS)
+    {
+        if (haveDDAtomOrdering(*cr))
+        {
+            /* Repartition the domain decomposition */
+            em_dd_partition_system(fplog,
+                                   mdlog,
+                                   count,
+                                   cr,
+                                   top_global,
+                                   inputrec,
+                                   mdModulesNotifiers,
+                                   imdSession,
+                                   pull_work,
+                                   ems,
+                                   top,
+                                   mdAtoms,
+                                   fr,
+                                   vsite,
+                                   constr,
+                                   nrnb,
+                                   wcycle);
+            ddpCountPairSearch = cr->dd->ddp_count;
+        }
+        else
+        {
+            // Without DD we increase the search counter here
+            ddpCountPairSearch++;
+            // Store the count in the state, so we check whether we later need
+            // to do pair search after resetting to this, by then, old state
+            ems->s.ddp_count = ddpCountPairSearch;
+        }
+    }
+
+    /* Store the local coordinates that will be used in the pair search, after we re-partitioned */
+    if (bufferSize > 0 && bNS)
+    {
+        ArrayRef<const RVec> localCoordinates =
+                constArrayRefFromArray(ems->s.x.data(), mdAtoms->mdatoms()->homenr);
+        setCoordinates(&pairSearchCoordinates, localCoordinates);
+    }
+
+    fr->longRangeNonbondeds->updateAfterPartition(*mdAtoms->mdatoms());
+
+    gmx_edsam* const ed = nullptr;
+
+    if (bNS)
+    {
+        if (fr->listedForcesGpu)
+        {
+            fr->listedForcesGpu->updateHaveInteractions(top->idef);
+        }
+        runScheduleWork->domainWork = setupDomainLifetimeWorkload(
+                *inputrec, *fr, pull_work, ed, *mdAtoms->mdatoms(), runScheduleWork->simulationWork);
+    }
+
+
+    const int legacyForceFlags = GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | GMX_FORCE_VIRIAL
+                                 | GMX_FORCE_ENERGY | (bNS ? GMX_FORCE_NS : 0);
+    runScheduleWork->stepWork = setupStepWorkload(legacyForceFlags,
+                                                  inputrec->mtsLevels,
+                                                  step,
+                                                  runScheduleWork->domainWork,
+                                                  runScheduleWork->simulationWork);
+
+    /* Calc force & energy on new trial position  */
+    /* do_force always puts the charge groups in the box and shifts again
+     * We do not unshift, so molecules are always whole in congrad.c
+     */
+    do_force(fplog,
+             cr,
+             ms,
+             *inputrec,
+             mdModulesNotifiers,
+             nullptr,
+             enforcedRotation,
+             imdSession,
+             pull_work,
+             count,
+             nrnb,
+             wcycle,
+             top,
+             ems->s.box,
+             ems->s.x.arrayRefWithPadding(),
+             {},
+             &ems->s.hist,
+             &ems->f.view(),
+             force_vir,
+             mdAtoms->mdatoms(),
+             enerd,
+             ems->s.lambda,
+             fr,
+             *runScheduleWork,
+             vsite,
+             mu_tot,
+             t,
+             ed,
+             fr->longRangeNonbondeds.get(),
+             DDBalanceRegionHandler(cr));
+
+    /* Clear the unused shake virial and pressure */
+    clear_mat(shake_vir);
+    clear_mat(pres);
+
+    /* Communicate stuff when parallel */
+    if (PAR(cr) && inputrec->eI != IntegrationAlgorithm::NM)
+    {
+        wallcycle_start(wcycle, WallCycleCounter::MoveE);
+
+        global_stat(*gstat,
+                    cr,
+                    enerd,
+                    force_vir,
+                    shake_vir,
+                    *inputrec,
+                    nullptr,
+                    nullptr,
+                    std::vector<real>(1, terminate),
+                    FALSE,
+                    CGLO_ENERGY | CGLO_PRESSURE | CGLO_CONSTRAINT,
+                    step,
+                    observablesReducer);
+
+        wallcycle_stop(wcycle, WallCycleCounter::MoveE);
+    }
+
+    ems->epot = enerd->term[F_EPOT];
+
+    if (constr)
+    {
+        /* Project out the constraint components of the force */
+        bool needsLogging  = false;
+        bool computeEnergy = false;
+        bool computeVirial = true;
+        dvdl_constr        = 0;
+        auto f             = ems->f.view().forceWithPadding();
+        constr->apply(needsLogging,
+                      computeEnergy,
+                      count,
+                      0,
+                      1.0,
+                      ems->s.x.arrayRefWithPadding(),
+                      f,
+                      f.unpaddedArrayRef(),
+                      ems->s.box,
+                      ems->s.lambda[FreeEnergyPerturbationCouplingType::Bonded],
+                      &dvdl_constr,
+                      gmx::ArrayRefWithPadding<RVec>(),
+                      computeVirial,
+                      shake_vir,
+                      gmx::ConstraintVariable::ForceDispl);
+        enerd->term[F_DVDL_CONSTR] += dvdl_constr;
+        m_add(force_vir, shake_vir, vir);
+    }
+    else
+    {
+        copy_mat(force_vir, vir);
+    }
+
+    clear_mat(ekin);
+    enerd->term[F_PRES] = calc_pres(fr->pbcType, inputrec->nwall, ems->s.box, ekin, vir, pres);
+
+    if (inputrec->efep != FreeEnergyPerturbationType::No)
+    {
+        accumulateKineticLambdaComponents(enerd, ems->s.lambda, *inputrec->fepvals);
+    }
+
+    if (EI_ENERGY_MINIMIZATION(inputrec->eI))
+    {
+        get_state_f_norm_max(cr, &(inputrec->opts), mdAtoms->mdatoms(), ems);
+    }
+}
+
+} // namespace
+
+//! Parallel utility summing energies and forces
+static double reorder_partsum(const t_commrec*  cr,
+                              const t_grpopts*  opts,
+                              const gmx_mtop_t& top_global,
+                              const em_state_t* s_min,
+                              const em_state_t* s_b)
+{
+    if (debug)
+    {
+        fprintf(debug, "Doing reorder_partsum\n");
+    }
+
+    auto fm = s_min->f.view().force();
+    auto fb = s_b->f.view().force();
+
+    /* Collect fm in a global vector fmg.
+     * This conflicts with the spirit of domain decomposition,
+     * but to fully optimize this a much more complicated algorithm is required.
+     */
+    const int natoms = top_global.natoms;
+    rvec*     fmg;
+    snew(fmg, natoms);
+
+    gmx::ArrayRef<const int> indicesMin = s_min->s.cg_gl;
+    int                      i          = 0;
+    for (int a : indicesMin)
+    {
+        copy_rvec(fm[i], fmg[a]);
+        i++;
+    }
+    gmx_sum(top_global.natoms * 3, fmg[0], cr);
+
+    /* Now we will determine the part of the sum for the cgs in state s_b */
+    gmx::ArrayRef<const int> indicesB = s_b->s.cg_gl;
+
+    double partsum                        = 0;
+    i                                     = 0;
+    int                                gf = 0;
+    gmx::ArrayRef<const unsigned char> grpnrFREEZE =
+            top_global.groups.groupNumbers[SimulationAtomGroupType::Freeze];
+    for (int a : indicesB)
+    {
+        if (!grpnrFREEZE.empty())
+        {
+            gf = grpnrFREEZE[i];
+        }
+        for (int m = 0; m < DIM; m++)
+        {
+            if (!opts->nFreeze[gf][m])
+            {
+                partsum += (fb[i][m] - fmg[a][m]) * fb[i][m];
+            }
+        }
+        i++;
+    }
+
+    sfree(fmg);
+
+    return partsum;
+}
+
+//! Print some stuff, like beta, whatever that means.
+static real pr_beta(const t_commrec*  cr,
+                    const t_grpopts*  opts,
+                    t_mdatoms*        mdatoms,
+                    const gmx_mtop_t& top_global,
+                    const em_state_t* s_min,
+                    const em_state_t* s_b)
+{
+    double sum;
+
+    /* This is just the classical Polak-Ribiere calculation of beta;
+     * it looks a bit complicated since we take freeze groups into account,
+     * and might have to sum it in parallel runs.
+     */
+
+    if (!haveDDAtomOrdering(*cr)
+        || (s_min->s.ddp_count == cr->dd->ddp_count && s_b->s.ddp_count == cr->dd->ddp_count))
+    {
+        auto fm = s_min->f.view().force();
+        auto fb = s_b->f.view().force();
+        sum     = 0;
+        int gf  = 0;
+        /* This part of code can be incorrect with DD,
+         * since the atom ordering in s_b and s_min might differ.
+         */
+        for (int i = 0; i < mdatoms->homenr; i++)
+        {
+            if (!mdatoms->cFREEZE.empty())
+            {
+                gf = mdatoms->cFREEZE[i];
+            }
+            for (int m = 0; m < DIM; m++)
+            {
+                if (!opts->nFreeze[gf][m])
+                {
+                    sum += (fb[i][m] - fm[i][m]) * fb[i][m];
+                }
+            }
+        }
+    }
+    else
+    {
+        /* We need to reorder cgs while summing */
+        sum = reorder_partsum(cr, opts, top_global, s_min, s_b);
+    }
+    if (PAR(cr))
+    {
+        gmx_sumd(1, &sum, cr);
+    }
+
+    return sum / gmx::square(s_min->fnorm);
+}
+
+namespace gmx
+{
+
+void LegacySimulator::do_cg()
+{
+    const char* CG = "Polak-Ribiere Conjugate Gradients";
+
+    gmx_global_stat_t gstat;
+    double            tmp, minstep;
+    real              stepsize;
+    real              a, b, c, beta = 0.0;
+    real              epot_repl = 0;
+    real              pnorm;
+    gmx_bool          converged, foundlower;
+    rvec              mu_tot = { 0 };
+    gmx_bool          do_log = FALSE, do_ene = FALSE, do_x, do_f;
+    tensor            vir, pres;
+    int               number_steps, neval = 0, nstcg = inputRec_->nstcgsteep;
+    int               m, step, nminstep;
+    auto*             mdatoms = mdAtoms_->mdatoms();
+
+    GMX_LOG(mdLog_.info)
+            .asParagraph()
+            .appendText(
+                    "Note that activating conjugate gradient energy minimization via the "
+                    "integrator .mdp option and the command gmx mdrun may "
+                    "be available in a different form in a future version of GROMACS, "
+                    "e.g. gmx minimize and an .mdp option.");
+
+    step = 0;
+
+    if (MAIN(cr_))
+    {
+        // In CG, the state is extended with a search direction
+        stateGlobal_->addEntry(StateEntry::Cgp);
+
+        // Initialize the search direction to zero
+        for (RVec& cg_p : stateGlobal_->cg_p)
+        {
+            cg_p = { 0, 0, 0 };
+        }
+    }
+
+    /* Create 4 states on the stack and extract pointers that we will swap */
+    em_state_t  s0{}, s1{}, s2{}, s3{};
+    em_state_t* s_min = &s0;
+    em_state_t* s_a   = &s1;
+    em_state_t* s_b   = &s2;
+    em_state_t* s_c   = &s3;
+
+    ObservablesReducer observablesReducer = observablesReducerBuilder_->build();
+
+    /* Init em and store the local state in s_min */
+    init_em(fpLog_,
+            mdLog_,
+            CG,
+            cr_,
+            inputRec_,
+            mdModulesNotifiers_,
+            imdSession_,
+            pullWork_,
+            stateGlobal_,
+            topGlobal_,
+            s_min,
+            top_,
+            nrnb_,
+            fr_,
+            mdAtoms_,
+            &gstat,
+            virtualSites_,
+            constr_,
+            nullptr);
+    const bool        simulationsShareState = false;
+    gmx_mdoutf*       outf                  = init_mdoutf(fpLog_,
+                                   nFile_,
+                                   fnm_,
+                                   mdrunOptions_,
+                                   cr_,
+                                   outputProvider_,
+                                   mdModulesNotifiers_,
+                                   inputRec_,
+                                   topGlobal_,
+                                   nullptr,
+                                   wallCycleCounters_,
+                                   StartingBehavior::NewSimulation,
+                                   simulationsShareState,
+                                   ms_);
+    gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
+                                   topGlobal_,
+                                   *inputRec_,
+                                   pullWork_,
+                                   nullptr,
+                                   false,
+                                   StartingBehavior::NewSimulation,
+                                   simulationsShareState,
+                                   mdModulesNotifiers_);
+
+    /* Print to log file */
+    print_em_start(fpLog_, cr_, wallTimeAccounting_, wallCycleCounters_, CG);
+
+    /* Max number of steps */
+    number_steps = inputRec_->nsteps;
+
+    if (MAIN(cr_))
+    {
+        sp_header(stderr, CG, inputRec_->em_tol, number_steps);
+    }
+    if (fpLog_)
+    {
+        sp_header(fpLog_, CG, inputRec_->em_tol, number_steps);
+    }
+
+    EnergyEvaluator energyEvaluator{ fpLog_,
+                                     mdLog_,
+                                     cr_,
+                                     ms_,
+                                     topGlobal_,
+                                     top_,
+                                     inputRec_,
+                                     mdModulesNotifiers_,
+                                     imdSession_,
+                                     pullWork_,
+                                     enforcedRotation_,
+                                     nrnb_,
+                                     wallCycleCounters_,
+                                     gstat,
+                                     &observablesReducer,
+                                     virtualSites_,
+                                     constr_,
+                                     mdAtoms_,
+                                     fr_,
+                                     runScheduleWork_,
+                                     enerd_,
+                                     -1,
+                                     {} };
+    /* Call the force routine and some auxiliary (neighboursearching etc.) */
+    /* do_force always puts the charge groups in the box and shifts again
+     * We do not unshift, so molecules are always whole in congrad.c
+     */
+    energyEvaluator.run(s_min, mu_tot, vir, pres, -1, TRUE, step);
+    observablesReducer.markAsReadyToReduce();
+
+    if (MAIN(cr_))
+    {
+        /* Copy stuff to the energy bin for easy printing etc. */
+        matrix nullBox = {};
+        energyOutput.addDataAtEnergyStep(false,
+                                         false,
+                                         static_cast<double>(step),
+                                         mdatoms->tmass,
+                                         enerd_,
+                                         nullptr,
+                                         nullBox,
+                                         PTCouplingArrays(),
+                                         0,
+                                         vir,
+                                         pres,
+                                         nullptr,
+                                         mu_tot,
+                                         constr_);
+
+        EnergyOutput::printHeader(fpLog_, step, step);
+        energyOutput.printStepToEnergyFile(
+                mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fpLog_, step, step, fr_->fcdata.get(), nullptr);
+    }
+
+    /* Estimate/guess the initial stepsize */
+    stepsize = inputRec_->em_stepsize / s_min->fnorm;
+
+    if (MAIN(cr_))
+    {
+        double sqrtNumAtoms = sqrt(static_cast<double>(stateGlobal_->numAtoms()));
+        fprintf(stderr, "   F-max             = %12.5e on atom %d\n", s_min->fmax, s_min->a_fmax + 1);
+        fprintf(stderr, "   F-Norm            = %12.5e\n", s_min->fnorm / sqrtNumAtoms);
+        fprintf(stderr, "\n");
+        /* and copy to the log file too... */
+        fprintf(fpLog_, "   F-max             = %12.5e on atom %d\n", s_min->fmax, s_min->a_fmax + 1);
+        fprintf(fpLog_, "   F-Norm            = %12.5e\n", s_min->fnorm / sqrtNumAtoms);
+        fprintf(fpLog_, "\n");
+    }
+    /* Start the loop over CG steps.
+     * Each successful step is counted, and we continue until
+     * we either converge or reach the max number of steps.
+     */
+    converged = FALSE;
+    for (step = 0; (number_steps < 0 || step <= number_steps) && !converged; step++)
+    {
+
+        /* start taking steps in a new direction
+         * First time we enter the routine, beta=0, and the direction is
+         * simply the negative gradient.
+         */
+
+        /* Calculate the new direction in p, and the gradient in this direction, gpa */
+        gmx::ArrayRef<gmx::RVec>       pm  = s_min->s.cg_p;
+        gmx::ArrayRef<const gmx::RVec> sfm = s_min->f.view().force();
+        double                         gpa = 0;
+        int                            gf  = 0;
+        for (int i = 0; i < mdatoms->homenr; i++)
+        {
+            if (!mdatoms->cFREEZE.empty())
+            {
+                gf = mdatoms->cFREEZE[i];
+            }
+            for (m = 0; m < DIM; m++)
+            {
+                if (!inputRec_->opts.nFreeze[gf][m])
+                {
+                    pm[i][m] = sfm[i][m] + beta * pm[i][m];
+                    gpa -= pm[i][m] * sfm[i][m];
+                    /* f is negative gradient, thus the sign */
+                }
+                else
+                {
+                    pm[i][m] = 0;
+                }
+            }
+        }
+
+        /* Sum the gradient along the line across CPUs */
+        if (PAR(cr_))
+        {
+            gmx_sumd(1, &gpa, cr_);
+        }
+
+        /* Calculate the norm of the search vector */
+        get_f_norm_max(cr_, &(inputRec_->opts), mdatoms, pm, &pnorm, nullptr, nullptr);
+
+        /* Just in case stepsize reaches zero due to numerical precision... */
+        if (stepsize <= 0)
+        {
+            stepsize = inputRec_->em_stepsize / pnorm;
+        }
+
+        /*
+         * Double check the value of the derivative in the search direction.
+         * If it is positive it must be due to the old information in the
+         * CG formula, so just remove that and start over with beta=0.
+         * This corresponds to a steepest descent step.
+         */
+        if (gpa > 0)
+        {
+            beta = 0;
+            step--;   /* Don't count this step since we are restarting */
+            continue; /* Go back to the beginning of the big for-loop */
+        }
+
+        /* Calculate minimum allowed stepsize, before the average (norm)
+         * relative change in coordinate is smaller than precision
+         */
+        minstep      = 0;
+        auto s_min_x = makeArrayRef(s_min->s.x);
+        for (int i = 0; i < mdatoms->homenr; i++)
+        {
+            for (m = 0; m < DIM; m++)
+            {
+                tmp = fabs(s_min_x[i][m]);
+                if (tmp < 1.0)
+                {
+                    tmp = 1.0;
+                }
+                tmp = pm[i][m] / tmp;
+                minstep += tmp * tmp;
+            }
+        }
+        /* Add up from all CPUs */
+        if (PAR(cr_))
+        {
+            gmx_sumd(1, &minstep, cr_);
+        }
+
+        minstep = GMX_REAL_EPS / sqrt(minstep / (3 * topGlobal_.natoms));
+
+        if (stepsize < minstep)
+        {
+            converged = TRUE;
+            break;
+        }
+
+        /* Write coordinates if necessary */
+        do_x = do_per_step(step, inputRec_->nstxout);
+        do_f = do_per_step(step, inputRec_->nstfout);
+
+        write_em_traj(
+                fpLog_, cr_, outf, do_x, do_f, nullptr, topGlobal_, inputRec_, step, s_min, stateGlobal_, observablesHistory_);
+
+        /* Take a step downhill.
+         * In theory, we should minimize the function along this direction.
+         * That is quite possible, but it turns out to take 5-10 function evaluations
+         * for each line. However, we dont really need to find the exact minimum -
+         * it is much better to start a new CG step in a modified direction as soon
+         * as we are close to it. This will save a lot of energy evaluations.
+         *
+         * In practice, we just try to take a single step.
+         * If it worked (i.e. lowered the energy), we increase the stepsize but
+         * the continue straight to the next CG step without trying to find any minimum.
+         * If it didn't work (higher energy), there must be a minimum somewhere between
+         * the old position and the new one.
+         *
+         * Due to the finite numerical accuracy, it turns out that it is a good idea
+         * to even accept a SMALL increase in energy, if the derivative is still downhill.
+         * This leads to lower final energies in the tests I've done. / Erik
+         */
+        s_a->epot = s_min->epot;
+        a         = 0.0;
+        c         = a + stepsize; /* reference position along line is zero */
+
+        if (haveDDAtomOrdering(*cr_) && s_min->s.ddp_count < cr_->dd->ddp_count)
+        {
+            em_dd_partition_system(fpLog_,
+                                   mdLog_,
+                                   step,
+                                   cr_,
+                                   topGlobal_,
+                                   inputRec_,
+                                   mdModulesNotifiers_,
+                                   imdSession_,
+                                   pullWork_,
+                                   s_min,
+                                   top_,
+                                   mdAtoms_,
+                                   fr_,
+                                   virtualSites_,
+                                   constr_,
+                                   nrnb_,
+                                   wallCycleCounters_);
+        }
+
+        /* Take a trial step (new coords in s_c) */
+        do_em_step(cr_, inputRec_, mdatoms, s_min, c, s_min->s.cg_p.constArrayRefWithPadding(), s_c, constr_, -1);
+
+        neval++;
+        /* Calculate energy for the trial step */
+        energyEvaluator.run(s_c, mu_tot, vir, pres, -1, FALSE, step);
+        observablesReducer.markAsReadyToReduce();
+
+        /* Calc derivative along line */
+        const rvec*                    pc  = s_c->s.cg_p.rvec_array();
+        gmx::ArrayRef<const gmx::RVec> sfc = s_c->f.view().force();
+        double                         gpc = 0;
+        for (int i = 0; i < mdatoms->homenr; i++)
+        {
+            for (m = 0; m < DIM; m++)
+            {
+                gpc -= pc[i][m] * sfc[i][m]; /* f is negative gradient, thus the sign */
+            }
+        }
+        /* Sum the gradient along the line across CPUs */
+        if (PAR(cr_))
+        {
+            gmx_sumd(1, &gpc, cr_);
+        }
+
+        /* This is the max amount of increase in energy we tolerate */
+        tmp = std::sqrt(GMX_REAL_EPS) * fabs(s_a->epot);
+
+        /* Accept the step if the energy is lower, or if it is not significantly higher
+         * and the line derivative is still negative.
+         */
+        if (s_c->epot < s_a->epot || (gpc < 0 && s_c->epot < (s_a->epot + tmp)))
+        {
+            foundlower = TRUE;
+            /* Great, we found a better energy. Increase step for next iteration
+             * if we are still going down, decrease it otherwise
+             */
+            if (gpc < 0)
+            {
+                stepsize *= 1.618034; /* The golden section */
+            }
+            else
+            {
+                stepsize *= 0.618034; /* 1/golden section */
+            }
+        }
+        else
+        {
+            /* New energy is the same or higher. We will have to do some work
+             * to find a smaller value in the interval. Take smaller step next time!
+             */
+            foundlower = FALSE;
+            stepsize *= 0.618034;
+        }
+
+
+        /* OK, if we didn't find a lower value we will have to locate one now - there must
+         * be one in the interval [a=0,c].
+         * The same thing is valid here, though: Don't spend dozens of iterations to find
+         * the line minimum. We try to interpolate based on the derivative at the endpoints,
+         * and only continue until we find a lower value. In most cases this means 1-2 iterations.
+         *
+         * I also have a safeguard for potentially really pathological functions so we never
+         * take more than 20 steps before we give up ...
+         *
+         * If we already found a lower value we just skip this step and continue to the update.
+         */
+        double gpb;
+        if (!foundlower)
+        {
+            nminstep = 0;
+
+            do
+            {
+                /* Select a new trial point.
+                 * If the derivatives at points a & c have different sign we interpolate to zero,
+                 * otherwise just do a bisection.
+                 */
+                if (gpa < 0 && gpc > 0)
+                {
+                    b = a + gpa * (a - c) / (gpc - gpa);
+                }
+                else
+                {
+                    b = 0.5 * (a + c);
+                }
+
+                /* safeguard if interpolation close to machine accuracy causes errors:
+                 * never go outside the interval
+                 */
+                if (b <= a || b >= c)
+                {
+                    b = 0.5 * (a + c);
+                }
+
+                if (haveDDAtomOrdering(*cr_) && s_min->s.ddp_count != cr_->dd->ddp_count)
+                {
+                    /* Reload the old state */
+                    em_dd_partition_system(fpLog_,
+                                           mdLog_,
+                                           -1,
+                                           cr_,
+                                           topGlobal_,
+                                           inputRec_,
+                                           mdModulesNotifiers_,
+                                           imdSession_,
+                                           pullWork_,
+                                           s_min,
+                                           top_,
+                                           mdAtoms_,
+                                           fr_,
+                                           virtualSites_,
+                                           constr_,
+                                           nrnb_,
+                                           wallCycleCounters_);
+                }
+
+                /* Take a trial step to this new point - new coords in s_b */
+                do_em_step(
+                        cr_, inputRec_, mdatoms, s_min, b, s_min->s.cg_p.constArrayRefWithPadding(), s_b, constr_, -1);
+
+                neval++;
+                /* Calculate energy for the trial step */
+                energyEvaluator.run(s_b, mu_tot, vir, pres, -1, FALSE, step);
+                observablesReducer.markAsReadyToReduce();
+
+                /* p does not change within a step, but since the domain decomposition
+                 * might change, we have to use cg_p of s_b here.
+                 */
+                const rvec*                    pb  = s_b->s.cg_p.rvec_array();
+                gmx::ArrayRef<const gmx::RVec> sfb = s_b->f.view().force();
+                gpb                                = 0;
+                for (int i = 0; i < mdatoms->homenr; i++)
+                {
+                    for (m = 0; m < DIM; m++)
+                    {
+                        gpb -= pb[i][m] * sfb[i][m]; /* f is negative gradient, thus the sign */
+                    }
+                }
+                /* Sum the gradient along the line across CPUs */
+                if (PAR(cr_))
+                {
+                    gmx_sumd(1, &gpb, cr_);
+                }
+
+                if (debug)
+                {
+                    fprintf(debug, "CGE: EpotA %f EpotB %f EpotC %f gpb %f\n", s_a->epot, s_b->epot, s_c->epot, gpb);
+                }
+
+                epot_repl = s_b->epot;
+
+                /* Keep one of the intervals based on the value of the derivative at the new point */
+                if (gpb > 0)
+                {
+                    /* Replace c endpoint with b */
+                    swap_em_state(&s_b, &s_c);
+                    c   = b;
+                    gpc = gpb;
+                }
+                else
+                {
+                    /* Replace a endpoint with b */
+                    swap_em_state(&s_b, &s_a);
+                    a   = b;
+                    gpa = gpb;
+                }
+
+                /*
+                 * Stop search as soon as we find a value smaller than the endpoints.
+                 * Never run more than 20 steps, no matter what.
+                 */
+                nminstep++;
+            } while ((epot_repl > s_a->epot || epot_repl > s_c->epot) && (nminstep < 20));
+
+            if (std::fabs(epot_repl - s_min->epot) < fabs(s_min->epot) * GMX_REAL_EPS || nminstep >= 20)
+            {
+                /* OK. We couldn't find a significantly lower energy.
+                 * If beta==0 this was steepest descent, and then we give up.
+                 * If not, set beta=0 and restart with steepest descent before quitting.
+                 */
+                if (beta == 0.0)
+                {
+                    /* Converged */
+                    converged = TRUE;
+                    break;
+                }
+                else
+                {
+                    /* Reset memory before giving up */
+                    beta = 0.0;
+                    continue;
+                }
+            }
+
+            /* Select min energy state of A & C, put the best in B.
+             */
+            if (s_c->epot < s_a->epot)
+            {
+                if (debug)
+                {
+                    fprintf(debug, "CGE: C (%f) is lower than A (%f), moving C to B\n", s_c->epot, s_a->epot);
+                }
+                swap_em_state(&s_b, &s_c);
+                gpb = gpc;
+            }
+            else
+            {
+                if (debug)
+                {
+                    fprintf(debug, "CGE: A (%f) is lower than C (%f), moving A to B\n", s_a->epot, s_c->epot);
+                }
+                swap_em_state(&s_b, &s_a);
+                gpb = gpa;
+            }
+        }
+        else
+        {
+            if (debug)
+            {
+                fprintf(debug, "CGE: Found a lower energy %f, moving C to B\n", s_c->epot);
+            }
+            swap_em_state(&s_b, &s_c);
+            gpb = gpc;
+        }
+
+        /* new search direction */
+        /* beta = 0 means forget all memory and restart with steepest descents. */
+        if (nstcg && ((step % nstcg) == 0))
+        {
+            beta = 0.0;
+        }
+        else
+        {
+            /* s_min->fnorm cannot be zero, because then we would have converged
+             * and broken out.
+             */
+
+            /* Polak-Ribiere update.
+             * Change to fnorm2/fnorm2_old for Fletcher-Reeves
+             */
+            beta = pr_beta(cr_, &inputRec_->opts, mdatoms, topGlobal_, s_min, s_b);
+        }
+        /* Limit beta to prevent oscillations */
+        if (fabs(beta) > 5.0)
+        {
+            beta = 0.0;
+        }
+
+
+        /* update positions */
+        swap_em_state(&s_min, &s_b);
+        gpa = gpb;
+
+        /* Print it if necessary */
+        if (MAIN(cr_))
+        {
+            if (mdrunOptions_.verbose)
+            {
+                double sqrtNumAtoms = sqrt(static_cast<double>(stateGlobal_->numAtoms()));
+                fprintf(stderr,
+                        "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
+                        step,
+                        s_min->epot,
+                        s_min->fnorm / sqrtNumAtoms,
+                        s_min->fmax,
+                        s_min->a_fmax + 1);
+                fflush(stderr);
+            }
+            /* Store the new (lower) energies */
+            matrix nullBox = {};
+            energyOutput.addDataAtEnergyStep(false,
+                                             false,
+                                             static_cast<double>(step),
+                                             mdatoms->tmass,
+                                             enerd_,
+                                             nullptr,
+                                             nullBox,
+                                             PTCouplingArrays(),
+                                             0,
+                                             vir,
+                                             pres,
+                                             nullptr,
+                                             mu_tot,
+                                             constr_);
+
+            do_log = do_per_step(step, inputRec_->nstlog);
+            do_ene = do_per_step(step, inputRec_->nstenergy);
+
+            imdSession_->fillEnergyRecord(step, TRUE);
+
+            if (do_log)
+            {
+                EnergyOutput::printHeader(fpLog_, step, step);
+            }
+            energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+                                               do_ene,
+                                               FALSE,
+                                               FALSE,
+                                               do_log ? fpLog_ : nullptr,
+                                               step,
+                                               step,
+                                               fr_->fcdata.get(),
+                                               nullptr);
+        }
+
+        /* Send energies and positions to the IMD client if bIMD is TRUE. */
+        if (MAIN(cr_) && imdSession_->run(step, TRUE, stateGlobal_->box, stateGlobal_->x, 0))
+        {
+            imdSession_->sendPositionsAndEnergies();
+        }
+
+        /* Stop when the maximum force lies below tolerance.
+         * If we have reached machine precision, converged is already set to true.
+         */
+        converged = converged || (s_min->fmax < inputRec_->em_tol);
+        observablesReducer.markAsReadyToReduce();
+    } /* End of the loop */
+
+    if (converged)
+    {
+        step--; /* we never took that last step in this case */
+    }
+    if (s_min->fmax > inputRec_->em_tol)
+    {
+        if (MAIN(cr_))
+        {
+            warn_step(fpLog_, inputRec_->em_tol, s_min->fmax, step - 1 == number_steps, FALSE);
+        }
+        converged = FALSE;
+    }
+
+    if (MAIN(cr_))
+    {
+        /* If we printed energy and/or logfile last step (which was the last step)
+         * we don't have to do it again, but otherwise print the final values.
+         */
+        if (!do_log)
+        {
+            /* Write final value to log since we didn't do anything the last step */
+            EnergyOutput::printHeader(fpLog_, step, step);
+        }
+        if (!do_ene || !do_log)
+        {
+            /* Write final energy file entries */
+            energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+                                               !do_ene,
+                                               FALSE,
+                                               FALSE,
+                                               !do_log ? fpLog_ : nullptr,
+                                               step,
+                                               step,
+                                               fr_->fcdata.get(),
+                                               nullptr);
+        }
+    }
+
+    /* Print some stuff... */
+    if (MAIN(cr_))
+    {
+        fprintf(stderr, "\nwriting lowest energy coordinates.\n");
+    }
+
+    /* IMPORTANT!
+     * For accurate normal mode calculation it is imperative that we
+     * store the last conformation into the full precision binary trajectory.
+     *
+     * However, we should only do it if we did NOT already write this step
+     * above (which we did if do_x or do_f was true).
+     */
+    /* Note that with 0 < nstfout != nstxout we can end up with two frames
+     * in the trajectory with the same step number.
+     */
+    do_x = !do_per_step(step, inputRec_->nstxout);
+    do_f = (inputRec_->nstfout > 0 && !do_per_step(step, inputRec_->nstfout));
+
+    write_em_traj(
+            fpLog_, cr_, outf, do_x, do_f, ftp2fn(efSTO, nFile_, fnm_), topGlobal_, inputRec_, step, s_min, stateGlobal_, observablesHistory_);
+
+
+    if (MAIN(cr_))
+    {
+        double sqrtNumAtoms = sqrt(static_cast<double>(stateGlobal_->numAtoms()));
+        print_converged(stderr, CG, inputRec_->em_tol, step, converged, number_steps, s_min, sqrtNumAtoms);
+        print_converged(fpLog_, CG, inputRec_->em_tol, step, converged, number_steps, s_min, sqrtNumAtoms);
+
+        fprintf(fpLog_, "\nPerformed %d energy evaluations in total.\n", neval);
+    }
+
+    finish_em(cr_, outf, wallTimeAccounting_, wallCycleCounters_);
+
+    /* To print the actual number of steps we needed somewhere */
+    walltime_accounting_set_nsteps_done(wallTimeAccounting_, step);
+}
+
+
+void LegacySimulator::do_lbfgs()
+{
+    static const char* LBFGS = "Low-Memory BFGS Minimizer";
+    em_state_t         ems;
+    gmx_global_stat_t  gstat;
+    auto*              mdatoms = mdAtoms_->mdatoms();
+
+    GMX_LOG(mdLog_.info)
+            .asParagraph()
+            .appendText(
+                    "Note that activating L-BFGS energy minimization via the "
+                    "integrator .mdp option and the command gmx mdrun may "
+                    "be available in a different form in a future version of GROMACS, "
+                    "e.g. gmx minimize and an .mdp option.");
+
+    if (haveDDAtomOrdering(*cr_))
+    {
+        gmx_fatal(FARGS, "L_BFGS is currently not supported");
+    }
+    if (PAR(cr_))
+    {
+        gmx_fatal(FARGS, "L-BFGS minimization only supports a single rank");
+    }
+
+    if (nullptr != constr_)
+    {
+        gmx_fatal(
+                FARGS,
+                "The combination of constraints and L-BFGS minimization is not implemented. Either "
+                "do not use constraints, or use another minimizer (e.g. steepest descent).");
+    }
+
+    const int n        = 3 * stateGlobal_->numAtoms();
+    const int nmaxcorr = inputRec_->nbfgscorr;
+
+    std::vector<real> p(n);
+    std::vector<real> rho(nmaxcorr);
+    std::vector<real> alpha(nmaxcorr);
+
+    std::vector<std::vector<real>> dx(nmaxcorr);
+    for (auto& dxCorr : dx)
+    {
+        dxCorr.resize(n);
+    }
+
+    std::vector<std::vector<real>> dg(nmaxcorr);
+    for (auto& dgCorr : dg)
+    {
+        dgCorr.resize(n);
+    }
+
+    int step  = 0;
+    int neval = 0;
+
+    ObservablesReducer observablesReducer = observablesReducerBuilder_->build();
+
+    /* Init em */
+    init_em(fpLog_,
+            mdLog_,
+            LBFGS,
+            cr_,
+            inputRec_,
+            mdModulesNotifiers_,
+            imdSession_,
+            pullWork_,
+            stateGlobal_,
+            topGlobal_,
+            &ems,
+            top_,
+            nrnb_,
+            fr_,
+            mdAtoms_,
+            &gstat,
+            virtualSites_,
+            constr_,
+            nullptr);
+    const bool        simulationsShareState = false;
+    gmx_mdoutf*       outf                  = init_mdoutf(fpLog_,
+                                   nFile_,
+                                   fnm_,
+                                   mdrunOptions_,
+                                   cr_,
+                                   outputProvider_,
+                                   mdModulesNotifiers_,
+                                   inputRec_,
+                                   topGlobal_,
+                                   nullptr,
+                                   wallCycleCounters_,
+                                   StartingBehavior::NewSimulation,
+                                   simulationsShareState,
+                                   ms_);
+    gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
+                                   topGlobal_,
+                                   *inputRec_,
+                                   pullWork_,
+                                   nullptr,
+                                   false,
+                                   StartingBehavior::NewSimulation,
+                                   simulationsShareState,
+                                   mdModulesNotifiers_);
+
+    const int start = 0;
+    const int end   = mdatoms->homenr;
+
+    /* We need 4 working states */
+    em_state_t  s0{}, s1{}, s2{}, s3{};
+    em_state_t* sa   = &s0;
+    em_state_t* sb   = &s1;
+    em_state_t* sc   = &s2;
+    em_state_t* last = &s3;
+    /* Initialize by copying the state from ems (we could skip x and f here) */
+    *sa = ems;
+    *sb = ems;
+    *sc = ems;
+
+    /* Print to log file */
+    print_em_start(fpLog_, cr_, wallTimeAccounting_, wallCycleCounters_, LBFGS);
+
+    /* Max number of steps */
+    const int number_steps = inputRec_->nsteps;
+
+    /* Create a 3*natoms index to tell whether each degree of freedom is frozen */
+    std::vector<bool> frozen(n);
+    int               gf = 0;
+    for (int i = start; i < end; i++)
+    {
+        if (!mdatoms->cFREEZE.empty())
+        {
+            gf = mdatoms->cFREEZE[i];
+        }
+        for (int m = 0; m < DIM; m++)
+        {
+            frozen[3 * i + m] = (inputRec_->opts.nFreeze[gf][m] != 0);
+        }
+    }
+    if (MAIN(cr_))
+    {
+        sp_header(stderr, LBFGS, inputRec_->em_tol, number_steps);
+    }
+    if (fpLog_)
+    {
+        sp_header(fpLog_, LBFGS, inputRec_->em_tol, number_steps);
+    }
+
+    if (virtualSites_)
+    {
+        virtualSites_->construct(stateGlobal_->x, {}, stateGlobal_->box, VSiteOperation::Positions);
+    }
+
+    /* Call the force routine and some auxiliary (neighboursearching etc.) */
+    /* do_force always puts the charge groups in the box and shifts again
+     * We do not unshift, so molecules are always whole
+     */
+    neval++;
+    EnergyEvaluator energyEvaluator{ fpLog_,
+                                     mdLog_,
+                                     cr_,
+                                     ms_,
+                                     topGlobal_,
+                                     top_,
+                                     inputRec_,
+                                     mdModulesNotifiers_,
+                                     imdSession_,
+                                     pullWork_,
+                                     enforcedRotation_,
+                                     nrnb_,
+                                     wallCycleCounters_,
+                                     gstat,
+                                     &observablesReducer,
+                                     virtualSites_,
+                                     constr_,
+                                     mdAtoms_,
+                                     fr_,
+                                     runScheduleWork_,
+                                     enerd_,
+                                     -1,
+                                     {} };
+    rvec            mu_tot;
+    tensor          vir;
+    tensor          pres;
+    energyEvaluator.run(&ems, mu_tot, vir, pres, -1, TRUE, step);
+
+    if (MAIN(cr_))
+    {
+        /* Copy stuff to the energy bin for easy printing etc. */
+        matrix nullBox = {};
+        energyOutput.addDataAtEnergyStep(false,
+                                         false,
+                                         static_cast<double>(step),
+                                         mdatoms->tmass,
+                                         enerd_,
+                                         nullptr,
+                                         nullBox,
+                                         PTCouplingArrays(),
+                                         0,
+                                         vir,
+                                         pres,
+                                         nullptr,
+                                         mu_tot,
+                                         constr_);
+
+        EnergyOutput::printHeader(fpLog_, step, step);
+        energyOutput.printStepToEnergyFile(
+                mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fpLog_, step, step, fr_->fcdata.get(), nullptr);
+    }
+
+    /* Set the initial step.
+     * since it will be multiplied by the non-normalized search direction
+     * vector (force vector the first time), we scale it by the
+     * norm of the force.
+     */
+
+    if (MAIN(cr_))
+    {
+        double sqrtNumAtoms = sqrt(static_cast<double>(stateGlobal_->numAtoms()));
+        fprintf(stderr, "Using %d BFGS correction steps.\n\n", nmaxcorr);
+        fprintf(stderr, "   F-max             = %12.5e on atom %d\n", ems.fmax, ems.a_fmax + 1);
+        fprintf(stderr, "   F-Norm            = %12.5e\n", ems.fnorm / sqrtNumAtoms);
+        fprintf(stderr, "\n");
+        /* and copy to the log file too... */
+        fprintf(fpLog_, "Using %d BFGS correction steps.\n\n", nmaxcorr);
+        fprintf(fpLog_, "   F-max             = %12.5e on atom %d\n", ems.fmax, ems.a_fmax + 1);
+        fprintf(fpLog_, "   F-Norm            = %12.5e\n", ems.fnorm / sqrtNumAtoms);
+        fprintf(fpLog_, "\n");
+    }
+
+    // Point is an index to the memory of search directions, where 0 is the first one.
+    int point = 0;
+
+    // Set initial search direction to the force (-gradient), or 0 for frozen particles.
+    real* fInit = static_cast<real*>(ems.f.view().force().data()[0]);
+    for (int i = 0; i < n; i++)
+    {
+        if (!frozen[i])
+        {
+            dx[point][i] = fInit[i]; /* Initial search direction */
+        }
+        else
+        {
+            dx[point][i] = 0;
+        }
+    }
+
+    // Stepsize will be modified during the search, and actually it is not critical
+    // (the main efficiency in the algorithm comes from changing directions), but
+    // we still need an initial value, so estimate it as the inverse of the norm
+    // so we take small steps where the potential fluctuates a lot.
+    double stepsize = 1.0 / ems.fnorm;
+
+    /* Start the loop over BFGS steps.
+     * Each successful step is counted, and we continue until
+     * we either converge or reach the max number of steps.
+     */
+
+    bool do_log = true;
+    bool do_ene = true;
+
+    int ncorr = 0;
+
+    /* Set the gradient from the force */
+    bool converged = false;
+    for (int step = 0; (number_steps < 0 || step <= number_steps) && !converged; step++)
+    {
+
+        /* Write coordinates if necessary */
+        const bool do_x = do_per_step(step, inputRec_->nstxout);
+        const bool do_f = do_per_step(step, inputRec_->nstfout);
+
+        int mdof_flags = 0;
+        if (do_x)
+        {
+            mdof_flags |= MDOF_X;
+        }
+
+        if (do_f)
+        {
+            mdof_flags |= MDOF_F;
+        }
+
+        if (inputRec_->bIMD)
+        {
+            mdof_flags |= MDOF_IMD;
+        }
+
+        gmx::WriteCheckpointDataHolder checkpointDataHolder;
+        mdoutf_write_to_trajectory_files(fpLog_,
+                                         cr_,
+                                         outf,
+                                         mdof_flags,
+                                         topGlobal_.natoms,
+                                         step,
+                                         static_cast<real>(step),
+                                         &ems.s,
+                                         stateGlobal_,
+                                         observablesHistory_,
+                                         ems.f.view().force(),
+                                         &checkpointDataHolder);
+
+        /* Do the linesearching in the direction dx[point][0..(n-1)] */
+
+        /* make s a pointer to current search direction - point=0 first time we get here */
+        gmx::ArrayRef<const real> s = dx[point];
+
+        const real* xx = static_cast<real*>(ems.s.x.rvec_array()[0]);
+        const real* ff = static_cast<real*>(ems.f.view().force().data()[0]);
+
+        // calculate line gradient in position A
+        double gpa = 0;
+        for (int i = 0; i < n; i++)
+        {
+            gpa -= s[i] * ff[i];
+        }
+
+        /* Calculate minimum allowed stepsize along the line, before the average (norm)
+         * relative change in coordinate is smaller than precision
+         */
+        double minstep = 0;
+        for (int i = 0; i < n; i++)
+        {
+            double tmp = fabs(xx[i]);
+            if (tmp < 1.0)
+            {
+                tmp = 1.0;
+            }
+            tmp = s[i] / tmp;
+            minstep += tmp * tmp;
+        }
+        minstep = GMX_REAL_EPS / sqrt(minstep / n);
+
+        if (stepsize < minstep)
+        {
+            converged = true;
+            break;
+        }
+
+        // Before taking any steps along the line, store the old position
+        *last            = ems;
+        real*      lastx = static_cast<real*>(last->s.x.data()[0]);
+        real*      lastf = static_cast<real*>(last->f.view().force().data()[0]);
+        const real Epot0 = ems.epot;
+
+        *sa = ems;
+
+        /* Take a step downhill.
+         * In theory, we should find the actual minimum of the function in this
+         * direction, somewhere along the line.
+         * That is quite possible, but it turns out to take 5-10 function evaluations
+         * for each line. However, we dont really need to find the exact minimum -
+         * it is much better to start a new BFGS step in a modified direction as soon
+         * as we are close to it. This will save a lot of energy evaluations.
+         *
+         * In practice, we just try to take a single step.
+         * If it worked (i.e. lowered the energy), we increase the stepsize but
+         * continue straight to the next BFGS step without trying to find any minimum,
+         * i.e. we change the search direction too. If the line was smooth, it is
+         * likely we are in a smooth region, and then it makes sense to take longer
+         * steps in the modified search direction too.
+         *
+         * If it didn't work (higher energy), there must be a minimum somewhere between
+         * the old position and the new one. Then we need to start by finding a lower
+         * value before we change search direction. Since the energy was apparently
+         * quite rough, we need to decrease the step size.
+         *
+         * Due to the finite numerical accuracy, it turns out that it is a good idea
+         * to accept a SMALL increase in energy, if the derivative is still downhill.
+         * This leads to lower final energies in the tests I've done. / Erik
+         */
+
+        // State "A" is the first position along the line.
+        // reference position along line is initially zero
+        real a = 0;
+
+        // Check stepsize first. We do not allow displacements
+        // larger than emstep.
+        //
+        real c;
+        real maxdelta;
+        do
+        {
+            // Pick a new position C by adding stepsize to A.
+            c = a + stepsize;
+
+            // Calculate what the largest change in any individual coordinate
+            // would be (translation along line * gradient along line)
+            maxdelta = 0;
+            for (int i = 0; i < n; i++)
+            {
+                real delta = c * s[i];
+                if (delta > maxdelta)
+                {
+                    maxdelta = delta;
+                }
+            }
+            // If any displacement is larger than the stepsize limit, reduce the step
+            if (maxdelta > inputRec_->em_stepsize)
+            {
+                stepsize *= 0.1;
+            }
+        } while (maxdelta > inputRec_->em_stepsize);
+
+        // Take a trial step and move the coordinate array xc[] to position C
+        real* xc = static_cast<real*>(sc->s.x.rvec_array()[0]);
+        for (int i = 0; i < n; i++)
+        {
+            xc[i] = lastx[i] + c * s[i];
+        }
+
+        neval++;
+        // Calculate energy for the trial step in position C
+        energyEvaluator.run(sc, mu_tot, vir, pres, step, FALSE, step);
+
+        // Calc line gradient in position C
+        real*  fc  = static_cast<real*>(sc->f.view().force()[0]);
+        double gpc = 0;
+        for (int i = 0; i < n; i++)
+        {
+            gpc -= s[i] * fc[i]; /* f is negative gradient, thus the sign */
+        }
+        /* Sum the gradient along the line across CPUs */
+        if (PAR(cr_))
+        {
+            gmx_sumd(1, &gpc, cr_);
+        }
+
+        // This is the max amount of increase in energy we tolerate.
+        // By allowing VERY small changes (close to numerical precision) we
+        // frequently find even better (lower) final energies.
+        double tmp = std::sqrt(GMX_REAL_EPS) * fabs(sa->epot);
+
+        // Accept the step if the energy is lower in the new position C (compared to A),
+        // or if it is not significantly higher and the line derivative is still negative.
+        bool foundlower = sc->epot < sa->epot || (gpc < 0 && sc->epot < (sa->epot + tmp));
+        // If true, great, we found a better energy. We no longer try to alter the
+        // stepsize, but simply accept this new better position. The we select a new
+        // search direction instead, which will be much more efficient than continuing
+        // to take smaller steps along a line. Set fnorm based on the new C position,
+        // which will be used to update the stepsize to 1/fnorm further down.
+
+        // If false, the energy is NOT lower in point C, i.e. it will be the same
+        // or higher than in point A. In this case it is pointless to move to point C,
+        // so we will have to do more iterations along the same line to find a smaller
+        // value in the interval [A=0.0,C].
+        // Here, A is still 0.0, but that will change when we do a search in the interval
+        // [0.0,C] below. That search we will do by interpolation or bisection rather
+        // than with the stepsize, so no need to modify it. For the next search direction
+        // it will be reset to 1/fnorm anyway.
+
+        double step_taken;
+        if (!foundlower)
+        {
+            // OK, if we didn't find a lower value we will have to locate one now - there must
+            // be one in the interval [a,c].
+            // The same thing is valid here, though: Don't spend dozens of iterations to find
+            // the line minimum. We try to interpolate based on the derivative at the endpoints,
+            // and only continue until we find a lower value. In most cases this means 1-2 iterations.
+            // I also have a safeguard for potentially really pathological functions so we never
+            // take more than 20 steps before we give up.
+            // If we already found a lower value we just skip this step and continue to the update.
+            real fnorm    = 0;
+            int  nminstep = 0;
+            do
+            {
+                // Select a new trial point B in the interval [A,C].
+                // If the derivatives at points a & c have different sign we interpolate to zero,
+                // otherwise just do a bisection since there might be multiple minima/maxima
+                // inside the interval.
+                real b;
+                if (gpa < 0 && gpc > 0)
+                {
+                    b = a + gpa * (a - c) / (gpc - gpa);
+                }
+                else
+                {
+                    b = 0.5 * (a + c);
+                }
+
+                /* safeguard if interpolation close to machine accuracy causes errors:
+                 * never go outside the interval
+                 */
+                if (b <= a || b >= c)
+                {
+                    b = 0.5 * (a + c);
+                }
+
+                // Take a trial step to point B
+                real* xb = static_cast<real*>(sb->s.x.rvec_array()[0]);
+                for (int i = 0; i < n; i++)
+                {
+                    xb[i] = lastx[i] + b * s[i];
+                }
+
+                neval++;
+                // Calculate energy for the trial step in point B
+                energyEvaluator.run(sb, mu_tot, vir, pres, step, FALSE, step);
+                fnorm = sb->fnorm;
+
+                // Calculate gradient in point B
+                real*  fb  = static_cast<real*>(sb->f.view().force()[0]);
+                double gpb = 0;
+                for (int i = 0; i < n; i++)
+                {
+                    gpb -= s[i] * fb[i]; /* f is negative gradient, thus the sign */
+                }
+                /* Sum the gradient along the line across CPUs */
+                if (PAR(cr_))
+                {
+                    gmx_sumd(1, &gpb, cr_);
+                }
+
+                // Keep one of the intervals [A,B] or [B,C] based on the value of the derivative
+                // at the new point B, and rename the endpoints of this new interval A and C.
+                if (gpb > 0)
+                {
+                    /* Replace c endpoint with b */
+                    c = b;
+                    /* copy state b to c */
+                    *sc = *sb;
+                }
+                else
+                {
+                    /* Replace a endpoint with b */
+                    a = b;
+                    /* copy state b to a */
+                    *sa = *sb;
+                }
+
+                /*
+                 * Stop search as soon as we find a value smaller than the endpoints,
+                 * or if the tolerance is below machine precision.
+                 * Never run more than 20 steps, no matter what.
+                 */
+                nminstep++;
+            } while ((sb->epot > sa->epot || sb->epot > sc->epot) && (nminstep < 20));
+
+            if (std::fabs(sb->epot - Epot0) < GMX_REAL_EPS || nminstep >= 20)
+            {
+                /* OK. We couldn't find a significantly lower energy.
+                 * If ncorr==0 this was steepest descent, and then we give up.
+                 * If not, reset memory to restart as steepest descent before quitting.
+                 */
+                if (ncorr == 0)
+                {
+                    /* Converged */
+                    converged = true;
+                    break;
+                }
+                else
+                {
+                    /* Reset memory */
+                    ncorr = 0;
+                    /* Search in gradient direction */
+                    for (int i = 0; i < n; i++)
+                    {
+                        dx[point][i] = ff[i];
+                    }
+                    /* Reset stepsize */
+                    stepsize = 1.0 / fnorm;
+                    continue;
+                }
+            }
+
+            /* Select min energy state of A & C, put the best in xx/ff/Epot
+             */
+            if (sc->epot < sa->epot)
+            {
+                /* Use state C */
+                ems        = *sc;
+                step_taken = c;
+            }
+            else
+            {
+                /* Use state A */
+                ems        = *sa;
+                step_taken = a;
+            }
+        }
+        else
+        {
+            /* found lower */
+            /* Use state C */
+            ems        = *sc;
+            step_taken = c;
+        }
+
+        /* Update the memory information, and calculate a new
+         * approximation of the inverse hessian
+         */
+
+        /* Have new data in Epot, xx, ff */
+        if (ncorr < nmaxcorr)
+        {
+            ncorr++;
+        }
+
+        for (int i = 0; i < n; i++)
+        {
+            dg[point][i] = lastf[i] - ff[i];
+            dx[point][i] *= step_taken;
+        }
+
+        real dgdg = 0;
+        real dgdx = 0;
+        for (int i = 0; i < n; i++)
+        {
+            dgdg += dg[point][i] * dg[point][i];
+            dgdx += dg[point][i] * dx[point][i];
+        }
+
+        const real diag = dgdx / dgdg;
+
+        rho[point] = 1.0 / dgdx;
+        point++;
+
+        if (point >= nmaxcorr)
+        {
+            point = 0;
+        }
+
+        /* Update */
+        for (int i = 0; i < n; i++)
+        {
+            p[i] = ff[i];
+        }
+
+        int cp = point;
+
+        /* Recursive update. First go back over the memory points */
+        for (int k = 0; k < ncorr; k++)
+        {
+            cp--;
+            if (cp < 0)
+            {
+                cp = ncorr - 1;
+            }
+
+            real sq = 0;
+            for (int i = 0; i < n; i++)
+            {
+                sq += dx[cp][i] * p[i];
+            }
+
+            alpha[cp] = rho[cp] * sq;
+
+            for (int i = 0; i < n; i++)
+            {
+                p[i] -= alpha[cp] * dg[cp][i];
+            }
+        }
+
+        for (int i = 0; i < n; i++)
+        {
+            p[i] *= diag;
+        }
+
+        /* And then go forward again */
+        for (int k = 0; k < ncorr; k++)
+        {
+            real yr = 0;
+            for (int i = 0; i < n; i++)
+            {
+                yr += p[i] * dg[cp][i];
+            }
+
+            real beta = rho[cp] * yr;
+            beta      = alpha[cp] - beta;
+
+            for (int i = 0; i < n; i++)
+            {
+                p[i] += beta * dx[cp][i];
+            }
+
+            cp++;
+            if (cp >= ncorr)
+            {
+                cp = 0;
+            }
+        }
+
+        for (int i = 0; i < n; i++)
+        {
+            if (!frozen[i])
+            {
+                dx[point][i] = p[i];
+            }
+            else
+            {
+                dx[point][i] = 0;
+            }
+        }
+
+        /* Print it if necessary */
+        if (MAIN(cr_))
+        {
+            if (mdrunOptions_.verbose)
+            {
+                double sqrtNumAtoms = sqrt(static_cast<double>(stateGlobal_->numAtoms()));
+                fprintf(stderr,
+                        "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
+                        step,
+                        ems.epot,
+                        ems.fnorm / sqrtNumAtoms,
+                        ems.fmax,
+                        ems.a_fmax + 1);
+                fflush(stderr);
+            }
+            /* Store the new (lower) energies */
+            matrix nullBox = {};
+            energyOutput.addDataAtEnergyStep(false,
+                                             false,
+                                             static_cast<double>(step),
+                                             mdatoms->tmass,
+                                             enerd_,
+                                             nullptr,
+                                             nullBox,
+                                             PTCouplingArrays(),
+                                             0,
+                                             vir,
+                                             pres,
+                                             nullptr,
+                                             mu_tot,
+                                             constr_);
+
+            do_log = do_per_step(step, inputRec_->nstlog);
+            do_ene = do_per_step(step, inputRec_->nstenergy);
+
+            imdSession_->fillEnergyRecord(step, TRUE);
+
+            if (do_log)
+            {
+                EnergyOutput::printHeader(fpLog_, step, step);
+            }
+            energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+                                               do_ene,
+                                               FALSE,
+                                               FALSE,
+                                               do_log ? fpLog_ : nullptr,
+                                               step,
+                                               step,
+                                               fr_->fcdata.get(),
+                                               nullptr);
+        }
+
+        /* Send x and E to IMD client, if bIMD is TRUE. */
+        if (imdSession_->run(step, TRUE, stateGlobal_->box, stateGlobal_->x, 0) && MAIN(cr_))
+        {
+            imdSession_->sendPositionsAndEnergies();
+        }
+
+        // Reset stepsize in we are doing more iterations
+        stepsize = 1.0;
+
+        /* Stop when the maximum force lies below tolerance.
+         * If we have reached machine precision, converged is already set to true.
+         */
+        converged = converged || (ems.fmax < inputRec_->em_tol);
+        observablesReducer.markAsReadyToReduce();
+    } /* End of the loop */
+
+    if (converged)
+    {
+        step--; /* we never took that last step in this case */
+    }
+    if (ems.fmax > inputRec_->em_tol)
+    {
+        if (MAIN(cr_))
+        {
+            warn_step(fpLog_, inputRec_->em_tol, ems.fmax, step - 1 == number_steps, FALSE);
+        }
+        converged = FALSE;
+    }
+
+    /* If we printed energy and/or logfile last step (which was the last step)
+     * we don't have to do it again, but otherwise print the final values.
+     */
+    if (!do_log) /* Write final value to log since we didn't do anythin last step */
+    {
+        EnergyOutput::printHeader(fpLog_, step, step);
+    }
+    if (!do_ene || !do_log) /* Write final energy file entries */
+    {
+        energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+                                           !do_ene,
+                                           FALSE,
+                                           FALSE,
+                                           !do_log ? fpLog_ : nullptr,
+                                           step,
+                                           step,
+                                           fr_->fcdata.get(),
+                                           nullptr);
+    }
+
+    /* Print some stuff... */
+    if (MAIN(cr_))
+    {
+        fprintf(stderr, "\nwriting lowest energy coordinates.\n");
+    }
+
+    /* IMPORTANT!
+     * For accurate normal mode calculation it is imperative that we
+     * store the last conformation into the full precision binary trajectory.
+     *
+     * However, we should only do it if we did NOT already write this step
+     * above (which we did if do_x or do_f was true).
+     */
+    const bool do_x = !do_per_step(step, inputRec_->nstxout);
+    const bool do_f = !do_per_step(step, inputRec_->nstfout);
+    write_em_traj(
+            fpLog_, cr_, outf, do_x, do_f, ftp2fn(efSTO, nFile_, fnm_), topGlobal_, inputRec_, step, &ems, stateGlobal_, observablesHistory_);
+
+    if (MAIN(cr_))
+    {
+        double sqrtNumAtoms = sqrt(static_cast<double>(stateGlobal_->numAtoms()));
+        print_converged(stderr, LBFGS, inputRec_->em_tol, step, converged, number_steps, &ems, sqrtNumAtoms);
+        print_converged(fpLog_, LBFGS, inputRec_->em_tol, step, converged, number_steps, &ems, sqrtNumAtoms);
+
+        fprintf(fpLog_, "\nPerformed %d energy evaluations in total.\n", neval);
+    }
+
+    finish_em(cr_, outf, wallTimeAccounting_, wallCycleCounters_);
+
+    /* To print the actual number of steps we needed somewhere */
+    walltime_accounting_set_nsteps_done(wallTimeAccounting_, step);
+}
+
+void LegacySimulator::do_steep()
+{
+    const char*       SD = "Steepest Descents";
+    gmx_global_stat_t gstat;
+    real              stepsize;
+    real              ustep;
+    gmx_bool          bDone, bAbort, do_x, do_f;
+    tensor            vir, pres;
+    rvec              mu_tot = { 0 };
+    int               nsteps;
+    int               count          = 0;
+    int               steps_accepted = 0;
+    auto*             mdatoms        = mdAtoms_->mdatoms();
+
+    GMX_LOG(mdLog_.info)
+            .asParagraph()
+            .appendText(
+                    "Note that activating steepest-descent energy minimization via the "
+                    "integrator .mdp option and the command gmx mdrun may "
+                    "be available in a different form in a future version of GROMACS, "
+                    "e.g. gmx minimize and an .mdp option.");
+
+    /* Create 2 states on the stack and extract pointers that we will swap */
+    em_state_t  s0{}, s1{};
+    em_state_t* s_min = &s0;
+    em_state_t* s_try = &s1;
+
+    ObservablesReducer observablesReducer = observablesReducerBuilder_->build();
+
+    /* Init em and store the local state in s_try */
+    init_em(fpLog_,
+            mdLog_,
+            SD,
+            cr_,
+            inputRec_,
+            mdModulesNotifiers_,
+            imdSession_,
+            pullWork_,
+            stateGlobal_,
+            topGlobal_,
+            s_try,
+            top_,
+            nrnb_,
+            fr_,
+            mdAtoms_,
+            &gstat,
+            virtualSites_,
+            constr_,
+            nullptr);
+    const bool        simulationsShareState = false;
+    gmx_mdoutf*       outf                  = init_mdoutf(fpLog_,
+                                   nFile_,
+                                   fnm_,
+                                   mdrunOptions_,
+                                   cr_,
+                                   outputProvider_,
+                                   mdModulesNotifiers_,
+                                   inputRec_,
+                                   topGlobal_,
+                                   nullptr,
+                                   wallCycleCounters_,
+                                   StartingBehavior::NewSimulation,
+                                   simulationsShareState,
+                                   ms_);
+    gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
+                                   topGlobal_,
+                                   *inputRec_,
+                                   pullWork_,
+                                   nullptr,
+                                   false,
+                                   StartingBehavior::NewSimulation,
+                                   simulationsShareState,
+                                   mdModulesNotifiers_);
+
+    /* Print to log file  */
+    print_em_start(fpLog_, cr_, wallTimeAccounting_, wallCycleCounters_, SD);
+
+    /* Set variables for stepsize (in nm). This is the largest
+     * step that we are going to make in any direction.
+     */
+    ustep    = inputRec_->em_stepsize;
+    stepsize = 0;
+
+    /* Max number of steps  */
+    nsteps = inputRec_->nsteps;
+
+    if (MAIN(cr_))
+    {
+        /* Print to the screen  */
+        sp_header(stderr, SD, inputRec_->em_tol, nsteps);
+    }
+    if (fpLog_)
+    {
+        sp_header(fpLog_, SD, inputRec_->em_tol, nsteps);
+    }
+    EnergyEvaluator energyEvaluator{ fpLog_,
+                                     mdLog_,
+                                     cr_,
+                                     ms_,
+                                     topGlobal_,
+                                     top_,
+                                     inputRec_,
+                                     mdModulesNotifiers_,
+                                     imdSession_,
+                                     pullWork_,
+                                     enforcedRotation_,
+                                     nrnb_,
+                                     wallCycleCounters_,
+                                     gstat,
+                                     &observablesReducer,
+                                     virtualSites_,
+                                     constr_,
+                                     mdAtoms_,
+                                     fr_,
+                                     runScheduleWork_,
+                                     enerd_,
+                                     -1,
+                                     {} };
+
+    /**** HERE STARTS THE LOOP ****
+     * count is the counter for the number of steps
+     * bDone will be TRUE when the minimization has converged
+     * bAbort will be TRUE when nsteps steps have been performed or when
+     * the stepsize becomes smaller than is reasonable for machine precision
+     */
+    count  = 0;
+    bDone  = FALSE;
+    bAbort = FALSE;
+    while (!bDone && !bAbort)
+    {
+        bAbort = (nsteps >= 0) && (count == nsteps);
+
+        /* set new coordinates, except for first step */
+        bool validStep = true;
+        if (count > 0)
+        {
+            validStep = do_em_step(
+                    cr_, inputRec_, mdatoms, s_min, stepsize, s_min->f.view().forceWithPadding(), s_try, constr_, count);
+        }
+
+        if (validStep)
+        {
+            energyEvaluator.run(s_try, mu_tot, vir, pres, count, count == 0, count);
+        }
+        else
+        {
+            // Signal constraint error during stepping with energy=inf
+            s_try->epot = std::numeric_limits<real>::infinity();
+        }
+
+        if (MAIN(cr_))
+        {
+            EnergyOutput::printHeader(fpLog_, count, count);
+        }
+
+        if (count == 0)
+        {
+            s_min->epot = s_try->epot;
+        }
+
+        /* Print it if necessary  */
+        if (MAIN(cr_))
+        {
+            if (mdrunOptions_.verbose)
+            {
+                fprintf(stderr,
+                        "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
+                        count,
+                        ustep,
+                        s_try->epot,
+                        s_try->fmax,
+                        s_try->a_fmax + 1,
+                        ((count == 0) || (s_try->epot < s_min->epot)) ? '\n' : '\r');
+                fflush(stderr);
+            }
+
+            if ((count == 0) || (s_try->epot < s_min->epot))
+            {
+                /* Store the new (lower) energies  */
+                matrix nullBox = {};
+                energyOutput.addDataAtEnergyStep(false,
+                                                 false,
+                                                 static_cast<double>(count),
+                                                 mdatoms->tmass,
+                                                 enerd_,
+                                                 nullptr,
+                                                 nullBox,
+                                                 PTCouplingArrays(),
+                                                 0,
+                                                 vir,
+                                                 pres,
+                                                 nullptr,
+                                                 mu_tot,
+                                                 constr_);
+
+                imdSession_->fillEnergyRecord(count, TRUE);
+
+                const bool do_dr = do_per_step(steps_accepted, inputRec_->nstdisreout);
+                const bool do_or = do_per_step(steps_accepted, inputRec_->nstorireout);
+                energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
+                                                   TRUE,
+                                                   do_dr,
+                                                   do_or,
+                                                   fpLog_,
+                                                   count,
+                                                   count,
+                                                   fr_->fcdata.get(),
+                                                   nullptr);
+                fflush(fpLog_);
+            }
+        }
+
+        /* Now if the new energy is smaller than the previous...
+         * or if this is the first step!
+         * or if we did random steps!
+         */
+
+        if ((count == 0) || (s_try->epot < s_min->epot))
+        {
+            steps_accepted++;
+
+            /* Test whether the convergence criterion is met...  */
+            bDone = (s_try->fmax < inputRec_->em_tol);
+
+            /* Copy the arrays for force, positions and energy  */
+            /* The 'Min' array always holds the coords and forces of the minimal
+               sampled energy  */
+            swap_em_state(&s_min, &s_try);
+            if (count > 0)
+            {
+                ustep *= 1.2;
+            }
+
+            /* Write to trn, if necessary */
+            do_x = do_per_step(steps_accepted, inputRec_->nstxout);
+            do_f = do_per_step(steps_accepted, inputRec_->nstfout);
+            write_em_traj(
+                    fpLog_, cr_, outf, do_x, do_f, nullptr, topGlobal_, inputRec_, count, s_min, stateGlobal_, observablesHistory_);
+        }
+        else
+        {
+            /* If energy is not smaller make the step smaller...  */
+            ustep *= 0.5;
+
+            if (haveDDAtomOrdering(*cr_) && s_min->s.ddp_count != cr_->dd->ddp_count)
+            {
+                /* Reload the old state */
+                em_dd_partition_system(fpLog_,
+                                       mdLog_,
+                                       count,
+                                       cr_,
+                                       topGlobal_,
+                                       inputRec_,
+                                       mdModulesNotifiers_,
+                                       imdSession_,
+                                       pullWork_,
+                                       s_min,
+                                       top_,
+                                       mdAtoms_,
+                                       fr_,
+                                       virtualSites_,
+                                       constr_,
+                                       nrnb_,
+                                       wallCycleCounters_);
+            }
+        }
+
+        // If the force is very small after finishing minimization,
+        // we risk dividing by zero when calculating the step size.
+        // So we check first if the minimization has stopped before
+        // trying to obtain a new step size.
+        if (!bDone)
+        {
+            /* Determine new step  */
+            stepsize = ustep / s_min->fmax;
+        }
+
+        /* Check if stepsize is too small, with 1 nm as a characteristic length */
+#if GMX_DOUBLE
+        if (count == nsteps || ustep < 1e-12)
+#else
+        if (count == nsteps || ustep < 1e-6)
+#endif
+        {
+            if (MAIN(cr_))
+            {
+                warn_step(fpLog_, inputRec_->em_tol, s_min->fmax, count == nsteps, constr_ != nullptr);
+            }
+            bAbort = TRUE;
+        }
+
+        /* Send IMD energies and positions, if bIMD is TRUE. */
+        if (imdSession_->run(count,
+                             TRUE,
+                             MAIN(cr_) ? stateGlobal_->box : nullptr,
+                             MAIN(cr_) ? stateGlobal_->x : gmx::ArrayRef<gmx::RVec>(),
+                             0)
+            && MAIN(cr_))
+        {
+            imdSession_->sendPositionsAndEnergies();
+        }
+
+        count++;
+        observablesReducer.markAsReadyToReduce();
+    } /* End of the loop  */
+
+    /* Print some data...  */
+    if (MAIN(cr_))
+    {
+        fprintf(stderr, "\nwriting lowest energy coordinates.\n");
+    }
+    write_em_traj(fpLog_,
+                  cr_,
+                  outf,
+                  TRUE,
+                  inputRec_->nstfout != 0,
+                  ftp2fn(efSTO, nFile_, fnm_),
+                  topGlobal_,
+                  inputRec_,
+                  count,
+                  s_min,
+                  stateGlobal_,
+                  observablesHistory_);
+
+    if (MAIN(cr_))
+    {
+        double sqrtNumAtoms = sqrt(static_cast<double>(stateGlobal_->numAtoms()));
+
+        print_converged(stderr, SD, inputRec_->em_tol, count, bDone, nsteps, s_min, sqrtNumAtoms);
+        print_converged(fpLog_, SD, inputRec_->em_tol, count, bDone, nsteps, s_min, sqrtNumAtoms);
+    }
+
+    finish_em(cr_, outf, wallTimeAccounting_, wallCycleCounters_);
+
+    walltime_accounting_set_nsteps_done(wallTimeAccounting_, count);
+}
+
+void LegacySimulator::do_nm()
+{
+    const char*         NM = "Normal Mode Analysis";
+    int                 nnodes;
+    gmx_global_stat_t   gstat;
+    tensor              vir, pres;
+    rvec                mu_tot = { 0 };
+    rvec*               dfdx;
+    gmx_bool            bSparse; /* use sparse matrix storage format */
+    size_t              sz;
+    gmx_sparsematrix_t* sparse_matrix = nullptr;
+    real*               full_matrix   = nullptr;
+
+    /* added with respect to mdrun */
+    int   row, col;
+    real  der_range = 10.0 * std::sqrt(GMX_REAL_EPS);
+    real  x_min;
+    bool  bIsMain = MAIN(cr_);
+    auto* mdatoms = mdAtoms_->mdatoms();
+
+    GMX_LOG(mdLog_.info)
+            .asParagraph()
+            .appendText(
+                    "Note that activating normal-mode analysis via the integrator "
+                    ".mdp option and the command gmx mdrun may "
+                    "be available in a different form in a future version of GROMACS, "
+                    "e.g. gmx normal-modes.");
+
+    if (constr_ != nullptr)
+    {
+        gmx_fatal(
+                FARGS,
+                "Constraints present with Normal Mode Analysis, this combination is not supported");
+    }
+
+    gmx_shellfc_t* shellfc;
+
+    em_state_t state_work{};
+
+    fr_->longRangeNonbondeds->updateAfterPartition(*mdAtoms_->mdatoms());
+    ObservablesReducer observablesReducer = observablesReducerBuilder_->build();
+
+    /* Init em and store the local state in state_minimum */
+    init_em(fpLog_,
+            mdLog_,
+            NM,
+            cr_,
+            inputRec_,
+            mdModulesNotifiers_,
+            imdSession_,
+            pullWork_,
+            stateGlobal_,
+            topGlobal_,
+            &state_work,
+            top_,
+            nrnb_,
+            fr_,
+            mdAtoms_,
+            &gstat,
+            virtualSites_,
+            constr_,
+            &shellfc);
+    const bool  simulationsShareState = false;
+    gmx_mdoutf* outf                  = init_mdoutf(fpLog_,
+                                   nFile_,
+                                   fnm_,
+                                   mdrunOptions_,
+                                   cr_,
+                                   outputProvider_,
+                                   mdModulesNotifiers_,
+                                   inputRec_,
+                                   topGlobal_,
+                                   nullptr,
+                                   wallCycleCounters_,
+                                   StartingBehavior::NewSimulation,
+                                   simulationsShareState,
+                                   ms_);
+
+    std::vector<int>       atom_index = get_atom_index(topGlobal_);
+    std::vector<gmx::RVec> fneg(atom_index.size(), { 0, 0, 0 });
+    snew(dfdx, atom_index.size());
+
+#if !GMX_DOUBLE
+    if (bIsMain)
+    {
+        fprintf(stderr,
+                "NOTE: This version of GROMACS has been compiled in single precision,\n"
+                "      which MIGHT not be accurate enough for normal mode analysis.\n"
+                "      GROMACS now uses sparse matrix storage, so the memory requirements\n"
+                "      are fairly modest even if you recompile in double precision.\n\n");
+    }
+#endif
+
+    /* Check if we can/should use sparse storage format.
+     *
+     * Sparse format is only useful when the Hessian itself is sparse, which it
+     * will be when we use a cutoff.
+     * For small systems (n<1000) it is easier to always use full matrix format, though.
+     */
+    if (usingFullElectrostatics(fr_->ic->eeltype) || fr_->rlist == 0.0)
+    {
+        GMX_LOG(mdLog_.warning)
+                .appendText("Non-cutoff electrostatics used, forcing full Hessian format.");
+        bSparse = FALSE;
+    }
+    else if (atom_index.size() < 1000)
+    {
+        GMX_LOG(mdLog_.warning)
+                .appendTextFormatted("Small system size (N=%zu), using full Hessian format.",
+                                     atom_index.size());
+        bSparse = FALSE;
+    }
+    else
+    {
+        GMX_LOG(mdLog_.warning).appendText("Using compressed symmetric sparse Hessian format.");
+        bSparse = TRUE;
+    }
+
+    /* Number of dimensions, based on real atoms, that is not vsites or shell */
+    sz = DIM * atom_index.size();
+
+    fprintf(stderr, "Allocating Hessian memory...\n\n");
+
+    if (bSparse)
+    {
+        sparse_matrix                       = gmx_sparsematrix_init(sz);
+        sparse_matrix->compressed_symmetric = TRUE;
+    }
+    else
+    {
+        snew(full_matrix, sz * sz);
+    }
+
+    /* Write start time and temperature */
+    print_em_start(fpLog_, cr_, wallTimeAccounting_, wallCycleCounters_, NM);
+
+    const int64_t numSteps = atom_index.size() * 2;
+    if (bIsMain)
+    {
+        fprintf(stderr,
+                "starting normal mode calculation '%s'\n%" PRId64 " steps.\n\n",
+                *(topGlobal_.name),
+                numSteps);
+    }
+
+    nnodes = cr_->nnodes;
+
+    /* Make evaluate_energy do a single node force calculation */
+    cr_->nnodes = 1;
+    EnergyEvaluator energyEvaluator{ fpLog_,
+                                     mdLog_,
+                                     cr_,
+                                     ms_,
+                                     topGlobal_,
+                                     top_,
+                                     inputRec_,
+                                     mdModulesNotifiers_,
+                                     imdSession_,
+                                     pullWork_,
+                                     enforcedRotation_,
+                                     nrnb_,
+                                     wallCycleCounters_,
+                                     gstat,
+                                     &observablesReducer,
+                                     virtualSites_,
+                                     constr_,
+                                     mdAtoms_,
+                                     fr_,
+                                     runScheduleWork_,
+                                     enerd_,
+                                     -1,
+                                     {} };
+    energyEvaluator.run(&state_work, mu_tot, vir, pres, -1, TRUE, 0);
+    cr_->nnodes = nnodes;
+
+    /* if forces are not small, warn user */
+    get_state_f_norm_max(cr_, &(inputRec_->opts), mdatoms, &state_work);
+
+    GMX_LOG(mdLog_.warning).appendTextFormatted("Maximum force:%12.5e", state_work.fmax);
+    if (state_work.fmax > 1.0e-3)
+    {
+        GMX_LOG(mdLog_.warning)
+                .appendText(
+                        "The force is probably not small enough to "
+                        "ensure that you are at a minimum.\n"
+                        "Be aware that negative eigenvalues may occur\n"
+                        "when the resulting matrix is diagonalized.");
+    }
+
+    /***********************************************************
+     *
+     *      Loop over all pairs in matrix
+     *
+     *      do_force called twice. Once with positive and
+     *      once with negative displacement
+     *
+     ************************************************************/
+
+    /* Steps are divided one by one over the nodes */
+    bool bNS          = true;
+    auto state_work_x = makeArrayRef(state_work.s.x);
+    auto state_work_f = state_work.f.view().force();
+    for (Index aid = cr_->nodeid; aid < ssize(atom_index); aid += nnodes)
+    {
+        size_t atom = atom_index[aid];
+        for (size_t d = 0; d < DIM; d++)
+        {
+            int64_t step = 0;
+            double  t    = 0;
+
+            x_min = state_work_x[atom][d];
+
+            for (unsigned int dx = 0; (dx < 2); dx++)
+            {
+                if (dx == 0)
+                {
+                    state_work_x[atom][d] = x_min - der_range;
+                }
+                else
+                {
+                    state_work_x[atom][d] = x_min + der_range;
+                }
+
+                /* Make evaluate_energy do a single node force calculation */
+                cr_->nnodes = 1;
+                if (shellfc)
+                {
+                    /* Now is the time to relax the shells */
+                    relax_shell_flexcon(fpLog_,
+                                        cr_,
+                                        ms_,
+                                        mdrunOptions_.verbose,
+                                        nullptr,
+                                        step,
+                                        inputRec_,
+                                        mdModulesNotifiers_,
+                                        imdSession_,
+                                        pullWork_,
+                                        bNS,
+                                        top_,
+                                        constr_,
+                                        enerd_,
+                                        state_work.s.numAtoms(),
+                                        state_work.s.x.arrayRefWithPadding(),
+                                        state_work.s.v.arrayRefWithPadding(),
+                                        state_work.s.box,
+                                        state_work.s.lambda,
+                                        &state_work.s.hist,
+                                        &state_work.f.view(),
+                                        vir,
+                                        *mdatoms,
+                                        fr_->longRangeNonbondeds.get(),
+                                        nrnb_,
+                                        wallCycleCounters_,
+                                        shellfc,
+                                        fr_,
+                                        *runScheduleWork_,
+                                        t,
+                                        mu_tot,
+                                        virtualSites_,
+                                        DDBalanceRegionHandler(nullptr));
+                    bNS = false;
+                    step++;
+                }
+                else
+                {
+                    energyEvaluator.run(&state_work, mu_tot, vir, pres, aid * 2 + dx, FALSE, step);
+                }
+
+                cr_->nnodes = nnodes;
+
+                if (dx == 0)
+                {
+                    std::copy(state_work_f.begin(), state_work_f.begin() + atom_index.size(), fneg.begin());
+                }
+            }
+
+            /* x is restored to original */
+            state_work_x[atom][d] = x_min;
+
+            for (size_t j = 0; j < atom_index.size(); j++)
+            {
+                for (size_t k = 0; (k < DIM); k++)
+                {
+                    dfdx[j][k] = -(state_work_f[atom_index[j]][k] - fneg[j][k]) / (2 * der_range);
+                }
+            }
+
+            if (!bIsMain)
+            {
+#if GMX_MPI
+#    define mpi_type GMX_MPI_REAL
+                MPI_Send(dfdx[0], atom_index.size() * DIM, mpi_type, MAIN(cr_), cr_->nodeid, cr_->mpi_comm_mygroup);
+#endif
+            }
+            else
+            {
+                for (Index node = 0; (node < nnodes && aid + node < ssize(atom_index)); node++)
+                {
+                    if (node > 0)
+                    {
+#if GMX_MPI
+                        MPI_Status stat;
+                        MPI_Recv(dfdx[0], atom_index.size() * DIM, mpi_type, node, node, cr_->mpi_comm_mygroup, &stat);
+#    undef mpi_type
+#endif
+                    }
+
+                    row = (aid + node) * DIM + d;
+
+                    for (size_t j = 0; j < atom_index.size(); j++)
+                    {
+                        for (size_t k = 0; k < DIM; k++)
+                        {
+                            col = j * DIM + k;
+
+                            if (bSparse)
+                            {
+                                if (col >= row && dfdx[j][k] != 0.0)
+                                {
+                                    gmx_sparsematrix_increment_value(sparse_matrix, row, col, dfdx[j][k]);
+                                }
+                            }
+                            else
+                            {
+                                full_matrix[row * sz + col] = dfdx[j][k];
+                            }
+                        }
+                    }
+                }
+            }
+
+            if (mdrunOptions_.verbose && fpLog_)
+            {
+                fflush(fpLog_);
+            }
+        }
+        /* write progress */
+        if (bIsMain && mdrunOptions_.verbose)
+        {
+            fprintf(stderr,
+                    "\rFinished step %d out of %td",
+                    std::min<int>(atom + nnodes, atom_index.size()),
+                    ssize(atom_index));
+            fflush(stderr);
+        }
+    }
+
+    if (bIsMain)
+    {
+        fprintf(stderr, "\n\nWriting Hessian...\n");
+        gmx_mtxio_write(ftp2fn(efMTX, nFile_, fnm_), sz, sz, full_matrix, sparse_matrix);
+    }
+
+    finish_em(cr_, outf, wallTimeAccounting_, wallCycleCounters_);
+
+    walltime_accounting_set_nsteps_done(wallTimeAccounting_, numSteps);
+}
+
+} // namespace gmx