hillclimber 0.1.6__cp314-cp314t-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl

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

@@ -0,0 +1,1506 @@
+/*
+ * 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 Implements the replica exchange routines.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_mdrun
+ */
+#include "gmxpre.h"
+
+#include "gromacs/utility/enumerationhelpers.h"
+#include "replicaexchange.h"
+
+#include "config.h"
+
+#include <cmath>
+
+#include <random>
+
+#include "gromacs/domdec/collect.h"
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdrunutility/multisim.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/enerdata.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
+#include "gromacs/random/threefry.h"
+#include "gromacs/random/uniformintdistribution.h"
+#include "gromacs/random/uniformrealdistribution.h"
+#include "gromacs/utility/enumerationhelpers.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/pleasecite.h"
+#include "gromacs/utility/smalloc.h"
+
+
+/* PLUMED */
+#include "../../../Plumed.h"
+extern int    plumedswitch;
+extern plumed plumedmain;
+/* END PLUMED */
+
+/* PLUMED HREX */
+extern int plumed_hrex;
+/* END PLUMED HREX */
+
+//! Helps cut off probability values.
+constexpr int c_probabilityCutoff = 100;
+
+/* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
+
+//! Rank in the multisimulation
+#define MSRANK(ms, nodeid) (nodeid)
+
+//! Enum for replica exchange flavours
+enum class ReplicaExchangeType : int
+{
+    Temperature,
+    Lambda,
+    EndSingle,
+    TemperatureLambda,
+    Count
+};
+/*! \brief Strings describing replica exchange flavours.
+ *
+ *  end_single_marker merely notes the end of single variable replica
+ *  exchange. All types higher than it are multiple replica exchange
+ *  methods.
+ *
+ * Eventually, should add 'pressure', 'temperature and pressure',
+ *  'lambda_and_pressure', 'temperature_lambda_pressure'?; Let's wait
+ *  until we feel better about the pressure control methods giving
+ *  exact ensembles.  Right now, we assume constant pressure */
+static const char* enumValueToString(ReplicaExchangeType enumValue)
+{
+    constexpr gmx::EnumerationArray<ReplicaExchangeType, const char*> replicateExchangeTypeNames = {
+        "temperature", "lambda", "end_single_marker", "temperature and lambda"
+    };
+    return replicateExchangeTypeNames[enumValue];
+}
+
+//! Working data for replica exchange.
+struct gmx_repl_ex
+{
+    //! Replica ID
+    int repl;
+    //! Total number of replica
+    int nrepl;
+    //! Temperature
+    real temp;
+    //! Replica exchange type from ReplicaExchangeType enum
+    ReplicaExchangeType type;
+    //! Quantity, e.g. temperature or lambda; first index is ere, second index is replica ID
+    gmx::EnumerationArray<ReplicaExchangeType, real*> q;
+    //! Use constant pressure and temperature
+    gmx_bool bNPT;
+    //! Replica pressures
+    real* pres;
+    //! Replica indices
+    int* ind;
+    //! Used for keeping track of all the replica swaps
+    int* allswaps;
+    //! Replica exchange interval (number of steps)
+    int nst;
+    //! Number of exchanges per interval
+    int nex;
+    //! Random seed
+    int seed;
+    //! Number of even and odd replica change attempts
+    int nattempt[2];
+    //! Sum of probabilities
+    real* prob_sum;
+    //! Number of moves between replicas i and j
+    int** nmoves;
+    //! i-th element of the array is the number of exchanges between replica i-1 and i
+    int* nexchange;
+
+    /*! \brief Helper arrays for replica exchange; allocated here
+     * so they don't have to be allocated each time */
+    //! \{
+    int*      destinations;
+    int**     cyclic;
+    int**     order;
+    int*      tmpswap;
+    gmx_bool* incycle;
+    gmx_bool* bEx;
+    //! \}
+
+    //! Helper arrays to hold the quantities that are exchanged.
+    //! \{
+    real*  prob;
+    real*  Epot;
+    real*  beta;
+    real*  Vol;
+    real** de;
+    //! \}
+};
+
+// TODO We should add Doxygen here some time.
+//! \cond
+
+static gmx_bool repl_quantity(const gmx_multisim_t* ms, struct gmx_repl_ex* re, ReplicaExchangeType ere, real q)
+{
+    real*    qall;
+    gmx_bool bDiff;
+    int      s;
+
+    snew(qall, ms->numSimulations_);
+    qall[re->repl] = q;
+    gmx_sum_sim(ms->numSimulations_, qall, ms);
+
+    /* PLUMED */
+    //bDiff = FALSE;
+    //for (s = 1; s < ms->numSimulations_; s++)
+    //{
+    //    if (fabs(qall[s] - qall[0]) > 1e-5) /* Each quantity normally has 2-4 significant digits */
+    //    {
+            bDiff = TRUE;
+    //    }
+    //}
+    /* PLUMED */
+
+    if (bDiff)
+    {
+        /* Set the replica exchange type and quantities */
+        re->type = ere;
+
+        snew(re->q[ere], re->nrepl);
+        for (s = 0; s < ms->numSimulations_; s++)
+        {
+            re->q[ere][s] = qall[s];
+        }
+    }
+    sfree(qall);
+    return bDiff;
+}
+
+gmx_repl_ex_t init_replica_exchange(FILE*                            fplog,
+                                    const gmx_multisim_t*            ms,
+                                    int                              numAtomsInSystem,
+                                    const t_inputrec*                ir,
+                                    const ReplicaExchangeParameters& replExParams)
+{
+    real                pres;
+    int                 i, j;
+    struct gmx_repl_ex* re;
+    gmx_bool            bTemp;
+    gmx_bool            bLambda = FALSE;
+
+    fprintf(fplog, "\nInitializing Replica Exchange\n");
+
+    if (!isMultiSim(ms) || ms->numSimulations_ == 1)
+    {
+        gmx_fatal(FARGS,
+                  "Nothing to exchange with only one replica, maybe you forgot to set the "
+                  "-multidir option of mdrun?");
+    }
+    if (replExParams.numExchanges < 0)
+    {
+        gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
+    }
+
+    if (!EI_DYNAMICS(ir->eI))
+    {
+        gmx_fatal(FARGS, "Replica exchange is only supported by dynamical simulations");
+        /* Note that PAR(cr) is defined by cr->nnodes > 1, which is
+         * distinct from isMultiSim(ms). A multi-simulation only runs
+         * with real MPI parallelism, but this does not imply PAR(cr)
+         * is true!
+         *
+         * Since we are using a dynamical integrator, the only
+         * decomposition is DD, so PAR(cr) and haveDDAtomOrdering(*cr) are
+         * synonymous. The only way for cr->nnodes > 1 to be true is
+         * if we are using DD. */
+    }
+
+    snew(re, 1);
+
+    re->repl  = ms->simulationIndex_;
+    re->nrepl = ms->numSimulations_;
+
+    fprintf(fplog, "Repl  There are %d replicas:\n", re->nrepl);
+
+    /* We only check that the number of atoms in the systms match.
+     * This, of course, do not guarantee that the systems are the same,
+     * but it does guarantee that we can perform replica exchange.
+     */
+    check_multi_int(fplog, ms, numAtomsInSystem, "the number of atoms", FALSE);
+    check_multi_int(fplog, ms, static_cast<int>(ir->eI), "the integrator", FALSE);
+    check_multi_int64(fplog, ms, ir->init_step + ir->nsteps, "init_step+nsteps", FALSE);
+    const int nst = replExParams.exchangeInterval;
+    check_multi_int64(
+            fplog, ms, (ir->init_step + nst - 1) / nst, "first exchange step: init_step/-replex", FALSE);
+    check_multi_int(fplog, ms, static_cast<int>(ir->etc), "the temperature coupling", FALSE);
+    check_multi_int(fplog, ms, ir->opts.ngtc, "the number of temperature coupling groups", FALSE);
+    check_multi_int(fplog, ms, static_cast<int>(ir->epc), "the pressure coupling", FALSE);
+    check_multi_int(fplog, ms, static_cast<int>(ir->efep), "free energy", FALSE);
+    check_multi_int(fplog, ms, ir->fepvals->n_lambda, "number of lambda states", FALSE);
+
+    re->temp = ir->opts.ref_t[0];
+    for (i = 1; (i < ir->opts.ngtc); i++)
+    {
+        if (ir->opts.ref_t[i] != re->temp)
+        {
+            fprintf(fplog,
+                    "\nWARNING: The temperatures of the different temperature coupling groups are "
+                    "not identical\n\n");
+            fprintf(stderr,
+                    "\nWARNING: The temperatures of the different temperature coupling groups are "
+                    "not identical\n\n");
+        }
+    }
+
+    re->type = ReplicaExchangeType::Count;
+    bTemp    = repl_quantity(ms, re, ReplicaExchangeType::Temperature, re->temp);
+    if (ir->efep != FreeEnergyPerturbationType::No)
+    {
+        bLambda = repl_quantity(
+                ms, re, ReplicaExchangeType::Lambda, static_cast<real>(ir->fepvals->init_fep_state));
+    }
+    if (re->type == ReplicaExchangeType::Count) /* nothing was assigned */
+    {
+        gmx_fatal(FARGS,
+                  "The properties of the %d systems are all the same, there is nothing to exchange",
+                  re->nrepl);
+    }
+    if (bLambda && bTemp)
+    {
+        re->type = ReplicaExchangeType::TemperatureLambda;
+    }
+
+    if (bTemp)
+    {
+        please_cite(fplog, "Sugita1999a");
+        if (ir->epc != PressureCoupling::No)
+        {
+            re->bNPT = TRUE;
+            fprintf(fplog, "Repl  Using Constant Pressure REMD.\n");
+            please_cite(fplog, "Okabe2001a");
+        }
+        if (ir->etc == TemperatureCoupling::Berendsen)
+        {
+            gmx_fatal(FARGS,
+                      "REMD with the %s thermostat does not produce correct potential energy "
+                      "distributions, consider using the %s thermostat instead",
+                      enumValueToString(ir->etc),
+                      enumValueToString(TemperatureCoupling::VRescale));
+        }
+    }
+    if (bLambda)
+    {
+        if (ir->fepvals->delta_lambda != 0) /* check this? */
+        {
+            gmx_fatal(FARGS, "delta_lambda is not zero");
+        }
+    }
+    if (re->bNPT)
+    {
+        snew(re->pres, re->nrepl);
+        if (ir->epct == PressureCouplingType::SurfaceTension)
+        {
+            pres = ir->ref_p[ZZ][ZZ];
+        }
+        else
+        {
+            pres = 0;
+            j    = 0;
+            for (i = 0; i < DIM; i++)
+            {
+                if (ir->compress[i][i] != 0)
+                {
+                    pres += ir->ref_p[i][i];
+                    j++;
+                }
+            }
+            pres /= j;
+        }
+        re->pres[re->repl] = pres;
+        gmx_sum_sim(re->nrepl, re->pres, ms);
+    }
+
+    /* Make an index for increasing replica order */
+    /* only makes sense if one or the other is varying, not both!
+       if both are varying, we trust the order the person gave. */
+    snew(re->ind, re->nrepl);
+    for (i = 0; i < re->nrepl; i++)
+    {
+        re->ind[i] = i;
+    }
+
+    /* PLUMED */
+    // plumed2: check if we want alternative patterns (i.e. for bias-exchange metaD)
+    // in those cases replicas can share the same temperature.
+    /*
+    if (re->type < ReplicaExchangeType::EndSingle)
+    {
+
+        for (i = 0; i < re->nrepl; i++)
+        {
+            for (j = i + 1; j < re->nrepl; j++)
+            {
+                if (re->q[re->type][re->ind[j]] < re->q[re->type][re->ind[i]])
+                {*/
+                    /* Unordered replicas are supposed to work, but there
+                     * is still an issues somewhere.
+                     * Note that at this point still re->ind[i]=i.
+                     */
+                 /*
+                    gmx_fatal(FARGS,
+                              "Replicas with indices %d < %d have %ss %g > %g, please order your "
+                              "replicas on increasing %s",
+                              i,
+                              j,
+                              enumValueToString(re->type),
+                              re->q[re->type][i],
+                              re->q[re->type][j],
+                              enumValueToString(re->type));
+                }
+                else if (re->q[re->type][re->ind[j]] == re->q[re->type][re->ind[i]])
+                {
+                    gmx_fatal(FARGS, "Two replicas have identical %ss", enumValueToString(re->type));
+                }
+            }
+        }
+    }
+    */
+    /* END PLUMED */
+
+    /* keep track of all the swaps, starting with the initial placement. */
+    snew(re->allswaps, re->nrepl);
+    for (i = 0; i < re->nrepl; i++)
+    {
+        re->allswaps[i] = re->ind[i];
+    }
+
+    switch (re->type)
+    {
+        case ReplicaExchangeType::Temperature:
+            fprintf(fplog, "\nReplica exchange in temperature\n");
+            for (i = 0; i < re->nrepl; i++)
+            {
+                fprintf(fplog, " %5.1f", re->q[re->type][re->ind[i]]);
+            }
+            fprintf(fplog, "\n");
+            break;
+        case ReplicaExchangeType::Lambda:
+            fprintf(fplog, "\nReplica exchange in lambda\n");
+            for (i = 0; i < re->nrepl; i++)
+            {
+                fprintf(fplog, " %3d", static_cast<int>(re->q[re->type][re->ind[i]]));
+            }
+            fprintf(fplog, "\n");
+            break;
+        case ReplicaExchangeType::TemperatureLambda:
+            fprintf(fplog, "\nReplica exchange in temperature and lambda state\n");
+            for (i = 0; i < re->nrepl; i++)
+            {
+                fprintf(fplog, " %5.1f", re->q[ReplicaExchangeType::Temperature][re->ind[i]]);
+            }
+            fprintf(fplog, "\n");
+            for (i = 0; i < re->nrepl; i++)
+            {
+                fprintf(fplog, " %5d", static_cast<int>(re->q[ReplicaExchangeType::Lambda][re->ind[i]]));
+            }
+            fprintf(fplog, "\n");
+            break;
+        default: gmx_incons("Unknown replica exchange quantity");
+    }
+    if (re->bNPT)
+    {
+        fprintf(fplog, "\nRepl  p");
+        for (i = 0; i < re->nrepl; i++)
+        {
+            fprintf(fplog, " %5.2f", re->pres[re->ind[i]]);
+        }
+
+        for (i = 0; i < re->nrepl; i++)
+        {
+            if ((i > 0) && (re->pres[re->ind[i]] < re->pres[re->ind[i - 1]]))
+            {
+                fprintf(fplog,
+                        "\nWARNING: The reference pressures decrease with increasing "
+                        "temperatures\n\n");
+                fprintf(stderr,
+                        "\nWARNING: The reference pressures decrease with increasing "
+                        "temperatures\n\n");
+            }
+        }
+    }
+    re->nst = nst;
+    if (replExParams.randomSeed == -1)
+    {
+        if (isMasterSim(ms))
+        {
+            re->seed = static_cast<int>(gmx::makeRandomSeed());
+        }
+        else
+        {
+            re->seed = 0;
+        }
+        gmx_sumi_sim(1, &(re->seed), ms);
+    }
+    else
+    {
+        re->seed = replExParams.randomSeed;
+    }
+    fprintf(fplog, "\nReplica exchange interval: %d\n", re->nst);
+    fprintf(fplog, "\nReplica random seed: %d\n", re->seed);
+
+    re->nattempt[0] = 0;
+    re->nattempt[1] = 0;
+
+    snew(re->prob_sum, re->nrepl);
+    snew(re->nexchange, re->nrepl);
+    snew(re->nmoves, re->nrepl);
+    for (i = 0; i < re->nrepl; i++)
+    {
+        snew(re->nmoves[i], re->nrepl);
+    }
+    fprintf(fplog, "Replica exchange information below: ex and x = exchange, pr = probability\n");
+
+    /* generate space for the helper functions so we don't have to snew each time */
+
+    snew(re->destinations, re->nrepl);
+    snew(re->incycle, re->nrepl);
+    snew(re->tmpswap, re->nrepl);
+    snew(re->cyclic, re->nrepl);
+    snew(re->order, re->nrepl);
+    for (i = 0; i < re->nrepl; i++)
+    {
+        snew(re->cyclic[i], re->nrepl + 1);
+        snew(re->order[i], re->nrepl);
+    }
+    /* allocate space for the functions storing the data for the replicas */
+    /* not all of these arrays needed in all cases, but they don't take
+       up much space, since the max size is nrepl**2 */
+    snew(re->prob, re->nrepl);
+    snew(re->bEx, re->nrepl);
+    snew(re->beta, re->nrepl);
+    snew(re->Vol, re->nrepl);
+    snew(re->Epot, re->nrepl);
+    snew(re->de, re->nrepl);
+    for (i = 0; i < re->nrepl; i++)
+    {
+        snew(re->de[i], re->nrepl);
+    }
+    re->nex = replExParams.numExchanges;
+    return re;
+}
+
+static void exchange_reals(const gmx_multisim_t gmx_unused* ms, int gmx_unused b, real* v, int n)
+{
+    real* buf;
+    int   i;
+
+    if (v)
+    {
+        snew(buf, n);
+#if GMX_MPI
+        /*
+           MPI_Sendrecv(v,  n*sizeof(real),MPI_BYTE,MSRANK(ms,b),0,
+           buf,n*sizeof(real),MPI_BYTE,MSRANK(ms,b),0,
+           ms->mastersComm_,MPI_STATUS_IGNORE);
+         */
+        {
+            MPI_Request mpi_req;
+
+            MPI_Isend(v, n * sizeof(real), MPI_BYTE, MSRANK(ms, b), 0, ms->mastersComm_, &mpi_req);
+            MPI_Recv(buf, n * sizeof(real), MPI_BYTE, MSRANK(ms, b), 0, ms->mastersComm_, MPI_STATUS_IGNORE);
+            MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+        }
+#endif
+        for (i = 0; i < n; i++)
+        {
+            v[i] = buf[i];
+        }
+        sfree(buf);
+    }
+}
+
+
+static void exchange_doubles(const gmx_multisim_t gmx_unused* ms, int gmx_unused b, double* v, int n)
+{
+    double* buf;
+    int     i;
+
+    if (v)
+    {
+        snew(buf, n);
+#if GMX_MPI
+        /*
+           MPI_Sendrecv(v,  n*sizeof(double),MPI_BYTE,MSRANK(ms,b),0,
+           buf,n*sizeof(double),MPI_BYTE,MSRANK(ms,b),0,
+           ms->mastersComm_,MPI_STATUS_IGNORE);
+         */
+        {
+            MPI_Request mpi_req;
+
+            MPI_Isend(v, n * sizeof(double), MPI_BYTE, MSRANK(ms, b), 0, ms->mastersComm_, &mpi_req);
+            MPI_Recv(buf, n * sizeof(double), MPI_BYTE, MSRANK(ms, b), 0, ms->mastersComm_, MPI_STATUS_IGNORE);
+            MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+        }
+#endif
+        for (i = 0; i < n; i++)
+        {
+            v[i] = buf[i];
+        }
+        sfree(buf);
+    }
+}
+
+static void exchange_rvecs(const gmx_multisim_t gmx_unused* ms, int gmx_unused b, rvec* v, int n)
+{
+    rvec* buf;
+    int   i;
+
+    if (v)
+    {
+        snew(buf, n);
+#if GMX_MPI
+        /*
+           MPI_Sendrecv(v[0],  n*sizeof(rvec),MPI_BYTE,MSRANK(ms,b),0,
+           buf[0],n*sizeof(rvec),MPI_BYTE,MSRANK(ms,b),0,
+           ms->mastersComm_,MPI_STATUS_IGNORE);
+         */
+        {
+            MPI_Request mpi_req;
+
+            MPI_Isend(v[0], n * sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0, ms->mastersComm_, &mpi_req);
+            MPI_Recv(buf[0], n * sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0, ms->mastersComm_, MPI_STATUS_IGNORE);
+            MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
+        }
+#endif
+        for (i = 0; i < n; i++)
+        {
+            copy_rvec(buf[i], v[i]);
+        }
+        sfree(buf);
+    }
+}
+
+/* PLUMED HREX */
+void exchange_state(const gmx_multisim_t* ms, int b, t_state* state)
+/* END PLUMED HREX */
+{
+    /* When t_state changes, this code should be updated. */
+    int ngtc, nnhpres;
+    ngtc    = state->ngtc * state->nhchainlength;
+    nnhpres = state->nnhpres * state->nhchainlength;
+    exchange_rvecs(ms, b, state->box, DIM);
+    exchange_rvecs(ms, b, state->box_rel, DIM);
+    exchange_rvecs(ms, b, state->boxv, DIM);
+    exchange_reals(ms, b, &(state->veta), 1);
+    exchange_reals(ms, b, &(state->vol0), 1);
+    exchange_rvecs(ms, b, state->svir_prev, DIM);
+    exchange_rvecs(ms, b, state->fvir_prev, DIM);
+    exchange_rvecs(ms, b, state->pres_prev, DIM);
+    exchange_doubles(ms, b, state->nosehoover_xi.data(), ngtc);
+    exchange_doubles(ms, b, state->nosehoover_vxi.data(), ngtc);
+    exchange_doubles(ms, b, state->nhpres_xi.data(), nnhpres);
+    exchange_doubles(ms, b, state->nhpres_vxi.data(), nnhpres);
+    exchange_doubles(ms, b, state->therm_integral.data(), state->ngtc);
+    exchange_doubles(ms, b, &state->baros_integral, 1);
+    exchange_rvecs(ms, b, state->x.rvec_array(), state->natoms);
+    exchange_rvecs(ms, b, state->v.rvec_array(), state->natoms);
+}
+
+/* PLUMED HREX */
+void copy_state_serial(const t_state* src, t_state* dest)
+/* END PLUMED HREX */
+{
+    if (dest != src)
+    {
+        /* Currently the local state is always a pointer to the global
+         * in serial, so we should never end up here.
+         * TODO: Implement a (trivial) t_state copy once converted to C++.
+         */
+        GMX_RELEASE_ASSERT(false, "State copying is currently not implemented in replica exchange");
+    }
+}
+
+static void scale_velocities(gmx::ArrayRef<gmx::RVec> velocities, real fac)
+{
+    for (auto& v : velocities)
+    {
+        v *= fac;
+    }
+}
+
+static void print_transition_matrix(FILE* fplog, int n, int** nmoves, const int* nattempt)
+{
+    int   i, j, ntot;
+    float Tprint;
+
+    ntot = nattempt[0] + nattempt[1];
+    fprintf(fplog, "\n");
+    fprintf(fplog, "Repl");
+    for (i = 0; i < n; i++)
+    {
+        fprintf(fplog, "    "); /* put the title closer to the center */
+    }
+    fprintf(fplog, "Empirical Transition Matrix\n");
+
+    fprintf(fplog, "Repl");
+    for (i = 0; i < n; i++)
+    {
+        fprintf(fplog, "%8d", (i + 1));
+    }
+    fprintf(fplog, "\n");
+
+    for (i = 0; i < n; i++)
+    {
+        fprintf(fplog, "Repl");
+        for (j = 0; j < n; j++)
+        {
+            Tprint = 0.0;
+            if (nmoves[i][j] > 0)
+            {
+                Tprint = nmoves[i][j] / (2.0 * ntot);
+            }
+            fprintf(fplog, "%8.4f", Tprint);
+        }
+        fprintf(fplog, "%3d\n", i);
+    }
+}
+
+static void print_ind(FILE* fplog, const char* leg, int n, int* ind, const gmx_bool* bEx)
+{
+    int i;
+
+    fprintf(fplog, "Repl %2s %2d", leg, ind[0]);
+    for (i = 1; i < n; i++)
+    {
+        fprintf(fplog, " %c %2d", (bEx != nullptr && bEx[i]) ? 'x' : ' ', ind[i]);
+    }
+    fprintf(fplog, "\n");
+}
+
+static void print_allswitchind(FILE* fplog, int n, int* pind, int* allswaps, int* tmpswap)
+{
+    int i;
+
+    for (i = 0; i < n; i++)
+    {
+        tmpswap[i] = allswaps[i];
+    }
+    for (i = 0; i < n; i++)
+    {
+        allswaps[i] = tmpswap[pind[i]];
+    }
+
+    fprintf(fplog, "\nAccepted Exchanges:   ");
+    for (i = 0; i < n; i++)
+    {
+        fprintf(fplog, "%d ", pind[i]);
+    }
+    fprintf(fplog, "\n");
+
+    /* the "Order After Exchange" is the state label corresponding to the configuration that
+       started in state listed in order, i.e.
+
+       3 0 1 2
+
+       means that the:
+       configuration starting in simulation 3 is now in simulation 0,
+       configuration starting in simulation 0 is now in simulation 1,
+       configuration starting in simulation 1 is now in simulation 2,
+       configuration starting in simulation 2 is now in simulation 3
+     */
+    fprintf(fplog, "Order After Exchange: ");
+    for (i = 0; i < n; i++)
+    {
+        fprintf(fplog, "%d ", allswaps[i]);
+    }
+    fprintf(fplog, "\n\n");
+}
+
+static void print_prob(FILE* fplog, const char* leg, int n, real* prob)
+{
+    int  i;
+    char buf[8];
+
+    fprintf(fplog, "Repl %2s ", leg);
+    for (i = 1; i < n; i++)
+    {
+        if (prob[i] >= 0)
+        {
+            sprintf(buf, "%4.2f", prob[i]);
+            fprintf(fplog, "  %3s", buf[0] == '1' ? "1.0" : buf + 1);
+        }
+        else
+        {
+            fprintf(fplog, "     ");
+        }
+    }
+    fprintf(fplog, "\n");
+}
+
+static void print_count(FILE* fplog, const char* leg, int n, int* count)
+{
+    int i;
+
+    fprintf(fplog, "Repl %2s ", leg);
+    for (i = 1; i < n; i++)
+    {
+        fprintf(fplog, " %4d", count[i]);
+    }
+    fprintf(fplog, "\n");
+}
+
+static real calc_delta(FILE* fplog, gmx_bool bPrint, struct gmx_repl_ex* re, int a, int b, int ap, int bp)
+{
+
+    real   ediff, dpV, delta = 0;
+    real*  Epot = re->Epot;
+    real*  Vol  = re->Vol;
+    real** de   = re->de;
+    real*  beta = re->beta;
+
+    /* Two cases; we are permuted and not.  In all cases, setting ap = a and bp = b will reduce
+       to the non permuted case */
+
+    switch (re->type)
+    {
+        case ReplicaExchangeType::Temperature:
+            /*
+             * Okabe et. al. Chem. Phys. Lett. 335 (2001) 435-439
+             */
+            ediff = Epot[b] - Epot[a];
+            delta = -(beta[bp] - beta[ap]) * ediff;
+            break;
+        case ReplicaExchangeType::Lambda:
+            /* two cases:  when we are permuted, and not.  */
+            /* non-permuted:
+               ediff =  E_new - E_old
+                     =  [H_b(x_a) + H_a(x_b)] - [H_b(x_b) + H_a(x_a)]
+                     =  [H_b(x_a) - H_a(x_a)] + [H_a(x_b) - H_b(x_b)]
+                     =  de[b][a] + de[a][b] */
+
+            /* permuted:
+               ediff =  E_new - E_old
+                     =  [H_bp(x_a) + H_ap(x_b)] - [H_bp(x_b) + H_ap(x_a)]
+                     =  [H_bp(x_a) - H_ap(x_a)] + [H_ap(x_b) - H_bp(x_b)]
+                     =  [H_bp(x_a) - H_a(x_a) + H_a(x_a) - H_ap(x_a)] + [H_ap(x_b) - H_b(x_b) + H_b(x_b) - H_bp(x_b)]
+                     =  [H_bp(x_a) - H_a(x_a)] - [H_ap(x_a) - H_a(x_a)] + [H_ap(x_b) - H_b(x_b)] - H_bp(x_b) - H_b(x_b)]
+                     =  (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b])    */
+            /* but, in the current code implementation, we flip configurations, not indices . . .
+               So let's examine that.
+                     =  [H_b(x_ap) - H_a(x_a)] - [H_a(x_ap) - H_a(x_a)] + [H_a(x_bp) - H_b(x_b)] - H_b(x_bp) - H_b(x_b)]
+                     =  [H_b(x_ap) - H_a(x_ap)]  + [H_a(x_bp) - H_b(x_pb)]
+                     = (de[b][ap] - de[a][ap]) + (de[a][bp] - de[b][bp]
+                     So, if we exchange b<=> bp and a<=> ap, we return to the same result.
+                     So the simple solution is to flip the
+                     position of perturbed and original indices in the tests.
+             */
+
+            ediff = (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b]);
+            delta = ediff * beta[a]; /* assume all same temperature in this case */
+            break;
+        case ReplicaExchangeType::TemperatureLambda:
+            /* not permuted:  */
+            /* delta =  reduced E_new - reduced E_old
+                     =  [beta_b H_b(x_a) + beta_a H_a(x_b)] - [beta_b H_b(x_b) + beta_a H_a(x_a)]
+                     =  [beta_b H_b(x_a) - beta_a H_a(x_a)] + [beta_a H_a(x_b) - beta_b H_b(x_b)]
+                     =  [beta_b dH_b(x_a) + beta_b H_a(x_a) - beta_a H_a(x_a)] +
+                        [beta_a dH_a(x_b) + beta_a H_b(x_b) - beta_b H_b(x_b)]
+                     =  [beta_b dH_b(x_a) + [beta_a dH_a(x_b) +
+                        beta_b (H_a(x_a) - H_b(x_b)]) - beta_a (H_a(x_a) - H_b(x_b))
+                     =  beta_b dH_b(x_a) + beta_a dH_a(x_b) - (beta_b - beta_a)(H_b(x_b) - H_a(x_a) */
+            /* delta = beta[b]*de[b][a] + beta[a]*de[a][b] - (beta[b] - beta[a])*(Epot[b] - Epot[a]; */
+            /* permuted (big breath!) */
+            /*   delta =  reduced E_new - reduced E_old
+                     =  [beta_bp H_bp(x_a) + beta_ap H_ap(x_b)] - [beta_bp H_bp(x_b) + beta_ap H_ap(x_a)]
+                     =  [beta_bp H_bp(x_a) - beta_ap H_ap(x_a)] + [beta_ap H_ap(x_b) - beta_bp H_bp(x_b)]
+                     =  [beta_bp H_bp(x_a) - beta_ap H_ap(x_a)] + [beta_ap H_ap(x_b) - beta_bp H_bp(x_b)]
+                        - beta_pb H_a(x_a) + beta_ap H_a(x_a) + beta_pb H_a(x_a) - beta_ap H_a(x_a)
+                        - beta_ap H_b(x_b) + beta_bp H_b(x_b) + beta_ap H_b(x_b) - beta_bp H_b(x_b)
+                     =  [(beta_bp H_bp(x_a) - beta_bp H_a(x_a)) - (beta_ap H_ap(x_a) - beta_ap H_a(x_a))] +
+                        [(beta_ap H_ap(x_b)  - beta_ap H_b(x_b)) - (beta_bp H_bp(x_b) - beta_bp H_b(x_b))]
+             + beta_pb H_a(x_a) - beta_ap H_a(x_a) + beta_ap H_b(x_b) - beta_bp H_b(x_b)
+                     =  [beta_bp (H_bp(x_a) - H_a(x_a)) - beta_ap (H_ap(x_a) - H_a(x_a))] +
+                        [beta_ap (H_ap(x_b) - H_b(x_b)) - beta_bp (H_bp(x_b) - H_b(x_b))]
+             + beta_pb (H_a(x_a) - H_b(x_b))  - beta_ap (H_a(x_a) - H_b(x_b))
+                     =  ([beta_bp de[bp][a] - beta_ap de[ap][a]) + beta_ap de[ap][b]  - beta_bp de[bp][b])
+             + (beta_pb-beta_ap)(H_a(x_a) - H_b(x_b))  */
+            delta = beta[bp] * (de[bp][a] - de[bp][b]) + beta[ap] * (de[ap][b] - de[ap][a])
+                    - (beta[bp] - beta[ap]) * (Epot[b] - Epot[a]);
+            break;
+        default: gmx_incons("Unknown replica exchange quantity");
+    }
+    if (bPrint)
+    {
+        fprintf(fplog, "Repl %d <-> %d  dE_term = %10.3e (kT)\n", a, b, delta);
+    }
+/* PLUMED HREX */
+/* this is necessary because with plumed HREX the energy contribution is
+   already taken into account */
+    if(plumed_hrex) delta=0.0;
+/* END PLUMED HREX */
+    if (re->bNPT)
+    {
+        /* revist the calculation for 5.0.  Might be some improvements. */
+        dpV = (beta[ap] * re->pres[ap] - beta[bp] * re->pres[bp]) * (Vol[b] - Vol[a]) / gmx::c_presfac;
+        if (bPrint)
+        {
+            fprintf(fplog, "  dpV = %10.3e  d = %10.3e\n", dpV, delta + dpV);
+        }
+        delta += dpV;
+    }
+    return delta;
+}
+
+static void test_for_replica_exchange(FILE*                 fplog,
+                                      const gmx_multisim_t* ms,
+                                      struct gmx_repl_ex*   re,
+                                      const gmx_enerdata_t* enerd,
+                                      real                  vol,
+                                      int64_t               step,
+                                      real                  time)
+{
+    int                                m, i, j, a, b, ap, bp, i0, i1, tmp;
+    real                               delta = 0;
+    gmx_bool                           bPrint, bMultiEx;
+    gmx_bool*                          bEx      = re->bEx;
+    real*                              prob     = re->prob;
+    int*                               pind     = re->destinations; /* permuted index */
+    gmx_bool                           bEpot    = FALSE;
+    gmx_bool                           bDLambda = FALSE;
+    gmx_bool                           bVol     = FALSE;
+    gmx::ThreeFry2x64<64>              rng(re->seed, gmx::RandomDomain::ReplicaExchange);
+    gmx::UniformRealDistribution<real> uniformRealDist;
+    gmx::UniformIntDistribution<int>   uniformNreplDist(0, re->nrepl - 1);
+
+    bMultiEx = (re->nex > 1); /* multiple exchanges at each state */
+    fprintf(fplog, "Replica exchange at step %" PRId64 " time %.5f\n", step, time);
+
+    if (re->bNPT)
+    {
+        for (i = 0; i < re->nrepl; i++)
+        {
+            re->Vol[i] = 0;
+        }
+        bVol              = TRUE;
+        re->Vol[re->repl] = vol;
+    }
+    if ((re->type == ReplicaExchangeType::Temperature || re->type == ReplicaExchangeType::TemperatureLambda))
+    {
+        for (i = 0; i < re->nrepl; i++)
+        {
+            re->Epot[i] = 0;
+        }
+        bEpot              = TRUE;
+        re->Epot[re->repl] = enerd->term[F_EPOT];
+        /* temperatures of different states*/
+        for (i = 0; i < re->nrepl; i++)
+        {
+            re->beta[i] = 1.0 / (re->q[ReplicaExchangeType::Temperature][i] * gmx::c_boltz);
+        }
+    }
+    else
+    {
+        for (i = 0; i < re->nrepl; i++)
+        {
+            re->beta[i] = 1.0 / (re->temp * gmx::c_boltz); /* we have a single temperature */
+        }
+    }
+    if (re->type == ReplicaExchangeType::Lambda || re->type == ReplicaExchangeType::TemperatureLambda)
+    {
+        bDLambda = TRUE;
+        /* lambda differences. */
+        /* de[i][j] is the energy of the jth simulation in the ith Hamiltonian
+           minus the energy of the jth simulation in the jth Hamiltonian */
+        for (i = 0; i < re->nrepl; i++)
+        {
+            for (j = 0; j < re->nrepl; j++)
+            {
+                re->de[i][j] = 0;
+            }
+        }
+        for (i = 0; i < re->nrepl; i++)
+        {
+            re->de[i][re->repl] =
+                    enerd->foreignLambdaTerms.deltaH(re->q[ReplicaExchangeType::Lambda][i]);
+        }
+    }
+
+    /* now actually do the communication */
+    if (bVol)
+    {
+        gmx_sum_sim(re->nrepl, re->Vol, ms);
+    }
+    if (bEpot)
+    {
+        gmx_sum_sim(re->nrepl, re->Epot, ms);
+    }
+    if (bDLambda)
+    {
+        for (i = 0; i < re->nrepl; i++)
+        {
+            gmx_sum_sim(re->nrepl, re->de[i], ms);
+        }
+    }
+
+    /* make a duplicate set of indices for shuffling */
+    for (i = 0; i < re->nrepl; i++)
+    {
+        pind[i] = re->ind[i];
+    }
+
+    rng.restart(step, 0);
+
+    /* PLUMED */
+    int plumed_test_exchange_pattern=0;
+    if(plumed_test_exchange_pattern && plumed_hrex) gmx_fatal(FARGS,"hrex not compatible with ad hoc exchange patterns");
+    /* END PLUMED */
+
+    if (bMultiEx)
+    {
+        /* multiple random switch exchange */
+        int nself = 0;
+
+
+        for (i = 0; i < re->nex + nself; i++)
+        {
+            // For now this is superfluous, but just in case we ever add more
+            // calls in different branches it is safer to always reset the distribution.
+            uniformNreplDist.reset();
+
+            /* randomly select a pair  */
+            /* in theory, could reduce this by identifying only which switches had a nonneglibible
+               probability of occurring (log p > -100) and only operate on those switches */
+            /* find out which state it is from, and what label that state currently has. Likely
+               more work that useful. */
+            i0 = uniformNreplDist(rng);
+            i1 = uniformNreplDist(rng);
+            if (i0 == i1)
+            {
+                nself++;
+                continue; /* self-exchange, back up and do it again */
+            }
+
+            a  = re->ind[i0]; /* what are the indices of these states? */
+            b  = re->ind[i1];
+            ap = pind[i0];
+            bp = pind[i1];
+
+            bPrint = FALSE; /* too noisy */
+            /* calculate the energy difference */
+            /* if the code changes to flip the STATES, rather than the configurations,
+               use the commented version of the code */
+            /* delta = calc_delta(fplog,bPrint,re,a,b,ap,bp); */
+            delta = calc_delta(fplog, bPrint, re, ap, bp, a, b);
+
+            /* we actually only use the first space in the prob and bEx array,
+               since there are actually many switches between pairs. */
+
+            if (delta <= 0)
+            {
+                /* accepted */
+                prob[0] = 1;
+                bEx[0]  = TRUE;
+            }
+            else
+            {
+                if (delta > c_probabilityCutoff)
+                {
+                    prob[0] = 0;
+                }
+                else
+                {
+                    prob[0] = exp(-delta);
+                }
+                // roll a number to determine if accepted. For now it is superfluous to
+                // reset, but just in case we ever add more calls in different branches
+                // it is safer to always reset the distribution.
+                uniformRealDist.reset();
+                bEx[0] = uniformRealDist(rng) < prob[0];
+            }
+            re->prob_sum[0] += prob[0];
+
+            if (bEx[0])
+            {
+                /* swap the states */
+                tmp      = pind[i0];
+                pind[i0] = pind[i1];
+                pind[i1] = tmp;
+            }
+        }
+        re->nattempt[0]++; /* keep track of total permutation trials here */
+        print_allswitchind(fplog, re->nrepl, pind, re->allswaps, re->tmpswap);
+    }
+    else
+    {
+        /* standard nearest neighbor replica exchange */
+
+        m = (step / re->nst) % 2;
+        /* PLUMED */
+        if(plumedswitch){
+          int partner=re->repl;
+          plumed_cmd(plumedmain,"getExchangesFlag",&plumed_test_exchange_pattern);
+          if(plumed_test_exchange_pattern>0){
+            int *list;
+            snew(list,re->nrepl);
+            plumed_cmd(plumedmain,"setNumberOfReplicas",&(re->nrepl));
+            plumed_cmd(plumedmain,"getExchangesList",list);
+            for(i=0; i<re->nrepl; i++) re->ind[i]=list[i];
+            sfree(list);
+          }
+
+          for(i=1; i<re->nrepl; i++) {
+            if (i % 2 != m) continue;
+            a = re->ind[i-1];
+            b = re->ind[i];
+            if(re->repl==a) partner=b;
+            if(re->repl==b) partner=a;
+          }
+          plumed_cmd(plumedmain,"GREX setPartner",&partner);
+          plumed_cmd(plumedmain,"GREX calculate",nullptr);
+          plumed_cmd(plumedmain,"GREX shareAllDeltaBias",nullptr);
+        }
+        /* END PLUMED */
+        for (i = 1; i < re->nrepl; i++)
+        {
+            a = re->ind[i - 1];
+            b = re->ind[i];
+
+            bPrint = (re->repl == a || re->repl == b);
+            if (i % 2 == m)
+            {
+                delta = calc_delta(fplog, bPrint, re, a, b, a, b);
+                /* PLUMED */
+                if(plumedswitch){
+                  real adb,bdb,dplumed;
+                  char buf[300];
+                  sprintf(buf,"GREX getDeltaBias %d",a); plumed_cmd(plumedmain,buf,&adb);
+                  sprintf(buf,"GREX getDeltaBias %d",b); plumed_cmd(plumedmain,buf,&bdb);
+                  dplumed=adb*re->beta[a]+bdb*re->beta[b];
+                  delta+=dplumed;
+                  if (bPrint)
+                    fprintf(fplog,"dplumed = %10.3e  dE_Term = %10.3e (kT)\n",dplumed,delta);
+                }
+                /* END PLUMED */
+                if (delta <= 0)
+                {
+                    /* accepted */
+                    prob[i] = 1;
+                    bEx[i]  = TRUE;
+                }
+                else
+                {
+                    if (delta > c_probabilityCutoff)
+                    {
+                        prob[i] = 0;
+                    }
+                    else
+                    {
+                        prob[i] = exp(-delta);
+                    }
+                    // roll a number to determine if accepted. For now it is superfluous to
+                    // reset, but just in case we ever add more calls in different branches
+                    // it is safer to always reset the distribution.
+                    uniformRealDist.reset();
+                    bEx[i] = uniformRealDist(rng) < prob[i];
+                }
+                re->prob_sum[i] += prob[i];
+
+                if (bEx[i])
+                {
+                  /* PLUMED */
+                  if(!plumed_test_exchange_pattern) {
+                    /* standard neighbour swapping */
+                    /* swap these two */
+                    tmp         = pind[i - 1];
+                    pind[i - 1] = pind[i];
+                    pind[i]     = tmp;
+                    re->nexchange[i]++; /* statistics for back compatibility */
+                  } else {
+                    /* alternative swapping patterns */
+                    tmp       = pind[a];
+                    pind[a]   = pind[b];
+                    pind[b]   = tmp;
+                    re->nexchange[i]++;  /* statistics for back compatibility */
+                  }
+                  /* END PLUMED */
+                }
+            }
+            else
+            {
+                prob[i] = -1;
+                bEx[i]  = FALSE;
+            }
+        }
+        /* print some statistics */
+        print_ind(fplog, "ex", re->nrepl, re->ind, bEx);
+        print_prob(fplog, "pr", re->nrepl, prob);
+        fprintf(fplog, "\n");
+        re->nattempt[m]++;
+    }
+
+    /* PLUMED */
+    if(plumed_test_exchange_pattern>0) {
+      for (i = 0; i < re->nrepl; i++)
+      {
+          re->ind[i] = i;
+      }
+    }
+    /* END PLUMED */
+
+    /* record which moves were made and accepted */
+    for (i = 0; i < re->nrepl; i++)
+    {
+        re->nmoves[re->ind[i]][pind[i]] += 1;
+        re->nmoves[pind[i]][re->ind[i]] += 1;
+    }
+    fflush(fplog); /* make sure we can see what the last exchange was */
+}
+
+static void cyclic_decomposition(const int* destinations, int** cyclic, gmx_bool* incycle, const int nrepl, int* nswap)
+{
+
+    int i, j, c, p;
+    int maxlen = 1;
+    for (i = 0; i < nrepl; i++)
+    {
+        incycle[i] = FALSE;
+    }
+    for (i = 0; i < nrepl; i++) /* one cycle for each replica */
+    {
+        if (incycle[i])
+        {
+            cyclic[i][0] = -1;
+            continue;
+        }
+        cyclic[i][0] = i;
+        incycle[i]   = TRUE;
+        c            = 1;
+        p            = i;
+        for (j = 0; j < nrepl; j++) /* potentially all cycles are part, but we will break first */
+        {
+            p = destinations[p]; /* start permuting */
+            if (p == i)
+            {
+                cyclic[i][c] = -1;
+                if (c > maxlen)
+                {
+                    maxlen = c;
+                }
+                break; /* we've reached the original element, the cycle is complete, and we marked the end. */
+            }
+            else
+            {
+                cyclic[i][c] = p; /* each permutation gives a new member of the cycle */
+                incycle[p]   = TRUE;
+                c++;
+            }
+        }
+    }
+    *nswap = maxlen - 1;
+
+    if (debug)
+    {
+        for (i = 0; i < nrepl; i++)
+        {
+            fprintf(debug, "Cycle %d:", i);
+            for (j = 0; j < nrepl; j++)
+            {
+                if (cyclic[i][j] < 0)
+                {
+                    break;
+                }
+                fprintf(debug, "%2d", cyclic[i][j]);
+            }
+            fprintf(debug, "\n");
+        }
+        fflush(debug);
+    }
+}
+
+static void compute_exchange_order(int** cyclic, int** order, const int nrepl, const int maxswap)
+{
+    int i, j;
+
+    for (j = 0; j < maxswap; j++)
+    {
+        for (i = 0; i < nrepl; i++)
+        {
+            if (cyclic[i][j + 1] >= 0)
+            {
+                order[cyclic[i][j + 1]][j] = cyclic[i][j];
+                order[cyclic[i][j]][j]     = cyclic[i][j + 1];
+            }
+        }
+        for (i = 0; i < nrepl; i++)
+        {
+            if (order[i][j] < 0)
+            {
+                order[i][j] = i; /* if it's not exchanging, it should stay this round*/
+            }
+        }
+    }
+
+    if (debug)
+    {
+        fprintf(debug, "Replica Exchange Order\n");
+        for (i = 0; i < nrepl; i++)
+        {
+            fprintf(debug, "Replica %d:", i);
+            for (j = 0; j < maxswap; j++)
+            {
+                if (order[i][j] < 0)
+                {
+                    break;
+                }
+                fprintf(debug, "%2d", order[i][j]);
+            }
+            fprintf(debug, "\n");
+        }
+        fflush(debug);
+    }
+}
+
+static void prepare_to_do_exchange(struct gmx_repl_ex* re, const int replica_id, int* maxswap, gmx_bool* bThisReplicaExchanged)
+{
+    int i, j;
+    /* Hold the cyclic decomposition of the (multiple) replica
+     * exchange. */
+    gmx_bool bAnyReplicaExchanged = FALSE;
+    *bThisReplicaExchanged        = FALSE;
+
+    for (i = 0; i < re->nrepl; i++)
+    {
+        if (re->destinations[i] != re->ind[i])
+        {
+            /* only mark as exchanged if the index has been shuffled */
+            bAnyReplicaExchanged = TRUE;
+            break;
+        }
+    }
+    if (bAnyReplicaExchanged)
+    {
+        /* reinitialize the placeholder arrays */
+        for (i = 0; i < re->nrepl; i++)
+        {
+            for (j = 0; j < re->nrepl; j++)
+            {
+                re->cyclic[i][j] = -1;
+                re->order[i][j]  = -1;
+            }
+        }
+
+        /* Identify the cyclic decomposition of the permutation (very
+         * fast if neighbor replica exchange). */
+        cyclic_decomposition(re->destinations, re->cyclic, re->incycle, re->nrepl, maxswap);
+
+        /* Now translate the decomposition into a replica exchange
+         * order at each step. */
+        compute_exchange_order(re->cyclic, re->order, re->nrepl, *maxswap);
+
+        /* Did this replica do any exchange at any point? */
+        for (j = 0; j < *maxswap; j++)
+        {
+            if (replica_id != re->order[replica_id][j])
+            {
+                *bThisReplicaExchanged = TRUE;
+                break;
+            }
+        }
+    }
+}
+
+gmx_bool replica_exchange(FILE*                 fplog,
+                          const t_commrec*      cr,
+                          const gmx_multisim_t* ms,
+                          struct gmx_repl_ex*   re,
+                          t_state*              state,
+                          const gmx_enerdata_t* enerd,
+                          t_state*              state_local,
+                          int64_t               step,
+                          real                  time)
+{
+    int j;
+    int replica_id = 0;
+    int exchange_partner;
+    int maxswap = 0;
+    /* Number of rounds of exchanges needed to deal with any multiple
+     * exchanges. */
+    /* Where each replica ends up after the exchange attempt(s). */
+    /* The order in which multiple exchanges will occur. */
+    gmx_bool bThisReplicaExchanged = FALSE;
+
+    /* PLUMED */
+    if(plumedswitch)plumed_cmd(plumedmain,"GREX prepare",nullptr);
+    /* END PLUMED */
+
+    if (MASTER(cr))
+    {
+        replica_id = re->repl;
+        test_for_replica_exchange(fplog, ms, re, enerd, det(state_local->box), step, time);
+        prepare_to_do_exchange(re, replica_id, &maxswap, &bThisReplicaExchanged);
+    }
+    /* Do intra-simulation broadcast so all processors belonging to
+     * each simulation know whether they need to participate in
+     * collecting the state. Otherwise, they might as well get on with
+     * the next thing to do. */
+    if (haveDDAtomOrdering(*cr))
+    {
+#if GMX_MPI
+        MPI_Bcast(&bThisReplicaExchanged, sizeof(gmx_bool), MPI_BYTE, MASTERRANK(cr), cr->mpi_comm_mygroup);
+#endif
+    }
+
+    if (bThisReplicaExchanged)
+    {
+        /* Exchange the states */
+        /* Collect the global state on the master node */
+        if (haveDDAtomOrdering(*cr))
+        {
+            dd_collect_state(cr->dd, state_local, state);
+        }
+        else
+        {
+            copy_state_serial(state_local, state);
+        }
+
+        if (MASTER(cr))
+        {
+            /* There will be only one swap cycle with standard replica
+             * exchange, but there may be multiple swap cycles if we
+             * allow multiple swaps. */
+
+            for (j = 0; j < maxswap; j++)
+            {
+                exchange_partner = re->order[replica_id][j];
+
+                if (exchange_partner != replica_id)
+                {
+                    /* Exchange the global states between the master nodes */
+                    if (debug)
+                    {
+                        fprintf(debug, "Exchanging %d with %d\n", replica_id, exchange_partner);
+                    }
+                    exchange_state(ms, exchange_partner, state);
+                }
+            }
+            /* For temperature-type replica exchange, we need to scale
+             * the velocities. */
+            if (re->type == ReplicaExchangeType::Temperature || re->type == ReplicaExchangeType::TemperatureLambda)
+            {
+                scale_velocities(
+                        state->v,
+                        std::sqrt(re->q[ReplicaExchangeType::Temperature][replica_id]
+                                  / re->q[ReplicaExchangeType::Temperature][re->destinations[replica_id]]));
+            }
+        }
+
+        /* With domain decomposition the global state is distributed later */
+        if (!haveDDAtomOrdering(*cr))
+        {
+            /* Copy the global state to the local state data structure */
+            copy_state_serial(state, state_local);
+        }
+    }
+
+    return bThisReplicaExchanged;
+}
+
+void print_replica_exchange_statistics(FILE* fplog, struct gmx_repl_ex* re)
+{
+    int i;
+
+    fprintf(fplog, "\nReplica exchange statistics\n");
+
+    if (re->nex == 0)
+    {
+        fprintf(fplog,
+                "Repl  %d attempts, %d odd, %d even\n",
+                re->nattempt[0] + re->nattempt[1],
+                re->nattempt[1],
+                re->nattempt[0]);
+
+        fprintf(fplog, "Repl  average probabilities:\n");
+        for (i = 1; i < re->nrepl; i++)
+        {
+            if (re->nattempt[i % 2] == 0)
+            {
+                re->prob[i] = 0;
+            }
+            else
+            {
+                re->prob[i] = re->prob_sum[i] / re->nattempt[i % 2];
+            }
+        }
+        print_ind(fplog, "", re->nrepl, re->ind, nullptr);
+        print_prob(fplog, "", re->nrepl, re->prob);
+
+        fprintf(fplog, "Repl  number of exchanges:\n");
+        print_ind(fplog, "", re->nrepl, re->ind, nullptr);
+        print_count(fplog, "", re->nrepl, re->nexchange);
+
+        fprintf(fplog, "Repl  average number of exchanges:\n");
+        for (i = 1; i < re->nrepl; i++)
+        {
+            if (re->nattempt[i % 2] == 0)
+            {
+                re->prob[i] = 0;
+            }
+            else
+            {
+                re->prob[i] = (static_cast<real>(re->nexchange[i])) / re->nattempt[i % 2];
+            }
+        }
+        print_ind(fplog, "", re->nrepl, re->ind, nullptr);
+        print_prob(fplog, "", re->nrepl, re->prob);
+
+        fprintf(fplog, "\n");
+    }
+    /* print the transition matrix */
+    print_transition_matrix(fplog, re->nrepl, re->nmoves, re->nattempt);
+}
+
+/* PLUMED HREX */
+int replica_exchange_get_repl(const gmx_repl_ex_t re){
+  return re->repl;
+};
+
+int replica_exchange_get_nrepl(const gmx_repl_ex_t re){
+  return re->nrepl;
+};
+/* END PLUMED HREX */
+//! \endcond