hillclimber 0.1.5__cp313-cp313-musllinux_1_2_aarch64.whl

plumed/_lib/lib/plumed/patches/gromacs-2023.5.diff/src/gromacs/mdlib/expanded.cpp

@@ -0,0 +1,1632 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright 2012- 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.
+ */
+
+/* PLUMED */
+#include "../../../Plumed.h"
+extern int    plumedswitch;
+extern plumed plumedmain;
+/* END PLUMED */
+
+#include "gmxpre.h"
+
+#include "expanded.h"
+
+#include <cmath>
+#include <cstdio>
+
+#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/mdtypes/enerdata.h"
+#include "gromacs/mdtypes/forcerec.h"
+#include "gromacs/mdtypes/group.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/uniformrealdistribution.h"
+#include "gromacs/utility/enumerationhelpers.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "expanded_internal.h"
+
+static void init_df_history_weights(df_history_t* dfhist, const t_expanded* expand, int nlim)
+{
+    int i;
+    dfhist->wl_delta = expand->init_wl_delta;
+    for (i = 0; i < nlim; i++)
+    {
+        dfhist->sum_weights[i] = expand->init_lambda_weights[i];
+        dfhist->sum_dg[i]      = expand->init_lambda_weights[i];
+    }
+}
+
+/* Eventually should contain all the functions needed to initialize expanded ensemble
+   before the md loop starts */
+void init_expanded_ensemble(gmx_bool bStateFromCP, const t_inputrec* ir, df_history_t* dfhist)
+{
+    if (!bStateFromCP)
+    {
+        init_df_history_weights(dfhist, ir->expandedvals.get(), ir->fepvals->n_lambda);
+    }
+}
+
+static void GenerateGibbsProbabilities(const real* ene, double* p_k, double* pks, int minfep, int maxfep)
+{
+
+    int  i;
+    real maxene;
+
+    *pks   = 0.0;
+    maxene = ene[minfep];
+    /* find the maximum value */
+    for (i = minfep; i <= maxfep; i++)
+    {
+        if (ene[i] > maxene)
+        {
+            maxene = ene[i];
+        }
+    }
+    /* find the denominator */
+    for (i = minfep; i <= maxfep; i++)
+    {
+        *pks += std::exp(ene[i] - maxene);
+    }
+    /*numerators*/
+    for (i = minfep; i <= maxfep; i++)
+    {
+        p_k[i] = std::exp(ene[i] - maxene) / *pks;
+    }
+}
+
+static void
+GenerateWeightedGibbsProbabilities(const real* ene, double* p_k, double* pks, int nlim, real* nvals, real delta)
+{
+
+    int   i;
+    real  maxene;
+    real* nene;
+    *pks = 0.0;
+
+    snew(nene, nlim);
+    for (i = 0; i < nlim; i++)
+    {
+        if (nvals[i] == 0)
+        {
+            /* add the delta, since we need to make sure it's greater than zero, and
+               we need a non-arbitrary number? */
+            nene[i] = ene[i] + std::log(nvals[i] + delta);
+        }
+        else
+        {
+            nene[i] = ene[i] + std::log(nvals[i]);
+        }
+    }
+
+    /* find the maximum value */
+    maxene = nene[0];
+    for (i = 0; i < nlim; i++)
+    {
+        if (nene[i] > maxene)
+        {
+            maxene = nene[i];
+        }
+    }
+
+    /* subtract off the maximum, avoiding overflow */
+    for (i = 0; i < nlim; i++)
+    {
+        nene[i] -= maxene;
+    }
+
+    /* find the denominator */
+    for (i = 0; i < nlim; i++)
+    {
+        *pks += std::exp(nene[i]);
+    }
+
+    /*numerators*/
+    for (i = 0; i < nlim; i++)
+    {
+        p_k[i] = std::exp(nene[i]) / *pks;
+    }
+    sfree(nene);
+}
+
+static int FindMinimum(const real* min_metric, int N)
+{
+
+    real min_val;
+    int  min_nval, nval;
+
+    min_nval = 0;
+    min_val  = min_metric[0];
+
+    for (nval = 0; nval < N; nval++)
+    {
+        if (min_metric[nval] < min_val)
+        {
+            min_val  = min_metric[nval];
+            min_nval = nval;
+        }
+    }
+    return min_nval;
+}
+
+static gmx_bool CheckHistogramRatios(int nhisto, const real* histo, real ratio)
+{
+
+    int      i;
+    real     nmean;
+    gmx_bool bIfFlat;
+
+    nmean = 0;
+    for (i = 0; i < nhisto; i++)
+    {
+        nmean += histo[i];
+    }
+
+    if (nmean == 0)
+    {
+        /* no samples! is bad!*/
+        bIfFlat = FALSE;
+        return bIfFlat;
+    }
+    nmean /= static_cast<real>(nhisto);
+
+    bIfFlat = TRUE;
+    for (i = 0; i < nhisto; i++)
+    {
+        /* make sure that all points are in the ratio < x <  1/ratio range  */
+        if (!((histo[i] / nmean < 1.0 / ratio) && (histo[i] / nmean > ratio)))
+        {
+            bIfFlat = FALSE;
+            break;
+        }
+    }
+    return bIfFlat;
+}
+
+static gmx_bool CheckIfDoneEquilibrating(int nlim, const t_expanded* expand, const df_history_t* dfhist, int64_t step)
+{
+
+    int      i, totalsamples;
+    gmx_bool bDoneEquilibrating = TRUE;
+    gmx_bool bIfFlat;
+
+    /* If we are doing slow growth to get initial values, we haven't finished equilibrating */
+    if (expand->lmc_forced_nstart > 0)
+    {
+        for (i = 0; i < nlim; i++)
+        {
+            if (dfhist->n_at_lam[i]
+                < expand->lmc_forced_nstart) /* we are still doing the initial sweep, so we're
+                                                definitely not done equilibrating*/
+            {
+                bDoneEquilibrating = FALSE;
+                break;
+            }
+        }
+    }
+    else
+    {
+        /* assume we have equilibrated the weights, then check to see if any of the conditions are not met */
+        bDoneEquilibrating = TRUE;
+
+        /* calculate the total number of samples */
+        switch (expand->elmceq)
+        {
+            case LambdaWeightWillReachEquilibrium::No:
+                /* We have not equilibrated, and won't, ever. */
+                bDoneEquilibrating = FALSE;
+                break;
+            case LambdaWeightWillReachEquilibrium::Yes:
+                /* we have equilibrated -- we're done */
+                bDoneEquilibrating = TRUE;
+                break;
+            case LambdaWeightWillReachEquilibrium::Steps:
+                /* first, check if we are equilibrating by steps, if we're still under */
+                if (step < expand->equil_steps)
+                {
+                    bDoneEquilibrating = FALSE;
+                }
+                break;
+            case LambdaWeightWillReachEquilibrium::Samples:
+                totalsamples = 0;
+                for (i = 0; i < nlim; i++)
+                {
+                    totalsamples += dfhist->n_at_lam[i];
+                }
+                if (totalsamples < expand->equil_samples)
+                {
+                    bDoneEquilibrating = FALSE;
+                }
+                break;
+            case LambdaWeightWillReachEquilibrium::NumAtLambda:
+                for (i = 0; i < nlim; i++)
+                {
+                    if (dfhist->n_at_lam[i]
+                        < expand->equil_n_at_lam) /* we are still doing the initial sweep, so we're
+                                                     definitely not done equilibrating*/
+                    {
+                        bDoneEquilibrating = FALSE;
+                        break;
+                    }
+                }
+                break;
+            case LambdaWeightWillReachEquilibrium::WLDelta:
+                if (EWL(expand->elamstats)) /* This check is in readir as well, but
+                                               just to be sure */
+                {
+                    if (dfhist->wl_delta > expand->equil_wl_delta)
+                    {
+                        bDoneEquilibrating = FALSE;
+                    }
+                }
+                break;
+            case LambdaWeightWillReachEquilibrium::Ratio:
+                /* we can use the flatness as a judge of good weights, as long as
+                   we're not doing minvar, or Wang-Landau.
+                   But turn off for now until we figure out exactly how we do this.
+                 */
+
+                if (!(EWL(expand->elamstats) || expand->elamstats == LambdaWeightCalculation::Minvar))
+                {
+                    /* we want to use flatness -avoiding- the forced-through samples.  Plus, we need
+                       to convert to floats for this histogram function. */
+
+                    real* modhisto;
+                    snew(modhisto, nlim);
+                    for (i = 0; i < nlim; i++)
+                    {
+                        modhisto[i] = 1.0 * (dfhist->n_at_lam[i] - expand->lmc_forced_nstart);
+                    }
+                    bIfFlat = CheckHistogramRatios(nlim, modhisto, expand->equil_ratio);
+                    sfree(modhisto);
+                    if (!bIfFlat)
+                    {
+                        bDoneEquilibrating = FALSE;
+                    }
+                }
+                break;
+            default: bDoneEquilibrating = TRUE; break;
+        }
+    }
+    return bDoneEquilibrating;
+}
+
+static gmx_bool UpdateWeights(int           nlim,
+                              t_expanded*   expand,
+                              df_history_t* dfhist,
+                              int           fep_state,
+                              const real*   scaled_lamee,
+                              const real*   weighted_lamee,
+                              int64_t       step)
+{
+    gmx_bool bSufficientSamples;
+    real     acceptanceWeight;
+    int      i;
+    int      min_nvalm, min_nvalp, maxc;
+    real     omega_m1_0, omega_p1_0;
+    real     zero_sum_weights;
+    real *omegam_array, *weightsm_array, *omegap_array, *weightsp_array, *varm_array, *varp_array,
+            *dwp_array, *dwm_array;
+    real    clam_varm, clam_varp, clam_osum, clam_weightsm, clam_weightsp, clam_minvar;
+    real *  lam_variance, *lam_dg;
+    double* p_k;
+    double  pks = 0;
+
+    /* Future potential todos for this function (see #3848):
+     *  - Update the names in the dhist structure to be clearer. Not done for now since this
+     *    a bugfix update and we are mininizing other code changes.
+     *  - Modularize the code some more.
+     *  - potentially merge with accelerated weight histogram functionality, since it's very similar.
+     */
+    /*  if we have equilibrated the expanded ensemble weights, we are not updating them, so exit now */
+    if (dfhist->bEquil)
+    {
+        return FALSE;
+    }
+
+    if (CheckIfDoneEquilibrating(nlim, expand, dfhist, step))
+    {
+        dfhist->bEquil = TRUE;
+        /* zero out the visited states so we know how many equilibrated states we have
+           from here on out.*/
+        for (i = 0; i < nlim; i++)
+        {
+            dfhist->n_at_lam[i] = 0;
+        }
+        return TRUE;
+    }
+
+    /* If we reached this far, we have not equilibrated yet, keep on
+       going resetting the weights */
+
+    if (EWL(expand->elamstats))
+    {
+        if (expand->elamstats
+            == LambdaWeightCalculation::WL) /* Using standard Wang-Landau for weight updates */
+        {
+            dfhist->sum_weights[fep_state] -= dfhist->wl_delta;
+            dfhist->wl_histo[fep_state] += 1.0;
+        }
+        else if (expand->elamstats == LambdaWeightCalculation::WWL)
+        /* Using weighted Wang-Landau for weight updates.
+         * Very closly equivalent to accelerated weight histogram approach
+         * applied to expanded ensemble. */
+        {
+            snew(p_k, nlim);
+
+            /* first increment count */
+            GenerateGibbsProbabilities(weighted_lamee, p_k, &pks, 0, nlim - 1);
+            for (i = 0; i < nlim; i++)
+            {
+                dfhist->wl_histo[i] += static_cast<real>(p_k[i]);
+            }
+
+            /* then increment weights (uses count) */
+            pks = 0.0;
+            GenerateWeightedGibbsProbabilities(
+                    weighted_lamee, p_k, &pks, nlim, dfhist->wl_histo, dfhist->wl_delta);
+
+            for (i = 0; i < nlim; i++)
+            {
+                dfhist->sum_weights[i] -= dfhist->wl_delta * static_cast<real>(p_k[i]);
+            }
+            /* Alternate definition, using logarithms. Shouldn't make very much difference! */
+            /*
+               real di;
+               for (i=0;i<nlim;i++)
+               {
+                di = (real)1.0 + dfhist->wl_delta*(real)p_k[i];
+                dfhist->sum_weights[i] -= log(di);
+               }
+             */
+            sfree(p_k);
+        }
+
+        zero_sum_weights = dfhist->sum_weights[0];
+        for (i = 0; i < nlim; i++)
+        {
+            dfhist->sum_weights[i] -= zero_sum_weights;
+        }
+    }
+
+    if (expand->elamstats == LambdaWeightCalculation::Barker
+        || expand->elamstats == LambdaWeightCalculation::Metropolis
+        || expand->elamstats == LambdaWeightCalculation::Minvar)
+    {
+        maxc = 2 * expand->c_range + 1;
+
+        snew(lam_dg, nlim);
+        snew(lam_variance, nlim);
+
+        snew(omegap_array, maxc);
+        snew(weightsp_array, maxc);
+        snew(varp_array, maxc);
+        snew(dwp_array, maxc);
+
+        snew(omegam_array, maxc);
+        snew(weightsm_array, maxc);
+        snew(varm_array, maxc);
+        snew(dwm_array, maxc);
+
+        /* unpack the values of the free energy differences and the
+         * variance in their estimates between nearby lambdas. We will
+         * only actually update 2 of these, the state we are currently
+         * at and the one we end up moving to
+         */
+
+        for (i = 0; i < nlim - 1; i++)
+        { /* only through the second to last */
+            lam_dg[i] = dfhist->sum_dg[i + 1] - dfhist->sum_dg[i];
+            lam_variance[i] =
+                    gmx::square(dfhist->sum_variance[i + 1]) - gmx::square(dfhist->sum_variance[i]);
+        }
+
+        /* accumulate running averages of thermodynamic averages for Bennett Acceptance Ratio-based
+         * estimates of the free energy .
+         * Rather than peforming self-consistent estimation of the free energies at each step,
+         * we keep track of an array of possible different free energies (cnvals),
+         * and we self-consistently choose the best one. The one that leads to a free energy estimate
+         * that is closest to itself is the best estimate of the free energy.  It is essentially a
+         * parallellized version of self-consistent iteration.  maxc is the number of these constants. */
+
+        for (int nval = 0; nval < maxc; nval++)
+        {
+            const real cnval = static_cast<real>(nval - expand->c_range);
+
+            /* Compute acceptance criterion weight to the state below this one for use in averages.
+             * Note we do not have to have just moved from that state to use this free energy
+             * estimate; these are essentially "virtual" moves. */
+
+            if (fep_state > 0)
+            {
+                const auto lambdaEnergyDifference =
+                        cnval - (scaled_lamee[fep_state] - scaled_lamee[fep_state - 1]);
+                acceptanceWeight =
+                        gmx::calculateAcceptanceWeight(expand->elamstats, lambdaEnergyDifference);
+                dfhist->accum_m[fep_state][nval] += acceptanceWeight;
+                dfhist->accum_m2[fep_state][nval] += acceptanceWeight * acceptanceWeight;
+            }
+
+            // Compute acceptance criterion weight to transition to the next state
+            if (fep_state < nlim - 1)
+            {
+                const auto lambdaEnergyDifference =
+                        -cnval + (scaled_lamee[fep_state + 1] - scaled_lamee[fep_state]);
+                acceptanceWeight =
+                        gmx::calculateAcceptanceWeight(expand->elamstats, lambdaEnergyDifference);
+                dfhist->accum_p[fep_state][nval] += acceptanceWeight;
+                dfhist->accum_p2[fep_state][nval] += acceptanceWeight * acceptanceWeight;
+            }
+
+            /* Determination of Metropolis transition and Barker transition weights */
+
+            int numObservationsCurrentState = dfhist->n_at_lam[fep_state];
+            /* determine the number of observations above and below the current state */
+            int numObservationsLowerState = 0;
+            if (fep_state > 0)
+            {
+                numObservationsLowerState = dfhist->n_at_lam[fep_state - 1];
+            }
+            int numObservationsHigherState = 0;
+            if (fep_state < nlim - 1)
+            {
+                numObservationsHigherState = dfhist->n_at_lam[fep_state + 1];
+            }
+
+            /* Calculate the biases for each expanded ensemble state that minimize the total
+             * variance, as implemented in Martinez-Veracoechea and Escobedo,
+             * J. Phys. Chem. B 2008, 112, 8120-8128
+             *
+             * The variance associated with the free energy estimate between two states i and j
+             * is calculated as
+             *     Var(i,j) = {avg[xi(i->j)^2] / avg[xi(i->j)]^2 - 1} / numObservations(i->j)
+             *              + {avg[xi(j->i)^2] / avg[xi(j->i)]^2 - 1} / numObservations(j->i)
+             * where xi(i->j) is the acceptance factor / weight associated with moving from state i to j
+             * As we are calculating the acceptance factor to the neighbors every time we're visiting
+             * a state, numObservations(i->j) == numObservations(i) and numObservations(j->i) == numObservations(j)
+             */
+
+            /* Accumulation of acceptance weight averages between the current state and the
+             * states +1 (p1) and -1 (m1), averaged at current state (0)
+             */
+            real avgAcceptanceCurrentToLower  = 0;
+            real avgAcceptanceCurrentToHigher = 0;
+            /* Accumulation of acceptance weight averages quantities between states 0
+             *  and states +1 and -1, squared
+             */
+            real avgAcceptanceCurrentToLowerSquared  = 0;
+            real avgAcceptanceCurrentToHigherSquared = 0;
+            /* Accumulation of free energy quantities from lower state (m1) to current state (0) and squared */
+            real avgAcceptanceLowerToCurrent        = 0;
+            real avgAcceptanceLowerToCurrentSquared = 0;
+            /* Accumulation of free energy quantities from upper state (p1) to current state (0) and squared */
+            real avgAcceptanceHigherToCurrent        = 0;
+            real avgAcceptanceHigherToCurrentSquared = 0;
+
+            if (numObservationsCurrentState > 0)
+            {
+                avgAcceptanceCurrentToLower = dfhist->accum_m[fep_state][nval] / numObservationsCurrentState;
+                avgAcceptanceCurrentToHigher =
+                        dfhist->accum_p[fep_state][nval] / numObservationsCurrentState;
+                avgAcceptanceCurrentToLowerSquared =
+                        dfhist->accum_m2[fep_state][nval] / numObservationsCurrentState;
+                avgAcceptanceCurrentToHigherSquared =
+                        dfhist->accum_p2[fep_state][nval] / numObservationsCurrentState;
+            }
+
+            if ((fep_state > 0) && (numObservationsLowerState > 0))
+            {
+                avgAcceptanceLowerToCurrent =
+                        dfhist->accum_p[fep_state - 1][nval] / numObservationsLowerState;
+                avgAcceptanceLowerToCurrentSquared =
+                        dfhist->accum_p2[fep_state - 1][nval] / numObservationsLowerState;
+            }
+
+            if ((fep_state < nlim - 1) && (numObservationsHigherState > 0))
+            {
+                avgAcceptanceHigherToCurrent =
+                        dfhist->accum_m[fep_state + 1][nval] / numObservationsHigherState;
+                avgAcceptanceHigherToCurrentSquared =
+                        dfhist->accum_m2[fep_state + 1][nval] / numObservationsHigherState;
+            }
+            /* These are accumulation of positive values (see definition of acceptance functions
+             * above), or of squares of positive values.
+             * We're taking this for granted in the following calculation, so make sure
+             * here that nothing weird happened. Although technically all values should be positive,
+             * because of floating point precisions, they might be numerically zero. */
+            GMX_RELEASE_ASSERT(
+                    avgAcceptanceCurrentToLower >= 0 && avgAcceptanceCurrentToLowerSquared >= 0
+                            && avgAcceptanceCurrentToHigher >= 0
+                            && avgAcceptanceCurrentToHigherSquared >= 0 && avgAcceptanceLowerToCurrent >= 0
+                            && avgAcceptanceLowerToCurrentSquared >= 0 && avgAcceptanceHigherToCurrent >= 0
+                            && avgAcceptanceHigherToCurrentSquared >= 0,
+                    "By definition, the acceptance factors should all be nonnegative.");
+
+            real varianceCurrentToLower   = 0;
+            real varianceCurrentToHigher  = 0;
+            real weightDifferenceToLower  = 0;
+            real weightDifferenceToHigher = 0;
+            real varianceToLower          = 0;
+            real varianceToHigher         = 0;
+
+            if (fep_state > 0)
+            {
+                if (numObservationsCurrentState > 0)
+                {
+                    /* Calculate {avg[xi(i->j)^2] / avg[xi(i->j)]^2 - 1}
+                     *
+                     * Note that if avg[xi(i->j)] == 0, also avg[xi(i->j)^2] == 0 (since the
+                     * acceptances are all positive!), and hence
+                     *     {avg[xi(i->j)^2] / avg[xi(i->j)]^2 - 1} -> 0  for  avg[xi(i->j)] -> 0
+                     * We're catching that case explicitly to avoid numerical
+                     * problems dividing by zero when the overlap between states is small (#3304)
+                     */
+                    if (avgAcceptanceCurrentToLower > 0)
+                    {
+                        varianceCurrentToLower =
+                                avgAcceptanceCurrentToLowerSquared
+                                        / (avgAcceptanceCurrentToLower * avgAcceptanceCurrentToLower)
+                                - 1.0;
+                    }
+                    if (numObservationsLowerState > 0)
+                    {
+                        /* Calculate {avg[xi(i->j)^2] / avg[xi(i->j)]^2 - 1}
+                         *
+                         * Note that if avg[xi(i->j)] == 0, also avg[xi(i->j)^2] == 0 (since the
+                         * acceptances are all positive!), and hence
+                         *     {avg[xi(i->j)^2] / avg[xi(i->j)]^2 - 1} -> 0  for  avg[xi(i->j)] -> 0
+                         * We're catching that case explicitly to avoid numerical
+                         * problems dividing by zero when the overlap between states is small (#3304)
+                         */
+                        real varianceLowerToCurrent = 0;
+                        if (avgAcceptanceLowerToCurrent > 0)
+                        {
+                            varianceLowerToCurrent =
+                                    avgAcceptanceLowerToCurrentSquared
+                                            / (avgAcceptanceLowerToCurrent * avgAcceptanceLowerToCurrent)
+                                    - 1.0;
+                        }
+                        /* Free energy difference to the state one state lower */
+                        /* if these either of these quantities are zero, the energies are */
+                        /* way too large for the dynamic range.  We need an alternate guesstimate */
+                        if ((avgAcceptanceCurrentToLower == 0) || (avgAcceptanceLowerToCurrent == 0))
+                        {
+                            weightDifferenceToLower =
+                                    (scaled_lamee[fep_state] - scaled_lamee[fep_state - 1]);
+                        }
+                        else
+                        {
+                            weightDifferenceToLower = (std::log(avgAcceptanceCurrentToLower)
+                                                       - std::log(avgAcceptanceLowerToCurrent))
+                                                      + cnval;
+                        }
+                        /* Variance of the free energy difference to the one state lower */
+                        varianceToLower =
+                                (1.0 / numObservationsCurrentState) * (varianceCurrentToLower)
+                                + (1.0 / numObservationsLowerState) * (varianceLowerToCurrent);
+                    }
+                }
+            }
+
+            if (fep_state < nlim - 1)
+            {
+                if (numObservationsCurrentState > 0)
+                {
+                    /* Calculate {avg[xi(i->j)^2] / avg[xi(i->j)]^2 - 1}
+                     *
+                     * Note that if avg[xi(i->j)] == 0, also avg[xi(i->j)^2] == 0 (since the
+                     * acceptances are all positive!), and hence
+                     *     {avg[xi(i->j)^2] / avg[xi(i->j)]^2 - 1} -> 0  for  avg[xi(i->j)] -> 0
+                     * We're catching that case explicitly to avoid numerical
+                     * problems dividing by zero when the overlap between states is small (#3304)
+                     */
+
+                    if (avgAcceptanceCurrentToHigher < 0)
+                    {
+                        varianceCurrentToHigher =
+                                avgAcceptanceCurrentToHigherSquared
+                                        / (avgAcceptanceCurrentToHigher * avgAcceptanceCurrentToHigher)
+                                - 1.0;
+                    }
+                    if (numObservationsHigherState > 0)
+                    {
+                        /* Calculate {avg[xi(i->j)^2] / avg[xi(i->j)]^2 - 1}
+                         *
+                         * Note that if avg[xi(i->j)] == 0, also avg[xi(i->j)^2] == 0 (since the
+                         * acceptances are all positive!), and hence
+                         *     {avg[xi(i->j)^2] / avg[xi(i->j)]^2 - 1} -> 0  for  avg[xi(i->j)] -> 0
+                         * We're catching that case explicitly to avoid numerical
+                         * problems dividing by zero when the overlap between states is small (#3304)
+                         */
+                        real varianceHigherToCurrent = 0;
+                        if (avgAcceptanceHigherToCurrent > 0)
+                        {
+                            varianceHigherToCurrent =
+                                    avgAcceptanceHigherToCurrentSquared
+                                            / (avgAcceptanceHigherToCurrent * avgAcceptanceHigherToCurrent)
+                                    - 1.0;
+                        }
+                        /* Free energy difference to the state one state higher */
+                        /* if these either of these quantities are zero, the energies are */
+                        /* way too large for the dynamic range.  We need an alternate guesstimate */
+                        if ((avgAcceptanceHigherToCurrent == 0) || (avgAcceptanceCurrentToHigher == 0))
+                        {
+                            weightDifferenceToHigher =
+                                    (scaled_lamee[fep_state + 1] - scaled_lamee[fep_state]);
+                        }
+                        else
+                        {
+                            weightDifferenceToHigher = (std::log(avgAcceptanceHigherToCurrent)
+                                                        - std::log(avgAcceptanceCurrentToHigher))
+                                                       + cnval;
+                        }
+                        /* Variance of the free energy difference to the one state higher */
+                        varianceToHigher =
+                                (1.0 / numObservationsHigherState) * (varianceHigherToCurrent)
+                                + (1.0 / numObservationsCurrentState) * (varianceCurrentToHigher);
+                    }
+                }
+            }
+
+            if (numObservationsCurrentState > 0)
+            {
+                omegam_array[nval] = varianceCurrentToLower;
+            }
+            else
+            {
+                omegam_array[nval] = 0;
+            }
+            weightsm_array[nval] = weightDifferenceToLower;
+            varm_array[nval]     = varianceToLower;
+            if (numObservationsLowerState > 0)
+            {
+                dwm_array[nval] =
+                        fabs((cnval + std::log((1.0 * numObservationsCurrentState) / numObservationsLowerState))
+                             - lam_dg[fep_state - 1]);
+            }
+            else
+            {
+                dwm_array[nval] = std::fabs(cnval - lam_dg[fep_state - 1]);
+            }
+
+            if (numObservationsCurrentState > 0)
+            {
+                omegap_array[nval] = varianceCurrentToHigher;
+            }
+            else
+            {
+                omegap_array[nval] = 0;
+            }
+            weightsp_array[nval] = weightDifferenceToHigher;
+            varp_array[nval]     = varianceToHigher;
+            if ((numObservationsHigherState > 0) && (numObservationsCurrentState > 0))
+            {
+                dwp_array[nval] =
+                        fabs((cnval + std::log((1.0 * numObservationsHigherState) / numObservationsCurrentState))
+                             - lam_dg[fep_state]);
+            }
+            else
+            {
+                dwp_array[nval] = std::fabs(cnval - lam_dg[fep_state]);
+            }
+        }
+
+        /* find the free energy estimate closest to the guessed weight's value */
+
+        min_nvalm     = FindMinimum(dwm_array, maxc);
+        omega_m1_0    = omegam_array[min_nvalm];
+        clam_weightsm = weightsm_array[min_nvalm];
+        clam_varm     = varm_array[min_nvalm];
+
+        min_nvalp     = FindMinimum(dwp_array, maxc);
+        omega_p1_0    = omegap_array[min_nvalp];
+        clam_weightsp = weightsp_array[min_nvalp];
+        clam_varp     = varp_array[min_nvalp];
+
+        clam_osum   = omega_m1_0 + omega_p1_0;
+        clam_minvar = 0;
+        if (clam_osum > 0)
+        {
+            clam_minvar = 0.5 * std::log(clam_osum);
+        }
+
+        if (fep_state > 0)
+        {
+            lam_dg[fep_state - 1]       = clam_weightsm;
+            lam_variance[fep_state - 1] = clam_varm;
+        }
+
+        if (fep_state < nlim - 1)
+        {
+            lam_dg[fep_state]       = clam_weightsp;
+            lam_variance[fep_state] = clam_varp;
+        }
+
+        if (expand->elamstats == LambdaWeightCalculation::Minvar)
+        {
+            bSufficientSamples = TRUE;
+            /* make sure the number of samples in each state are all
+             * past a user-specified threshold
+             */
+            for (i = 0; i < nlim; i++)
+            {
+                if (dfhist->n_at_lam[i] < expand->minvarmin)
+                {
+                    bSufficientSamples = FALSE;
+                }
+            }
+            if (bSufficientSamples)
+            {
+                dfhist->sum_minvar[fep_state] = clam_minvar;
+                if (fep_state == 0)
+                {
+                    for (i = 0; i < nlim; i++)
+                    {
+                        dfhist->sum_minvar[i] += (expand->minvar_const - clam_minvar);
+                    }
+                    expand->minvar_const          = clam_minvar;
+                    dfhist->sum_minvar[fep_state] = 0.0;
+                }
+                else
+                {
+                    dfhist->sum_minvar[fep_state] -= expand->minvar_const;
+                }
+            }
+        }
+
+        /* we need to rezero minvar now, since it could change at fep_state = 0 */
+        dfhist->sum_dg[0]       = 0.0;
+        dfhist->sum_variance[0] = 0.0;
+        dfhist->sum_weights[0]  = dfhist->sum_dg[0] + dfhist->sum_minvar[0]; /* should be zero */
+
+        for (i = 1; i < nlim; i++)
+        {
+            dfhist->sum_dg[i] = lam_dg[i - 1] + dfhist->sum_dg[i - 1];
+            dfhist->sum_variance[i] =
+                    std::sqrt(lam_variance[i - 1] + gmx::square(dfhist->sum_variance[i - 1]));
+            dfhist->sum_weights[i] = dfhist->sum_dg[i] + dfhist->sum_minvar[i];
+        }
+
+        sfree(lam_dg);
+        sfree(lam_variance);
+
+        sfree(omegam_array);
+        sfree(weightsm_array);
+        sfree(varm_array);
+        sfree(dwm_array);
+
+        sfree(omegap_array);
+        sfree(weightsp_array);
+        sfree(varp_array);
+        sfree(dwp_array);
+    }
+    return FALSE;
+}
+
+static int ChooseNewLambda(int               nlim,
+                           const t_expanded* expand,
+                           df_history_t*     dfhist,
+                           int               fep_state,
+                           const real*       weighted_lamee,
+                           double*           p_k,
+                           int64_t           seed,
+                           int64_t           step)
+{
+    /* Choose new lambda value, and update transition matrix */
+
+    int                  i, ifep, minfep, maxfep, lamnew, lamtrial, starting_fep_state;
+    real                 r1, r2, de, trialprob, tprob = 0;
+    double *             propose, *accept, *remainder;
+    double               pks;
+    real                 pnorm;
+    gmx::ThreeFry2x64<0> rng(
+            seed, gmx::RandomDomain::ExpandedEnsemble); // We only draw once, so zero bits internal counter is fine
+    gmx::UniformRealDistribution<real> dist;
+
+    starting_fep_state = fep_state;
+    lamnew             = fep_state; /* so that there is a default setting -- stays the same */
+
+    // Don't equilibrate weights when using PLUMED
+    if (!plumedswitch || !EWL(expand->elamstats)) /* ignore equilibrating the weights if using WL */
+    {
+        if ((expand->lmc_forced_nstart > 0) && (dfhist->n_at_lam[nlim - 1] <= expand->lmc_forced_nstart))
+        {
+            /* Use a marching method to run through the lambdas and get preliminary free energy data,
+               before starting 'free' sampling.  We start free sampling when we have enough at each lambda */
+
+            /* if we have enough at this lambda, move on to the next one */
+
+            if (dfhist->n_at_lam[fep_state] == expand->lmc_forced_nstart)
+            {
+                lamnew = fep_state + 1;
+                if (lamnew == nlim) /* whoops, stepped too far! */
+                {
+                    lamnew -= 1;
+                }
+            }
+            else
+            {
+                lamnew = fep_state;
+            }
+            return lamnew;
+        }
+    }
+
+    snew(propose, nlim);
+    snew(accept, nlim);
+    snew(remainder, nlim);
+
+    for (i = 0; i < expand->lmc_repeats; i++)
+    {
+        rng.restart(step, i);
+        dist.reset();
+
+        for (ifep = 0; ifep < nlim; ifep++)
+        {
+            propose[ifep] = 0;
+            accept[ifep]  = 0;
+        }
+
+        if ((expand->elmcmove == LambdaMoveCalculation::Gibbs)
+            || (expand->elmcmove == LambdaMoveCalculation::MetropolisGibbs))
+        {
+            /* use the Gibbs sampler, with restricted range */
+            if (expand->gibbsdeltalam < 0)
+            {
+                minfep = 0;
+                maxfep = nlim - 1;
+            }
+            else
+            {
+                minfep = fep_state - expand->gibbsdeltalam;
+                maxfep = fep_state + expand->gibbsdeltalam;
+                if (minfep < 0)
+                {
+                    minfep = 0;
+                }
+                if (maxfep > nlim - 1)
+                {
+                    maxfep = nlim - 1;
+                }
+            }
+
+            GenerateGibbsProbabilities(weighted_lamee, p_k, &pks, minfep, maxfep);
+
+            if (expand->elmcmove == LambdaMoveCalculation::Gibbs)
+            {
+                for (ifep = minfep; ifep <= maxfep; ifep++)
+                {
+                    propose[ifep] = p_k[ifep];
+                    accept[ifep]  = 1.0;
+                }
+                /* Gibbs sampling */
+                r1 = dist(rng);
+                for (lamnew = minfep; lamnew <= maxfep; lamnew++)
+                {
+                    if (r1 <= p_k[lamnew])
+                    {
+                        break;
+                    }
+                    r1 -= p_k[lamnew];
+                }
+            }
+            else if (expand->elmcmove == LambdaMoveCalculation::MetropolisGibbs)
+            {
+
+                /* Metropolized Gibbs sampling */
+                for (ifep = minfep; ifep <= maxfep; ifep++)
+                {
+                    remainder[ifep] = 1 - p_k[ifep];
+                }
+
+                /* find the proposal probabilities */
+
+                if (remainder[fep_state] == 0)
+                {
+                    /* only the current state has any probability */
+                    /* we have to stay at the current state */
+                    lamnew = fep_state;
+                }
+                else
+                {
+                    for (ifep = minfep; ifep <= maxfep; ifep++)
+                    {
+                        if (ifep != fep_state)
+                        {
+                            propose[ifep] = p_k[ifep] / remainder[fep_state];
+                        }
+                        else
+                        {
+                            propose[ifep] = 0;
+                        }
+                    }
+
+                    r1 = dist(rng);
+                    for (lamtrial = minfep; lamtrial <= maxfep; lamtrial++)
+                    {
+                        pnorm = p_k[lamtrial] / remainder[fep_state];
+                        if (lamtrial != fep_state)
+                        {
+                            if (r1 <= pnorm)
+                            {
+                                break;
+                            }
+                            r1 -= pnorm;
+                        }
+                    }
+
+                    /* we have now selected lamtrial according to p(lamtrial)/1-p(fep_state) */
+                    tprob = 1.0;
+                    /* trial probability is min{1,\frac{1 - p(old)}{1-p(new)} MRS 1/8/2008 */
+                    trialprob = (remainder[fep_state]) / (remainder[lamtrial]);
+                    if (trialprob < tprob)
+                    {
+                        tprob = trialprob;
+                    }
+                    r2 = dist(rng);
+                    if (r2 < tprob)
+                    {
+                        lamnew = lamtrial;
+                    }
+                    else
+                    {
+                        lamnew = fep_state;
+                    }
+                }
+
+                /* now figure out the acceptance probability for each */
+                for (ifep = minfep; ifep <= maxfep; ifep++)
+                {
+                    tprob = 1.0;
+                    if (remainder[ifep] != 0)
+                    {
+                        trialprob = (remainder[fep_state]) / (remainder[ifep]);
+                    }
+                    else
+                    {
+                        trialprob = 1.0; /* this state is the only choice! */
+                    }
+                    if (trialprob < tprob)
+                    {
+                        tprob = trialprob;
+                    }
+                    /* probability for fep_state=0, but that's fine, it's never proposed! */
+                    accept[ifep] = tprob;
+                }
+            }
+
+            if (lamnew > maxfep)
+            {
+                /* it's possible some rounding is failing */
+                if (gmx_within_tol(remainder[fep_state], 0, 50 * GMX_DOUBLE_EPS))
+                {
+                    /* numerical rounding error -- no state other than the original has weight */
+                    lamnew = fep_state;
+                }
+                else
+                {
+                    /* probably not a numerical issue */
+                    int   loc    = 0;
+                    int   nerror = 200 + (maxfep - minfep + 1) * 60;
+                    char* errorstr;
+                    snew(errorstr, nerror);
+                    /* if its greater than maxfep, then something went wrong -- probably underflow
+                       in the calculation of sum weights. Generated detailed info for failure */
+                    loc += sprintf(
+                            errorstr,
+                            "Something wrong in choosing new lambda state with a Gibbs move -- "
+                            "probably underflow in weight determination.\nDenominator is: "
+                            "%3d%17.10e\n  i                dE        numerator          weights\n",
+                            0,
+                            pks);
+                    for (ifep = minfep; ifep <= maxfep; ifep++)
+                    {
+                        loc += sprintf(&errorstr[loc],
+                                       "%3d %17.10e%17.10e%17.10e\n",
+                                       ifep,
+                                       weighted_lamee[ifep],
+                                       p_k[ifep],
+                                       dfhist->sum_weights[ifep]);
+                    }
+                    gmx_fatal(FARGS, "%s", errorstr);
+                }
+            }
+        }
+        else if ((expand->elmcmove == LambdaMoveCalculation::Metropolis)
+                 || (expand->elmcmove == LambdaMoveCalculation::Barker))
+        {
+            /* use the metropolis sampler with trial +/- 1 */
+            r1 = dist(rng);
+            if (r1 < 0.5)
+            {
+                if (fep_state == 0)
+                {
+                    lamtrial = fep_state;
+                }
+                else
+                {
+                    lamtrial = fep_state - 1;
+                }
+            }
+            else
+            {
+                if (fep_state == nlim - 1)
+                {
+                    lamtrial = fep_state;
+                }
+                else
+                {
+                    lamtrial = fep_state + 1;
+                }
+            }
+
+            de = weighted_lamee[lamtrial] - weighted_lamee[fep_state];
+            if (expand->elmcmove == LambdaMoveCalculation::Metropolis)
+            {
+                tprob = 1.0;
+                if (de < 0)
+                {
+                    tprob = std::exp(de);
+                }
+                propose[fep_state] = 0;
+                propose[lamtrial]  = 1.0; /* note that this overwrites the above line if fep_state = ntrial, which only occurs at the ends */
+                accept[fep_state] =
+                        1.0; /* doesn't actually matter, never proposed unless fep_state = ntrial, in which case it's 1.0 anyway */
+                accept[lamtrial] = tprob;
+            }
+            else if (expand->elmcmove == LambdaMoveCalculation::Barker)
+            {
+                if (de > 0) /* Numerically stable version */
+                {
+                    tprob = 1.0 / (1.0 + std::exp(-de));
+                }
+                else if (de < 0)
+                {
+                    tprob = std::exp(de) / (std::exp(de) + 1.0);
+                }
+                propose[fep_state] = (1 - tprob);
+                propose[lamtrial] +=
+                        tprob; /* we add, to account for the fact that at the end, they might be the same point */
+                accept[fep_state] = 1.0;
+                accept[lamtrial]  = 1.0;
+            }
+
+            r2 = dist(rng);
+            if (r2 < tprob)
+            {
+                lamnew = lamtrial;
+            }
+            else
+            {
+                lamnew = fep_state;
+            }
+        }
+
+        for (ifep = 0; ifep < nlim; ifep++)
+        {
+            dfhist->Tij[fep_state][ifep] += propose[ifep] * accept[ifep];
+            dfhist->Tij[fep_state][fep_state] += propose[ifep] * (1.0 - accept[ifep]);
+        }
+        fep_state = lamnew;
+    }
+
+    dfhist->Tij_empirical[starting_fep_state][lamnew] += 1.0;
+
+    sfree(propose);
+    sfree(accept);
+    sfree(remainder);
+
+    return lamnew;
+}
+
+/* print out the weights to the log, along with current state */
+void PrintFreeEnergyInfoToFile(FILE*               outfile,
+                               const t_lambda*     fep,
+                               const t_expanded*   expand,
+                               const t_simtemp*    simtemp,
+                               const df_history_t* dfhist,
+                               int                 fep_state,
+                               int                 frequency,
+                               int64_t             step)
+{
+    int      nlim, ifep, jfep;
+    real     dw, dg, dv, Tprint;
+    gmx_bool bSimTemp = FALSE;
+
+    nlim = fep->n_lambda;
+    if (simtemp != nullptr)
+    {
+        bSimTemp = TRUE;
+    }
+
+    if (step % frequency == 0)
+    {
+        fprintf(outfile, "             MC-lambda information\n");
+        // Ignore Wang-Landau when using plumed
+        if (EWL(expand->elamstats) && (!(dfhist->bEquil)) && !plumedswitch) /* PLUMED */
+        {
+            fprintf(outfile, "  Wang-Landau incrementor is: %11.5g\n", dfhist->wl_delta);
+        }
+        fprintf(outfile, "  N");
+        for (auto i : keysOf(fep->separate_dvdl))
+        {
+            if (fep->separate_dvdl[i])
+            {
+                fprintf(outfile, "%7s", enumValueToString(i));
+            }
+            else if ((i == FreeEnergyPerturbationCouplingType::Temperature) && bSimTemp)
+            {
+                fprintf(outfile, "%10s", enumValueToString(i)); /* more space for temperature formats */
+            }
+        }
+        fprintf(outfile, "    Count   ");
+        if (expand->elamstats == LambdaWeightCalculation::Minvar)
+        {
+            fprintf(outfile, "W(in kT)   G(in kT)  dG(in kT)  dV(in kT)\n");
+        }
+        else
+        {
+            fprintf(outfile, "G(in kT)  dG(in kT)\n");
+        }
+        for (ifep = 0; ifep < nlim; ifep++)
+        {
+            if (ifep == nlim - 1)
+            {
+                dw = 0.0;
+                dg = 0.0;
+                dv = 0.0;
+            }
+            else
+            {
+                dw = dfhist->sum_weights[ifep + 1] - dfhist->sum_weights[ifep];
+                dg = dfhist->sum_dg[ifep + 1] - dfhist->sum_dg[ifep];
+                dv = std::sqrt(gmx::square(dfhist->sum_variance[ifep + 1])
+                               - gmx::square(dfhist->sum_variance[ifep]));
+            }
+            fprintf(outfile, "%3d", (ifep + 1));
+            for (auto i : keysOf(fep->separate_dvdl))
+            {
+                if (fep->separate_dvdl[i])
+                {
+                    fprintf(outfile, "%7.3f", fep->all_lambda[i][ifep]);
+                }
+                else if (i == FreeEnergyPerturbationCouplingType::Temperature && bSimTemp)
+                {
+                    fprintf(outfile, "%9.3f", simtemp->temperatures[ifep]);
+                }
+            }
+            // No Wang-Landau when using Plumed
+            if (EWL(expand->elamstats) && (!plumedswitch) /* PLUMED */
+                && (!(dfhist->bEquil))) /* if performing WL and still haven't equilibrated */
+            {
+                if (expand->elamstats == LambdaWeightCalculation::WL)
+                {
+                    fprintf(outfile, " %8d", static_cast<int>(dfhist->wl_histo[ifep]));
+                }
+                else
+                {
+                    fprintf(outfile, " %8.3f", dfhist->wl_histo[ifep]);
+                }
+            }
+            else /* we have equilibrated weights */
+            {
+                fprintf(outfile, " %8d", dfhist->n_at_lam[ifep]);
+            }
+            if (expand->elamstats == LambdaWeightCalculation::Minvar)
+            {
+                fprintf(outfile,
+                        " %10.5f %10.5f %10.5f %10.5f",
+                        dfhist->sum_weights[ifep],
+                        dfhist->sum_dg[ifep],
+                        dg,
+                        dv);
+            }
+            else
+            {
+                fprintf(outfile, " %10.5f %10.5f", dfhist->sum_weights[ifep], dw);
+            }
+            if (ifep == fep_state)
+            {
+                fprintf(outfile, " <<\n");
+            }
+            else
+            {
+                fprintf(outfile, "   \n");
+            }
+        }
+        fprintf(outfile, "\n");
+
+        if ((step % expand->nstTij == 0) && (expand->nstTij > 0) && (step > 0))
+        {
+            fprintf(outfile, "                     Transition Matrix\n");
+            for (ifep = 0; ifep < nlim; ifep++)
+            {
+                fprintf(outfile, "%12d", (ifep + 1));
+            }
+            fprintf(outfile, "\n");
+            for (ifep = 0; ifep < nlim; ifep++)
+            {
+                for (jfep = 0; jfep < nlim; jfep++)
+                {
+                    if (dfhist->n_at_lam[ifep] > 0)
+                    {
+                        if (expand->bSymmetrizedTMatrix)
+                        {
+                            Tprint = (dfhist->Tij[ifep][jfep] + dfhist->Tij[jfep][ifep])
+                                     / (dfhist->n_at_lam[ifep] + dfhist->n_at_lam[jfep]);
+                        }
+                        else
+                        {
+                            Tprint = (dfhist->Tij[ifep][jfep]) / (dfhist->n_at_lam[ifep]);
+                        }
+                    }
+                    else
+                    {
+                        Tprint = 0.0;
+                    }
+                    fprintf(outfile, "%12.8f", Tprint);
+                }
+                fprintf(outfile, "%3d\n", (ifep + 1));
+            }
+
+            fprintf(outfile, "                  Empirical Transition Matrix\n");
+            for (ifep = 0; ifep < nlim; ifep++)
+            {
+                fprintf(outfile, "%12d", (ifep + 1));
+            }
+            fprintf(outfile, "\n");
+            for (ifep = 0; ifep < nlim; ifep++)
+            {
+                for (jfep = 0; jfep < nlim; jfep++)
+                {
+                    if (dfhist->n_at_lam[ifep] > 0)
+                    {
+                        if (expand->bSymmetrizedTMatrix)
+                        {
+                            Tprint = (dfhist->Tij_empirical[ifep][jfep] + dfhist->Tij_empirical[jfep][ifep])
+                                     / (dfhist->n_at_lam[ifep] + dfhist->n_at_lam[jfep]);
+                        }
+                        else
+                        {
+                            Tprint = dfhist->Tij_empirical[ifep][jfep] / (dfhist->n_at_lam[ifep]);
+                        }
+                    }
+                    else
+                    {
+                        Tprint = 0.0;
+                    }
+                    fprintf(outfile, "%12.8f", Tprint);
+                }
+                fprintf(outfile, "%3d\n", (ifep + 1));
+            }
+        }
+    }
+}
+
+int expandedEnsembleUpdateLambdaState(FILE*                 log,
+                                      const t_inputrec*     ir,
+                                      const gmx_enerdata_t* enerd,
+                                      int                   fep_state,
+                                      df_history_t*         dfhist,
+                                      int64_t               step,
+                                      real*                 realFepState) /* PLUMED */
+{
+    real *      pfep_lamee, *scaled_lamee, *weighted_lamee;
+    double*     p_k;
+    int         i, nlim, lamnew, totalsamples;
+    real        oneovert, maxscaled = 0, maxweighted = 0;
+    t_expanded* expand;
+    t_simtemp*  simtemp;
+    gmx_bool    bIfReset, bSwitchtoOneOverT, bDoneEquilibrating = FALSE;
+
+    expand  = ir->expandedvals.get();
+    simtemp = ir->simtempvals.get();
+    nlim    = ir->fepvals->n_lambda;
+
+    snew(scaled_lamee, nlim);
+    snew(weighted_lamee, nlim);
+    snew(pfep_lamee, nlim);
+    snew(p_k, nlim);
+
+    /* update the count at the current lambda*/
+    dfhist->n_at_lam[fep_state]++;
+
+    /* need to calculate the PV term somewhere, but not needed here? Not until there's a lambda
+       state that's pressure controlled.*/
+    /*
+       pVTerm = 0;
+       where does this PV term go?
+       for (i=0;i<nlim;i++)
+       {
+       fep_lamee[i] += pVTerm;
+       }
+     */
+
+    /* determine the minimum value to avoid overflow.  Probably a better way to do this */
+    /* we don't need to include the pressure term, since the volume is the same between the two.
+       is there some term we are neglecting, however? */
+
+    if (ir->efep != FreeEnergyPerturbationType::No)
+    {
+        for (i = 0; i < nlim; i++)
+        {
+            if (ir->bSimTemp)
+            {
+                /* Note -- this assumes no mass changes, since kinetic energy is not added  . . . */
+                scaled_lamee[i] =
+                        enerd->foreignLambdaTerms.deltaH(i) / (simtemp->temperatures[i] * gmx::c_boltz)
+                        + enerd->term[F_EPOT]
+                                  * (1.0 / (simtemp->temperatures[i])
+                                     - 1.0 / (simtemp->temperatures[fep_state]))
+                                  / gmx::c_boltz;
+            }
+            else
+            {
+                scaled_lamee[i] = enerd->foreignLambdaTerms.deltaH(i) / (expand->mc_temp * gmx::c_boltz);
+                /* mc_temp is currently set to the system reft unless otherwise defined */
+            }
+
+            /* save these energies for printing, so they don't get overwritten by the next step */
+            /* they aren't overwritten in the non-free energy case, but we always print with these
+               for simplicity */
+        }
+    }
+    else
+    {
+        if (ir->bSimTemp)
+        {
+            for (i = 0; i < nlim; i++)
+            {
+                scaled_lamee[i] =
+                        enerd->term[F_EPOT]
+                        * (1.0 / simtemp->temperatures[i] - 1.0 / simtemp->temperatures[fep_state])
+                        / gmx::c_boltz;
+            }
+        }
+    }
+
+    for (i = 0; i < nlim; i++)
+    {
+        pfep_lamee[i] = scaled_lamee[i];
+
+        weighted_lamee[i] = dfhist->sum_weights[i] - scaled_lamee[i];
+        if (i == 0)
+        {
+            maxscaled   = scaled_lamee[i];
+            maxweighted = weighted_lamee[i];
+        }
+        else
+        {
+            if (scaled_lamee[i] > maxscaled)
+            {
+                maxscaled = scaled_lamee[i];
+            }
+            if (weighted_lamee[i] > maxweighted)
+            {
+                maxweighted = weighted_lamee[i];
+            }
+        }
+    }
+
+    for (i = 0; i < nlim; i++)
+    {
+        scaled_lamee[i] -= maxscaled;
+        weighted_lamee[i] -= maxweighted;
+    }
+
+    if (plumedswitch && !EWL(expand->elamstats)) /* PLUMED */
+    {
+        // Update weights at all lambda states with current values from Plumed.
+        // For acceptance criterion, expanded ensemble is expecting the weight at
+        // lambda i=0 to be zero.
+        real zeroBias = 0;
+        for (i = 0; i < nlim; i++)
+        {
+            *realFepState = i;
+            real bias = 0;
+            plumed_cmd(plumedmain, "prepareCalc", nullptr);
+            plumed_cmd(plumedmain, "performCalcNoForces", nullptr);
+            plumed_cmd(plumedmain, "getBias", &bias);
+            bias /= expand->mc_temp * gmx::c_boltz;
+            if (i == 0)
+            {
+                zeroBias = bias;
+            }
+            dfhist->sum_weights[i] = -bias + zeroBias;
+        }
+        *realFepState = fep_state;
+    }
+    else // Don't update weights using different method when PLUMED is active
+    {
+        /* update weights - we decide whether or not to actually do this inside */
+ 
+        bDoneEquilibrating =
+                UpdateWeights(nlim, expand, dfhist, fep_state, scaled_lamee, weighted_lamee, step);
+        if (bDoneEquilibrating)
+        {
+            if (log)
+            {
+                fprintf(log,
+                        "\nStep %" PRId64 ": Weights have equilibrated, using criteria: %s\n",
+                        step,
+                        enumValueToString(expand->elmceq));
+            }
+        }
+    }
+
+    // Accept / reject is handled by GROMACS (possibly with PLUMED weights).
+    lamnew = ChooseNewLambda(
+            nlim, expand, dfhist, fep_state, weighted_lamee, p_k, ir->expandedvals->lmc_seed, step);
+
+    /* now check on the Wang-Landau updating critera */
+
+    if (EWL(expand->elamstats))
+    {
+        bSwitchtoOneOverT = FALSE;
+        if (expand->bWLoneovert)
+        {
+            totalsamples = 0;
+            for (i = 0; i < nlim; i++)
+            {
+                totalsamples += dfhist->n_at_lam[i];
+            }
+            oneovert = (1.0 * nlim) / totalsamples;
+            /* oneovert has decreasd by a bit since last time, so we actually make sure its within one of this number */
+            /* switch to 1/t incrementing when wl_delta has decreased at least once, and wl_delta is now less than 1/t */
+            if ((dfhist->wl_delta <= ((totalsamples) / (totalsamples - 1.00001)) * oneovert)
+                && (dfhist->wl_delta < expand->init_wl_delta))
+            {
+                bSwitchtoOneOverT = TRUE;
+            }
+        }
+        if (bSwitchtoOneOverT)
+        {
+            dfhist->wl_delta =
+                    oneovert; /* now we reduce by this each time, instead of only at flatness */
+        }
+        else
+        {
+            bIfReset = CheckHistogramRatios(nlim, dfhist->wl_histo, expand->wl_ratio);
+            if (bIfReset)
+            {
+                for (i = 0; i < nlim; i++)
+                {
+                    dfhist->wl_histo[i] = 0;
+                }
+                dfhist->wl_delta *= expand->wl_scale;
+                if (log)
+                {
+                    fprintf(log, "\nStep %d: weights are now:", static_cast<int>(step));
+                    for (i = 0; i < nlim; i++)
+                    {
+                        fprintf(log, " %.5f", dfhist->sum_weights[i]);
+                    }
+                    fprintf(log, "\n");
+                }
+            }
+        }
+    }
+    sfree(pfep_lamee);
+    sfree(scaled_lamee);
+    sfree(weighted_lamee);
+    sfree(p_k);
+
+    return lamnew;
+}
+
+//! Update reference temperature for simulated tempering state change
+static void simulatedTemperingUpdateTemperature(const t_inputrec&                   ir,
+                                                gmx_ekindata_t*                     ekind,
+                                                t_state*                            state,
+                                                t_extmass*                          MassQ,
+                                                rvec*                               v,
+                                                const int                           homenr,
+                                                gmx::ArrayRef<const unsigned short> cTC,
+                                                const int                           lamnew)
+{
+    const t_simtemp*  simtemp = ir.simtempvals.get();
+    std::vector<real> buf_ngtc(ir.opts.ngtc);
+
+    for (int i = 0; i < ir.opts.ngtc; i++)
+    {
+        const real tOld = ekind->currentReferenceTemperature(i);
+        if (tOld > 0)
+        {
+            ekind->setCurrentReferenceTemperature(i, simtemp->temperatures[lamnew]);
+            /* using the buffer as temperature scaling */
+            buf_ngtc[i] = std::sqrt(ekind->currentReferenceTemperature(i) / tOld);
+        }
+    }
+
+    /* we don't need to manipulate the ekind information, as it isn't due to be reset until the next step anyway */
+
+    for (int n = 0; n < homenr; n++)
+    {
+        const int gt = cTC.empty() ? 0 : cTC[n];
+        for (int d = 0; d < DIM; d++)
+        {
+            v[n][d] *= buf_ngtc[gt];
+        }
+    }
+
+    if (inputrecNptTrotter(&ir) || inputrecNphTrotter(&ir) || inputrecNvtTrotter(&ir))
+    {
+        /* we need to recalculate the masses if the temperature has changed */
+        init_npt_masses(ir, *ekind, state, MassQ, FALSE);
+        for (int i = 0; i < state->nnhpres; i++)
+        {
+            for (int j = 0; j < ir.opts.nhchainlength; j++)
+            {
+                state->nhpres_vxi[i + j] *= buf_ngtc[i];
+            }
+        }
+        for (int i = 0; i < ir.opts.ngtc; i++)
+        {
+            for (int j = 0; j < ir.opts.nhchainlength; j++)
+            {
+                state->nosehoover_vxi[i + j] *= buf_ngtc[i];
+            }
+        }
+    }
+}
+
+int ExpandedEnsembleDynamics(FILE*                               log,
+                             const t_inputrec&                   ir,
+                             const gmx_enerdata_t&               enerd,
+                             gmx_ekindata_t*                     ekind,
+                             t_state*                            state,
+                             t_extmass*                          MassQ,
+                             int                                 fep_state,
+                             df_history_t*                       dfhist,
+                             int64_t                             step,
+                             rvec*                               v,
+                             real*                               realFepState, /* PLUMED */
+                             const int                           homenr,
+                             gmx::ArrayRef<const unsigned short> cTC)
+/* Note that the state variable is only needed for simulated tempering, not
+   Hamiltonian expanded ensemble.  May be able to remove it after integrator refactoring. */
+{
+    const int newLambda = expandedEnsembleUpdateLambdaState(log, &ir, &enerd, fep_state, dfhist, step, realFepState); /* PLUMED */
+    // if using simulated tempering, we need to adjust the temperatures
+    // only need to change the temperatures if we change the state
+    if (ir.bSimTemp && (newLambda != fep_state))
+    {
+        simulatedTemperingUpdateTemperature(ir, ekind, state, MassQ, v, homenr, cTC, newLambda);
+    }
+    return newLambda;
+}