/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
 * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
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 * as published by the Free Software Foundation; either version 2.1
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 */
#include "gmxpre.h"

#include <cmath>
#include <cstdlib>
#include <cstring>

#include <algorithm>

#include "gromacs/commandline/pargs.h"
#include "gromacs/commandline/viewit.h"
#include "gromacs/correlationfunctions/autocorr.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/gstat.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/energyoutput.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"

static const int NOTSET = -23451;

typedef struct
{
    real sum;
    real sum2;
} exactsum_t;

typedef struct
{
    real*       ener;
    exactsum_t* es;
    gmx_bool    bExactStat;
    double      av;
    double      rmsd;
    double      ee;
    double      slope;
} enerdat_t;

typedef struct
{
    int64_t    nsteps;
    int64_t    npoints;
    int        nframes;
    int*       step;
    int*       steps;
    int*       points;
    enerdat_t* s;
    gmx_bool   bHaveSums;
} enerdata_t;

static void done_enerdata_t(int nset, enerdata_t* edat)
{
    sfree(edat->step);
    sfree(edat->steps);
    sfree(edat->points);
    for (int i = 0; i < nset; i++)
    {
        sfree(edat->s[i].ener);
        sfree(edat->s[i].es);
    }
    sfree(edat->s);
}

static void chomp(char* buf)
{
    int len = std::strlen(buf);

    while ((len > 0) && (buf[len - 1] == '\n'))
    {
        buf[len - 1] = '\0';
        len--;
    }
}

static int* select_by_name(int nre, gmx_enxnm_t* nm, int* nset)
{
    gmx_bool*   bE;
    int         k, kk, j, i, nmatch, nind, nss;
    int*        set;
    gmx_bool    bEOF, bVerbose = TRUE, bLong = FALSE;
    char *      ptr, buf[STRLEN];
    const char* fm4   = "%3d  %-14s";
    const char* fm2   = "%3d  %-34s";
    char**      newnm = nullptr;

    if ((getenv("GMX_ENER_VERBOSE")) != nullptr)
    {
        bVerbose = FALSE;
    }

    fprintf(stderr, "\n");
    fprintf(stderr, "Select the terms you want from the following list by\n");
    fprintf(stderr, "selecting either (part of) the name or the number or a combination.\n");
    fprintf(stderr, "End your selection with an empty line or a zero.\n");
    fprintf(stderr, "-------------------------------------------------------------------\n");

    snew(newnm, nre);
    j = 0;
    for (k = 0; k < nre; k++)
    {
        newnm[k] = gmx_strdup(nm[k].name);
        /* Insert dashes in all the names */
        while ((ptr = std::strchr(newnm[k], ' ')) != nullptr)
        {
            *ptr = '-';
        }
        if (bVerbose)
        {
            if (j == 0)
            {
                if (k > 0)
                {
                    fprintf(stderr, "\n");
                }
                bLong = FALSE;
                for (kk = k; kk < k + 4; kk++)
                {
                    if (kk < nre && std::strlen(nm[kk].name) > 14)
                    {
                        bLong = TRUE;
                    }
                }
            }
            else
            {
                fprintf(stderr, " ");
            }
            if (!bLong)
            {
                fprintf(stderr, fm4, k + 1, newnm[k]);
                j++;
                if (j == 4)
                {
                    j = 0;
                }
            }
            else
            {
                fprintf(stderr, fm2, k + 1, newnm[k]);
                j++;
                if (j == 2)
                {
                    j = 0;
                }
            }
        }
    }
    if (bVerbose)
    {
        fprintf(stderr, "\n\n");
    }

    snew(bE, nre);

    bEOF = FALSE;
    while (!bEOF && (fgets2(buf, STRLEN - 1, stdin)))
    {
        /* Remove newlines */
        chomp(buf);

        /* Remove spaces */
        trim(buf);

        /* Empty line means end of input */
        bEOF = (std::strlen(buf) == 0);
        if (!bEOF)
        {
            ptr = buf;
            do
            {
                if (!bEOF)
                {
                    /* First try to read an integer */
                    nss = sscanf(ptr, "%d", &nind);
                    if (nss == 1)
                    {
                        /* Zero means end of input */
                        if (nind == 0)
                        {
                            bEOF = TRUE;
                        }
                        else if ((1 <= nind) && (nind <= nre))
                        {
                            bE[nind - 1] = TRUE;
                        }
                        else
                        {
                            fprintf(stderr, "number %d is out of range\n", nind);
                        }
                    }
                    else
                    {
                        /* Now try to read a string */
                        nmatch = 0;
                        for (nind = 0; nind < nre; nind++)
                        {
                            if (gmx_strcasecmp(newnm[nind], ptr) == 0)
                            {
                                bE[nind] = TRUE;
                                nmatch++;
                            }
                        }
                        if (nmatch == 0)
                        {
                            i      = std::strlen(ptr);
                            nmatch = 0;
                            for (nind = 0; nind < nre; nind++)
                            {
                                if (gmx_strncasecmp(newnm[nind], ptr, i) == 0)
                                {
                                    bE[nind] = TRUE;
                                    nmatch++;
                                }
                            }
                            if (nmatch == 0)
                            {
                                fprintf(stderr, "String '%s' does not match anything\n", ptr);
                            }
                        }
                    }
                }
                /* Look for the first space, and remove spaces from there */
                if ((ptr = std::strchr(ptr, ' ')) != nullptr)
                {
                    trim(ptr);
                }
            } while (!bEOF && ((ptr != nullptr) && (std::strlen(ptr) > 0)));
        }
    }

    snew(set, nre);
    for (i = (*nset) = 0; (i < nre); i++)
    {
        if (bE[i])
        {
            set[(*nset)++] = i;
        }
    }

    sfree(bE);

    if (*nset == 0)
    {
        gmx_fatal(FARGS, "No energy terms selected");
    }

    for (i = 0; (i < nre); i++)
    {
        sfree(newnm[i]);
    }
    sfree(newnm);

    return set;
}

static void get_dhdl_parms(const char* topnm, t_inputrec* ir)
{
    gmx_mtop_t mtop;
    int        natoms;
    matrix     box;

    /* all we need is the ir to be able to write the label */
    read_tpx(topnm, ir, box, &natoms, nullptr, nullptr, &mtop);
}

static void einstein_visco(const char*             fn,
                           const char*             fni,
                           int                     nsets,
                           int                     nint,
                           real**                  eneint,
                           real                    V,
                           real                    T,
                           double                  dt,
                           const gmx_output_env_t* oenv)
{
    FILE * fp0, *fp1;
    double av[4], avold[4];
    double fac, di;
    int    i, j, m, nf4;

    nf4 = nint / 4 + 1;

    for (i = 0; i <= nsets; i++)
    {
        avold[i] = 0;
    }
    fp0 = xvgropen(fni, "Shear viscosity integral", "Time (ps)", "(kg m\\S-1\\N s\\S-1\\N ps)", oenv);
    fp1 = xvgropen(fn, "Shear viscosity using Einstein relation", "Time (ps)",
                   "(kg m\\S-1\\N s\\S-1\\N)", oenv);
    for (i = 0; i < nf4; i++)
    {
        for (m = 0; m <= nsets; m++)
        {
            av[m] = 0;
        }
        for (j = 0; j < nint - i; j++)
        {
            for (m = 0; m < nsets; m++)
            {
                di = gmx::square(eneint[m][j + i] - eneint[m][j]);

                av[m] += di;
                av[nsets] += di / nsets;
            }
        }
        /* Convert to SI for the viscosity */
        fac = (V * NANO * NANO * NANO * PICO * 1e10) / (2 * BOLTZMANN * T) / (nint - i);
        fprintf(fp0, "%10g", i * dt);
        for (m = 0; (m <= nsets); m++)
        {
            av[m] = fac * av[m];
            fprintf(fp0, "  %10g", av[m]);
        }
        fprintf(fp0, "\n");
        fprintf(fp1, "%10g", (i + 0.5) * dt);
        for (m = 0; (m <= nsets); m++)
        {
            fprintf(fp1, "  %10g", (av[m] - avold[m]) / dt);
            avold[m] = av[m];
        }
        fprintf(fp1, "\n");
    }
    xvgrclose(fp0);
    xvgrclose(fp1);
}

typedef struct
{
    int64_t np;
    double  sum;
    double  sav;
    double  sav2;
} ee_sum_t;

typedef struct
{
    int      b;
    ee_sum_t sum;
    int64_t  nst;
    int64_t  nst_min;
} ener_ee_t;

static void clear_ee_sum(ee_sum_t* ees)
{
    ees->sav  = 0;
    ees->sav2 = 0;
    ees->np   = 0;
    ees->sum  = 0;
}

static void add_ee_sum(ee_sum_t* ees, double sum, int np)
{
    ees->np += np;
    ees->sum += sum;
}

static void add_ee_av(ee_sum_t* ees)
{
    double av;

    av = ees->sum / ees->np;
    ees->sav += av;
    ees->sav2 += av * av;
    ees->np  = 0;
    ees->sum = 0;
}

static double calc_ee2(int nb, ee_sum_t* ees)
{
    return (ees->sav2 / nb - gmx::square(ees->sav / nb)) / (nb - 1);
}

static void set_ee_av(ener_ee_t* eee)
{
    if (debug)
    {
        char buf[STEPSTRSIZE];
        fprintf(debug, "Storing average for err.est.: %s steps\n", gmx_step_str(eee->nst, buf));
    }
    add_ee_av(&eee->sum);
    eee->b++;
    if (eee->b == 1 || eee->nst < eee->nst_min)
    {
        eee->nst_min = eee->nst;
    }
    eee->nst = 0;
}

static void calc_averages(int nset, enerdata_t* edat, int nbmin, int nbmax)
{
    int         nb, i, f, nee;
    double      sum, sum2, sump, see2;
    int64_t     np, p, bound_nb;
    enerdat_t*  ed;
    exactsum_t* es;
    gmx_bool    bAllZero;
    double      x, sx, sy, sxx, sxy;
    ener_ee_t*  eee;

    /* Check if we have exact statistics over all points */
    for (i = 0; i < nset; i++)
    {
        ed             = &edat->s[i];
        ed->bExactStat = FALSE;
        if (edat->bHaveSums)
        {
            /* All energy file sum entries 0 signals no exact sums.
             * But if all energy values are 0, we still have exact sums.
             */
            bAllZero = TRUE;
            for (f = 0; f < edat->nframes && !ed->bExactStat; f++)
            {
                if (ed->ener[i] != 0)
                {
                    bAllZero = FALSE;
                }
                ed->bExactStat = (ed->es[f].sum != 0);
            }
            if (bAllZero)
            {
                ed->bExactStat = TRUE;
            }
        }
    }

    snew(eee, nbmax + 1);
    for (i = 0; i < nset; i++)
    {
        ed = &edat->s[i];

        sum  = 0;
        sum2 = 0;
        np   = 0;
        sx   = 0;
        sy   = 0;
        sxx  = 0;
        sxy  = 0;
        for (nb = nbmin; nb <= nbmax; nb++)
        {
            eee[nb].b = 0;
            clear_ee_sum(&eee[nb].sum);
            eee[nb].nst     = 0;
            eee[nb].nst_min = 0;
        }
        for (f = 0; f < edat->nframes; f++)
        {
            es = &ed->es[f];

            if (ed->bExactStat)
            {
                /* Add the sum and the sum of variances to the totals. */
                p    = edat->points[f];
                sump = es->sum;
                sum2 += es->sum2;
                if (np > 0)
                {
                    sum2 += gmx::square(sum / np - (sum + es->sum) / (np + p)) * np * (np + p) / p;
                }
            }
            else
            {
                /* Add a single value to the sum and sum of squares. */
                p    = 1;
                sump = ed->ener[f];
                sum2 += gmx::square(sump);
            }

            /* sum has to be increased after sum2 */
            np += p;
            sum += sump;

            /* For the linear regression use variance 1/p.
             * Note that sump is the sum, not the average, so we don't need p*.
             */
            x = edat->step[f] - 0.5 * (edat->steps[f] - 1);
            sx += p * x;
            sy += sump;
            sxx += p * x * x;
            sxy += x * sump;

            for (nb = nbmin; nb <= nbmax; nb++)
            {
                /* Check if the current end step is closer to the desired
                 * block boundary than the next end step.
                 */
                bound_nb = (edat->step[0] - 1) * nb + edat->nsteps * (eee[nb].b + 1);
                if (eee[nb].nst > 0 && bound_nb - edat->step[f - 1] * nb < edat->step[f] * nb - bound_nb)
                {
                    set_ee_av(&eee[nb]);
                }
                if (f == 0)
                {
                    eee[nb].nst = 1;
                }
                else
                {
                    eee[nb].nst += edat->step[f] - edat->step[f - 1];
                }
                if (ed->bExactStat)
                {
                    add_ee_sum(&eee[nb].sum, es->sum, edat->points[f]);
                }
                else
                {
                    add_ee_sum(&eee[nb].sum, edat->s[i].ener[f], 1);
                }
                bound_nb = (edat->step[0] - 1) * nb + edat->nsteps * (eee[nb].b + 1);
                if (edat->step[f] * nb >= bound_nb)
                {
                    set_ee_av(&eee[nb]);
                }
            }
        }

        edat->s[i].av = sum / np;
        if (ed->bExactStat)
        {
            edat->s[i].rmsd = std::sqrt(sum2 / np);
        }
        else
        {
            edat->s[i].rmsd = std::sqrt(sum2 / np - gmx::square(edat->s[i].av));
        }

        if (edat->nframes > 1)
        {
            edat->s[i].slope = (np * sxy - sx * sy) / (np * sxx - sx * sx);
        }
        else
        {
            edat->s[i].slope = 0;
        }

        nee  = 0;
        see2 = 0;
        for (nb = nbmin; nb <= nbmax; nb++)
        {
            /* Check if we actually got nb blocks and if the smallest
             * block is not shorter than 80% of the average.
             */
            if (debug)
            {
                char buf1[STEPSTRSIZE], buf2[STEPSTRSIZE];
                fprintf(debug, "Requested %d blocks, we have %d blocks, min %s nsteps %s\n", nb,
                        eee[nb].b, gmx_step_str(eee[nb].nst_min, buf1), gmx_step_str(edat->nsteps, buf2));
            }
            if (eee[nb].b == nb && 5 * nb * eee[nb].nst_min >= 4 * edat->nsteps)
            {
                see2 += calc_ee2(nb, &eee[nb].sum);
                nee++;
            }
        }
        if (nee > 0)
        {
            edat->s[i].ee = std::sqrt(see2 / nee);
        }
        else
        {
            edat->s[i].ee = -1;
        }
    }
    sfree(eee);
}

static enerdata_t* calc_sum(int nset, enerdata_t* edat, int nbmin, int nbmax)
{
    enerdata_t* esum;
    enerdat_t*  s;
    int         f, i;
    double      sum;

    snew(esum, 1);
    *esum = *edat;
    snew(esum->s, 1);
    s = &esum->s[0];
    snew(s->ener, esum->nframes);
    snew(s->es, esum->nframes);

    s->bExactStat = TRUE;
    s->slope      = 0;
    for (i = 0; i < nset; i++)
    {
        if (!edat->s[i].bExactStat)
        {
            s->bExactStat = FALSE;
        }
        s->slope += edat->s[i].slope;
    }

    for (f = 0; f < edat->nframes; f++)
    {
        sum = 0;
        for (i = 0; i < nset; i++)
        {
            sum += edat->s[i].ener[f];
        }
        s->ener[f] = sum;
        sum        = 0;
        for (i = 0; i < nset; i++)
        {
            sum += edat->s[i].es[f].sum;
        }
        s->es[f].sum  = sum;
        s->es[f].sum2 = 0;
    }

    calc_averages(1, esum, nbmin, nbmax);

    return esum;
}

static void ee_pr(double ee, int buflen, char* buf)
{
    snprintf(buf, buflen, "%s", "--");
    if (ee >= 0)
    {
        /* Round to two decimals by printing. */
        char tmp[100];
        snprintf(tmp, sizeof(tmp), "%.1e", ee);
        double rnd = gmx::doubleFromString(tmp);
        snprintf(buf, buflen, "%g", rnd);
    }
}

static void remove_drift(int nset, int nbmin, int nbmax, real dt, enerdata_t* edat)
{
    /* Remove the drift by performing a fit to y = ax+b.
       Uses 5 iterations. */
    int    i, j, k;
    double delta;

    edat->npoints = edat->nframes;
    edat->nsteps  = edat->nframes;

    for (k = 0; (k < 5); k++)
    {
        for (i = 0; (i < nset); i++)
        {
            delta = edat->s[i].slope * dt;

            if (nullptr != debug)
            {
                fprintf(debug, "slope for set %d is %g\n", i, edat->s[i].slope);
            }

            for (j = 0; (j < edat->nframes); j++)
            {
                edat->s[i].ener[j] -= j * delta;
                edat->s[i].es[j].sum  = 0;
                edat->s[i].es[j].sum2 = 0;
            }
        }
        calc_averages(nset, edat, nbmin, nbmax);
    }
}

static void calc_fluctuation_props(FILE*       fp,
                                   gmx_bool    bDriftCorr,
                                   real        dt,
                                   int         nset,
                                   int         nmol,
                                   char**      leg,
                                   enerdata_t* edat,
                                   int         nbmin,
                                   int         nbmax)
{
    int    i, j;
    double vv, v, h, varv, hh, varh, tt, cv, cp, alpha, kappa, dcp, varet;
    double NANO3;
    enum
    {
        eVol,
        eEnth,
        eTemp,
        eEtot,
        eNR
    };
    const char* my_ener[] = { "Volume", "Enthalpy", "Temperature", "Total Energy" };
    int         ii[eNR];

    NANO3 = NANO * NANO * NANO;
    if (!bDriftCorr)
    {
        fprintf(fp,
                "\nYou may want to use the -driftcorr flag in order to correct\n"
                "for spurious drift in the graphs. Note that this is not\n"
                "a substitute for proper equilibration and sampling!\n");
    }
    else
    {
        remove_drift(nset, nbmin, nbmax, dt, edat);
    }
    for (i = 0; (i < eNR); i++)
    {
        for (ii[i] = 0; (ii[i] < nset && (gmx_strcasecmp(leg[ii[i]], my_ener[i]) != 0)); ii[i]++) {}
/*        if (ii[i] < nset)
            fprintf(fp,"Found %s data.\n",my_ener[i]);
 */ }
/* Compute it all! */
alpha = kappa = cp = dcp = cv = NOTSET;

/* Temperature */
tt = NOTSET;
if (ii[eTemp] < nset)
{
    tt = edat->s[ii[eTemp]].av;
}
/* Volume */
vv = varv = NOTSET;
if ((ii[eVol] < nset) && (ii[eTemp] < nset))
{
    vv    = edat->s[ii[eVol]].av * NANO3;
    varv  = gmx::square(edat->s[ii[eVol]].rmsd * NANO3);
    kappa = (varv / vv) / (BOLTZMANN * tt);
}
/* Enthalpy */
hh = varh = NOTSET;
if ((ii[eEnth] < nset) && (ii[eTemp] < nset))
{
    hh   = KILO * edat->s[ii[eEnth]].av / AVOGADRO;
    varh = gmx::square(KILO * edat->s[ii[eEnth]].rmsd / AVOGADRO);
    cp   = AVOGADRO * ((varh / nmol) / (BOLTZMANN * tt * tt));
}
/* Total energy */
if ((ii[eEtot] < nset) && (hh == NOTSET) && (tt != NOTSET))
{
    /* Only compute cv in constant volume runs, which we can test
       by checking whether the enthalpy was computed.
     */
    varet = gmx::square(edat->s[ii[eEtot]].rmsd);
    cv    = KILO * ((varet / nmol) / (BOLTZ * tt * tt));
}
/* Alpha, dcp */
if ((ii[eVol] < nset) && (ii[eEnth] < nset) && (ii[eTemp] < nset))
{
    double v_sum, h_sum, vh_sum, v_aver, h_aver, vh_aver;
    vh_sum = v_sum = h_sum = 0;
    for (j = 0; (j < edat->nframes); j++)
    {
        v = edat->s[ii[eVol]].ener[j] * NANO3;
        h = KILO * edat->s[ii[eEnth]].ener[j] / AVOGADRO;
        v_sum += v;
        h_sum += h;
        vh_sum += (v * h);
    }
    vh_aver = vh_sum / edat->nframes;
    v_aver  = v_sum / edat->nframes;
    h_aver  = h_sum / edat->nframes;
    alpha   = (vh_aver - v_aver * h_aver) / (v_aver * BOLTZMANN * tt * tt);
    dcp     = (v_aver * AVOGADRO / nmol) * tt * gmx::square(alpha) / (kappa);
}

if (tt != NOTSET)
{
    if (nmol < 2)
    {
        fprintf(fp, "\nWARNING: nmol = %d, this may not be what you want.\n", nmol);
    }
    fprintf(fp, "\nTemperature dependent fluctuation properties at T = %g.\n", tt);
    fprintf(fp, "\nHeat capacities obtained from fluctuations do *not* include\n");
    fprintf(fp, "quantum corrections. If you want to get a more accurate estimate\n");
    fprintf(fp, "please use the g_dos program.\n\n");
    fprintf(fp,
            "WARNING: Please verify that your simulations are converged and perform\n"
            "a block-averaging error analysis (not implemented in g_energy yet)\n");

    if (debug != nullptr)
    {
        if (varv != NOTSET)
        {
            fprintf(fp, "varv  =  %10g (m^6)\n", varv * AVOGADRO / nmol);
        }
    }
    if (vv != NOTSET)
    {
        fprintf(fp, "Volume                                   = %10g m^3/mol\n", vv * AVOGADRO / nmol);
    }
    if (varh != NOTSET)
    {
        fprintf(fp, "Enthalpy                                 = %10g kJ/mol\n",
                hh * AVOGADRO / (KILO * nmol));
    }
    if (alpha != NOTSET)
    {
        fprintf(fp, "Coefficient of Thermal Expansion Alpha_P = %10g (1/K)\n", alpha);
    }
    if (kappa != NOTSET)
    {
        fprintf(fp, "Isothermal Compressibility Kappa         = %10g (m^3/J)\n", kappa);
        fprintf(fp, "Adiabatic bulk modulus                   = %10g (J/m^3)\n", 1.0 / kappa);
    }
    if (cp != NOTSET)
    {
        fprintf(fp, "Heat capacity at constant pressure Cp    = %10g J/(mol K)\n", cp);
    }
    if (cv != NOTSET)
    {
        fprintf(fp, "Heat capacity at constant volume Cv      = %10g J/(mol K)\n", cv);
    }
    if (dcp != NOTSET)
    {
        fprintf(fp, "Cp-Cv                                    =  %10g J/(mol K)\n", dcp);
    }
    please_cite(fp, "Allen1987a");
}
else
{
    fprintf(fp, "You should select the temperature in order to obtain fluctuation properties.\n");
}
}

static void analyse_ener(gmx_bool                bCorr,
                         const char*             corrfn,
                         const char*             eviscofn,
                         const char*             eviscoifn,
                         gmx_bool                bFee,
                         gmx_bool                bSum,
                         gmx_bool                bFluct,
                         gmx_bool                bVisco,
                         const char*             visfn,
                         int                     nmol,
                         int64_t                 start_step,
                         double                  start_t,
                         int64_t                 step,
                         double                  t,
                         real                    reftemp,
                         enerdata_t*             edat,
                         int                     nset,
                         const int               set[],
                         const gmx_bool*         bIsEner,
                         char**                  leg,
                         gmx_enxnm_t*            enm,
                         real                    Vaver,
                         real                    ezero,
                         int                     nbmin,
                         int                     nbmax,
                         const gmx_output_env_t* oenv)
{
    FILE* fp;
    /* Check out the printed manual for equations! */
    double      Dt, aver, stddev, errest, delta_t, totaldrift;
    enerdata_t* esum = nullptr;
    real        integral, intBulk, Temp = 0, Pres = 0;
    real        pr_aver, pr_stddev, pr_errest;
    double      beta = 0, expE, expEtot, *fee = nullptr;
    int64_t     nsteps;
    int         nexact, nnotexact;
    int         i, j, nout;
    char        buf[256], eebuf[100];

    nsteps = step - start_step + 1;
    if (nsteps < 1)
    {
        fprintf(stdout, "Not enough steps (%s) for statistics\n", gmx_step_str(nsteps, buf));
    }
    else
    {
        /* Calculate the time difference */
        delta_t = t - start_t;

        fprintf(stdout, "\nStatistics over %s steps [ %.4f through %.4f ps ], %d data sets\n",
                gmx_step_str(nsteps, buf), start_t, t, nset);

        calc_averages(nset, edat, nbmin, nbmax);

        if (bSum)
        {
            esum = calc_sum(nset, edat, nbmin, nbmax);
        }

        if (!edat->bHaveSums)
        {
            nexact    = 0;
            nnotexact = nset;
        }
        else
        {
            nexact    = 0;
            nnotexact = 0;
            for (i = 0; (i < nset); i++)
            {
                if (edat->s[i].bExactStat)
                {
                    nexact++;
                }
                else
                {
                    nnotexact++;
                }
            }
        }

        if (nnotexact == 0)
        {
            fprintf(stdout, "All statistics are over %s points\n", gmx_step_str(edat->npoints, buf));
        }
        else if (nexact == 0 || edat->npoints == edat->nframes)
        {
            fprintf(stdout, "All statistics are over %d points (frames)\n", edat->nframes);
        }
        else
        {
            fprintf(stdout, "The term%s", nnotexact == 1 ? "" : "s");
            for (i = 0; (i < nset); i++)
            {
                if (!edat->s[i].bExactStat)
                {
                    fprintf(stdout, " '%s'", leg[i]);
                }
            }
            fprintf(stdout, " %s has statistics over %d points (frames)\n",
                    nnotexact == 1 ? "is" : "are", edat->nframes);
            fprintf(stdout, "All other statistics are over %s points\n", gmx_step_str(edat->npoints, buf));
        }
        fprintf(stdout, "\n");

        fprintf(stdout, "%-24s %10s %10s %10s %10s", "Energy", "Average", "Err.Est.", "RMSD",
                "Tot-Drift");
        if (bFee)
        {
            fprintf(stdout, "  %10s\n", "-kT ln<e^(E/kT)>");
        }
        else
        {
            fprintf(stdout, "\n");
        }
        fprintf(stdout,
                "-------------------------------------------------------------------------------"
                "\n");

        /* Initiate locals, only used with -sum */
        expEtot = 0;
        if (bFee)
        {
            beta = 1.0 / (BOLTZ * reftemp);
            snew(fee, nset);
        }
        for (i = 0; (i < nset); i++)
        {
            aver   = edat->s[i].av;
            stddev = edat->s[i].rmsd;
            errest = edat->s[i].ee;

            if (bFee)
            {
                expE = 0;
                for (j = 0; (j < edat->nframes); j++)
                {
                    expE += std::exp(beta * (edat->s[i].ener[j] - aver) / nmol);
                }
                if (bSum)
                {
                    expEtot += expE / edat->nframes;
                }

                fee[i] = std::log(expE / edat->nframes) / beta + aver / nmol;
            }
            if (std::strstr(leg[i], "empera") != nullptr)
            {
                Temp = aver;
            }
            else if (std::strstr(leg[i], "olum") != nullptr)
            {
                Vaver = aver;
            }
            else if (std::strstr(leg[i], "essure") != nullptr)
            {
                Pres = aver;
            }
            if (bIsEner[i])
            {
                pr_aver   = aver / nmol - ezero;
                pr_stddev = stddev / nmol;
                pr_errest = errest / nmol;
            }
            else
            {
                pr_aver   = aver;
                pr_stddev = stddev;
                pr_errest = errest;
            }

            /* Multiply the slope in steps with the number of steps taken */
            totaldrift = (edat->nsteps - 1) * edat->s[i].slope;
            if (bIsEner[i])
            {
                totaldrift /= nmol;
            }

            ee_pr(pr_errest, sizeof(eebuf), eebuf);
            fprintf(stdout, "%-24s %10g %10s %10g %10g", leg[i], pr_aver, eebuf, pr_stddev, totaldrift);
            if (bFee)
            {
                fprintf(stdout, "  %10g", fee[i]);
            }

            fprintf(stdout, "  (%s)\n", enm[set[i]].unit);

            if (bFluct)
            {
                for (j = 0; (j < edat->nframes); j++)
                {
                    edat->s[i].ener[j] -= aver;
                }
            }
        }
        if (bSum)
        {
            totaldrift = (edat->nsteps - 1) * esum->s[0].slope;
            ee_pr(esum->s[0].ee / nmol, sizeof(eebuf), eebuf);
            fprintf(stdout, "%-24s %10g %10s %10s %10g  (%s)", "Total", esum->s[0].av / nmol, eebuf,
                    "--", totaldrift / nmol, enm[set[0]].unit);
            /* pr_aver,pr_stddev,a,totaldrift */
            if (bFee)
            {
                fprintf(stdout, "  %10g  %10g\n", std::log(expEtot) / beta + esum->s[0].av / nmol,
                        std::log(expEtot) / beta);
            }
            else
            {
                fprintf(stdout, "\n");
            }
        }

        /* Do correlation function */
        if (edat->nframes > 1)
        {
            Dt = delta_t / (edat->nframes - 1);
        }
        else
        {
            Dt = 0;
        }
        if (bVisco)
        {
            const char* leg[] = { "Shear", "Bulk" };
            real        factor;
            real**      eneset;
            real**      eneint;

            /* Assume pressure tensor is in Pxx Pxy Pxz Pyx Pyy Pyz Pzx Pzy Pzz */

            /* Symmetrise tensor! (and store in first three elements)
             * And subtract average pressure!
             */
            snew(eneset, 12);
            for (i = 0; i < 12; i++)
            {
                snew(eneset[i], edat->nframes);
            }
            for (i = 0; (i < edat->nframes); i++)
            {
                eneset[0][i] = 0.5 * (edat->s[1].ener[i] + edat->s[3].ener[i]);
                eneset[1][i] = 0.5 * (edat->s[2].ener[i] + edat->s[6].ener[i]);
                eneset[2][i] = 0.5 * (edat->s[5].ener[i] + edat->s[7].ener[i]);
                for (j = 3; j <= 11; j++)
                {
                    eneset[j][i] = edat->s[j].ener[i];
                }
                eneset[11][i] -= Pres;
            }

            /* Determine integrals of the off-diagonal pressure elements */
            snew(eneint, 3);
            for (i = 0; i < 3; i++)
            {
                snew(eneint[i], edat->nframes + 1);
            }
            eneint[0][0] = 0;
            eneint[1][0] = 0;
            eneint[2][0] = 0;
            for (i = 0; i < edat->nframes; i++)
            {
                eneint[0][i + 1] =
                        eneint[0][i]
                        + 0.5 * (edat->s[1].es[i].sum + edat->s[3].es[i].sum) * Dt / edat->points[i];
                eneint[1][i + 1] =
                        eneint[1][i]
                        + 0.5 * (edat->s[2].es[i].sum + edat->s[6].es[i].sum) * Dt / edat->points[i];
                eneint[2][i + 1] =
                        eneint[2][i]
                        + 0.5 * (edat->s[5].es[i].sum + edat->s[7].es[i].sum) * Dt / edat->points[i];
            }

            einstein_visco(eviscofn, eviscoifn, 3, edat->nframes + 1, eneint, Vaver, Temp, Dt, oenv);

            for (i = 0; i < 3; i++)
            {
                sfree(eneint[i]);
            }
            sfree(eneint);

            /*do_autocorr(corrfn,buf,nenergy,3,eneset,Dt,eacNormal,TRUE);*/
            /* Do it for shear viscosity */
            std::strcpy(buf, "Shear Viscosity");
            low_do_autocorr(corrfn, oenv, buf, edat->nframes, 3, (edat->nframes + 1) / 2, eneset,
                            Dt, eacNormal, 1, TRUE, FALSE, FALSE, 0.0, 0.0, 0);

            /* Now for bulk viscosity */
            std::strcpy(buf, "Bulk Viscosity");
            low_do_autocorr(corrfn, oenv, buf, edat->nframes, 1, (edat->nframes + 1) / 2,
                            &(eneset[11]), Dt, eacNormal, 1, TRUE, FALSE, FALSE, 0.0, 0.0, 0);

            factor = (Vaver * 1e-26 / (BOLTZMANN * Temp)) * Dt;
            fp     = xvgropen(visfn, buf, "Time (ps)", "\\8h\\4 (cp)", oenv);
            xvgr_legend(fp, asize(leg), leg, oenv);

            /* Use trapezium rule for integration */
            integral = 0;
            intBulk  = 0;
            nout     = get_acfnout();
            if ((nout < 2) || (nout >= edat->nframes / 2))
            {
                nout = edat->nframes / 2;
            }
            for (i = 1; (i < nout); i++)
            {
                integral += 0.5 * (eneset[0][i - 1] + eneset[0][i]) * factor;
                intBulk += 0.5 * (eneset[11][i - 1] + eneset[11][i]) * factor;
                fprintf(fp, "%10g  %10g  %10g\n", (i * Dt), integral, intBulk);
            }
            xvgrclose(fp);

            for (i = 0; i < 12; i++)
            {
                sfree(eneset[i]);
            }
            sfree(eneset);
        }
        else if (bCorr)
        {
            if (bFluct)
            {
                std::strcpy(buf, "Autocorrelation of Energy Fluctuations");
            }
            else
            {
                std::strcpy(buf, "Energy Autocorrelation");
            }
#if 0
            do_autocorr(corrfn, oenv, buf, edat->nframes,
                        bSum ? 1                 : nset,
                        bSum ? &edat->s[nset-1].ener : eneset,
                        (delta_t/edat->nframes), eacNormal, FALSE);
#endif
        }
    }
}

static void print_time(FILE* fp, double t)
{
    fprintf(fp, "%12.6f", t);
}

static void print1(FILE* fp, gmx_bool bDp, real e)
{
    if (bDp)
    {
        fprintf(fp, "  %16.12f", e);
    }
    else
    {
        fprintf(fp, "  %10.6f", e);
    }
}

static void fec(const char*             ene2fn,
                const char*             runavgfn,
                real                    reftemp,
                int                     nset,
                const int               set[],
                char*                   leg[],
                enerdata_t*             edat,
                double                  time[],
                const gmx_output_env_t* oenv)
{
    const char*  ravgleg[] = { "\\8D\\4E = E\\sB\\N-E\\sA\\N", "<e\\S-\\8D\\4E/kT\\N>\\s0..t\\N" };
    FILE*        fp;
    ener_file_t  enx;
    int          timecheck, nenergy, nenergy2, maxenergy;
    int          i, j;
    gmx_bool     bCont;
    real         aver, beta;
    real**       eneset2;
    double       dE, sum;
    gmx_enxnm_t* enm = nullptr;
    t_enxframe*  fr;
    char         buf[22];

    /* read second energy file */
    snew(fr, 1);
    enm = nullptr;
    enx = open_enx(ene2fn, "r");
    do_enxnms(enx, &(fr->nre), &enm);

    snew(eneset2, nset + 1);
    nenergy2  = 0;
    maxenergy = 0;
    timecheck = 0;
    do
    {
        /* This loop searches for the first frame (when -b option is given),
         * or when this has been found it reads just one energy frame
         */
        do
        {
            bCont = do_enx(enx, fr);

            if (bCont)
            {
                timecheck = check_times(fr->t);
            }

        } while (bCont && (timecheck < 0));

        /* Store energies for analysis afterwards... */
        if ((timecheck == 0) && bCont)
        {
            if (fr->nre > 0)
            {
                if (nenergy2 >= maxenergy)
                {
                    maxenergy += 1000;
                    for (i = 0; i <= nset; i++)
                    {
                        srenew(eneset2[i], maxenergy);
                    }
                }
                GMX_RELEASE_ASSERT(time != nullptr, "trying to dereference NULL time pointer");

                if (fr->t != time[nenergy2])
                {
                    fprintf(stderr, "\nWARNING time mismatch %g!=%g at frame %s\n", fr->t,
                            time[nenergy2], gmx_step_str(fr->step, buf));
                }
                for (i = 0; i < nset; i++)
                {
                    eneset2[i][nenergy2] = fr->ener[set[i]].e;
                }
                nenergy2++;
            }
        }
    } while (bCont && (timecheck == 0));

    /* check */
    if (edat->nframes != nenergy2)
    {
        fprintf(stderr, "\nWARNING file length mismatch %d!=%d\n", edat->nframes, nenergy2);
    }
    nenergy = std::min(edat->nframes, nenergy2);

    /* calculate fe difference dF = -kT ln < exp(-(E_B-E_A)/kT) >_A */
    fp = nullptr;
    if (runavgfn)
    {
        fp = xvgropen(runavgfn, "Running average free energy difference", "Time (" unit_time ")",
                      "\\8D\\4E (" unit_energy ")", oenv);
        xvgr_legend(fp, asize(ravgleg), ravgleg, oenv);
    }
    fprintf(stdout, "\n%-24s %10s\n", "Energy", "dF = -kT ln < exp(-(EB-EA)/kT) >A");
    sum  = 0;
    beta = 1.0 / (BOLTZ * reftemp);
    for (i = 0; i < nset; i++)
    {
        if (gmx_strcasecmp(leg[i], enm[set[i]].name) != 0)
        {
            fprintf(stderr, "\nWARNING energy set name mismatch %s!=%s\n", leg[i], enm[set[i]].name);
        }
        for (j = 0; j < nenergy; j++)
        {
            dE = eneset2[i][j] - edat->s[i].ener[j];
            sum += std::exp(-dE * beta);
            if (fp)
            {
                fprintf(fp, "%10g %10g %10g\n", time[j], dE, -BOLTZ * reftemp * std::log(sum / (j + 1)));
            }
        }
        aver = -BOLTZ * reftemp * std::log(sum / nenergy);
        fprintf(stdout, "%-24s %10g\n", leg[i], aver);
    }
    if (fp)
    {
        xvgrclose(fp);
    }
    sfree(fr);
}


static void do_dhdl(t_enxframe*             fr,
                    const t_inputrec*       ir,
                    FILE**                  fp_dhdl,
                    const char*             filename,
                    gmx_bool                bDp,
                    int*                    blocks,
                    int*                    hists,
                    int*                    samples,
                    int*                    nlambdas,
                    const gmx_output_env_t* oenv)
{
    const char *dhdl = "dH/d\\lambda", *deltag = "\\DeltaH", *lambda = "\\lambda";
    char        title[STRLEN], label_x[STRLEN], label_y[STRLEN], legend[STRLEN];
    char        buf[STRLEN];
    int         nblock_hist = 0, nblock_dh = 0, nblock_dhcoll = 0;
    int         i, j, k;
    /* coll data */
    double       temp = 0, start_time = 0, delta_time = 0, start_lambda = 0;
    static int   setnr             = 0;
    double*      native_lambda_vec = nullptr;
    const char** lambda_components = nullptr;
    int          n_lambda_vec      = 0;
    bool         firstPass         = true;

    /* now count the blocks & handle the global dh data */
    for (i = 0; i < fr->nblock; i++)
    {
        if (fr->block[i].id == enxDHHIST)
        {
            nblock_hist++;
        }
        else if (fr->block[i].id == enxDH)
        {
            nblock_dh++;
        }
        else if (fr->block[i].id == enxDHCOLL)
        {
            nblock_dhcoll++;
            if ((fr->block[i].nsub < 1) || (fr->block[i].sub[0].type != xdr_datatype_double)
                || (fr->block[i].sub[0].nr < 5))
            {
                gmx_fatal(FARGS, "Unexpected block data");
            }

            /* read the data from the DHCOLL block */
            temp         = fr->block[i].sub[0].dval[0];
            start_time   = fr->block[i].sub[0].dval[1];
            delta_time   = fr->block[i].sub[0].dval[2];
            start_lambda = fr->block[i].sub[0].dval[3];
            if (fr->block[i].nsub > 1)
            {
                if (firstPass)
                {
                    n_lambda_vec = fr->block[i].sub[1].ival[1];
                    snew(lambda_components, n_lambda_vec);
                    snew(native_lambda_vec, n_lambda_vec);
                    firstPass = false;
                }
                else
                {
                    if (n_lambda_vec != fr->block[i].sub[1].ival[1])
                    {
                        gmx_fatal(FARGS, "Unexpected change of basis set in lambda");
                    }
                }
                for (j = 0; j < n_lambda_vec; j++)
                {
                    native_lambda_vec[j] = fr->block[i].sub[0].dval[5 + j];
                    lambda_components[j] = efpt_singular_names[fr->block[i].sub[1].ival[2 + j]];
                }
            }
        }
    }
    // Clean up!
    sfree(native_lambda_vec);
    sfree(lambda_components);
    if (nblock_hist == 0 && nblock_dh == 0)
    {
        /* don't do anything */
        return;
    }
    if (nblock_hist > 0 && nblock_dh > 0)
    {
        gmx_fatal(FARGS,
                  "This energy file contains both histogram dhdl data and non-histogram dhdl data. "
                  "Don't know what to do.");
    }
    if (!*fp_dhdl)
    {
        if (nblock_dh > 0)
        {
            /* we have standard, non-histogram data --
               call open_dhdl to open the file */
            /* TODO this is an ugly hack that needs to be fixed: this will only
               work if the order of data is always the same and if we're
               only using the g_energy compiled with the mdrun that produced
               the ener.edr. */
            *fp_dhdl = open_dhdl(filename, ir, oenv);
        }
        else
        {
            sprintf(title, "N(%s)", deltag);
            sprintf(label_x, "%s (%s)", deltag, unit_energy);
            sprintf(label_y, "Samples");
            *fp_dhdl = xvgropen_type(filename, title, label_x, label_y, exvggtXNY, oenv);
            sprintf(buf, "T = %g (K), %s = %g", temp, lambda, start_lambda);
            xvgr_subtitle(*fp_dhdl, buf, oenv);
        }
    }

    (*hists) += nblock_hist;
    (*blocks) += nblock_dh;
    (*nlambdas) = nblock_hist + nblock_dh;

    /* write the data */
    if (nblock_hist > 0)
    {
        int64_t sum = 0;
        /* histograms */
        for (i = 0; i < fr->nblock; i++)
        {
            t_enxblock* blk = &(fr->block[i]);
            if (blk->id == enxDHHIST)
            {
                double  foreign_lambda, dx;
                int64_t x0;
                int     nhist, derivative;

                /* check the block types etc. */
                if ((blk->nsub < 2) || (blk->sub[0].type != xdr_datatype_double)
                    || (blk->sub[1].type != xdr_datatype_int64) || (blk->sub[0].nr < 2)
                    || (blk->sub[1].nr < 2))
                {
                    gmx_fatal(FARGS, "Unexpected block data in file");
                }
                foreign_lambda = blk->sub[0].dval[0];
                dx             = blk->sub[0].dval[1];
                nhist          = blk->sub[1].lval[0];
                derivative     = blk->sub[1].lval[1];
                for (j = 0; j < nhist; j++)
                {
                    const char* lg[1];
                    x0 = blk->sub[1].lval[2 + j];

                    if (!derivative)
                    {
                        sprintf(legend, "N(%s(%s=%g) | %s=%g)", deltag, lambda, foreign_lambda,
                                lambda, start_lambda);
                    }
                    else
                    {
                        sprintf(legend, "N(%s | %s=%g)", dhdl, lambda, start_lambda);
                    }

                    lg[0] = legend;
                    xvgr_new_dataset(*fp_dhdl, setnr, 1, lg, oenv);
                    setnr++;
                    for (k = 0; k < blk->sub[j + 2].nr; k++)
                    {
                        int    hist;
                        double xmin, xmax;

                        hist = blk->sub[j + 2].ival[k];
                        xmin = (x0 + k) * dx;
                        xmax = (x0 + k + 1) * dx;
                        fprintf(*fp_dhdl, "%g %d\n%g %d\n", xmin, hist, xmax, hist);
                        sum += hist;
                    }
                    /* multiple histogram data blocks in one histogram
                       mean that the second one is the reverse of the first one:
                       for dhdl derivatives, it's important to know both the
                       maximum and minimum values */
                    dx = -dx;
                }
            }
        }
        (*samples) += static_cast<int>(sum / nblock_hist);
    }
    else
    {
        /* raw dh */
        int len = 0;

        for (i = 0; i < fr->nblock; i++)
        {
            t_enxblock* blk = &(fr->block[i]);
            if (blk->id == enxDH)
            {
                if (len == 0)
                {
                    len = blk->sub[2].nr;
                }
                else
                {
                    if (len != blk->sub[2].nr)
                    {
                        gmx_fatal(FARGS, "Length inconsistency in dhdl data");
                    }
                }
            }
        }
        (*samples) += len;

        for (i = 0; i < len; i++)
        {
            double time = start_time + delta_time * i;

            fprintf(*fp_dhdl, "%.4f ", time);

            for (j = 0; j < fr->nblock; j++)
            {
                t_enxblock* blk = &(fr->block[j]);
                if (blk->id == enxDH)
                {
                    double value;
                    if (blk->sub[2].type == xdr_datatype_float)
                    {
                        value = blk->sub[2].fval[i];
                    }
                    else
                    {
                        value = blk->sub[2].dval[i];
                    }
                    /* we need to decide which data type it is based on the count*/

                    if (j == 1 && ir->bExpanded)
                    {
                        fprintf(*fp_dhdl, "%4d",
                                static_cast<int>(value)); /* if expanded ensembles and zero, this is a state value, it's an integer. We need a cleaner conditional than if j==1! */
                    }
                    else
                    {
                        if (bDp)
                        {
                            fprintf(*fp_dhdl, " %#.12g", value); /* print normal precision */
                        }
                        else
                        {
                            fprintf(*fp_dhdl, " %#.8g", value); /* print normal precision */
                        }
                    }
                }
            }
            fprintf(*fp_dhdl, "\n");
        }
    }
}


int gmx_energy(int argc, char* argv[])
{
    const char* desc[] = {
        "[THISMODULE] extracts energy components",
        "from an energy file. The user is prompted to interactively",
        "select the desired energy terms.[PAR]",

        "Average, RMSD, and drift are calculated with full precision from the",
        "simulation (see printed manual). Drift is calculated by performing",
        "a least-squares fit of the data to a straight line. The reported total drift",
        "is the difference of the fit at the first and last point.",
        "An error estimate of the average is given based on a block averages",
        "over 5 blocks using the full-precision averages. The error estimate",
        "can be performed over multiple block lengths with the options",
        "[TT]-nbmin[tt] and [TT]-nbmax[tt].",
        "[BB]Note[bb] that in most cases the energy files contains averages over all",
        "MD steps, or over many more points than the number of frames in",
        "energy file. This makes the [THISMODULE] statistics output more accurate",
        "than the [REF].xvg[ref] output. When exact averages are not present in the energy",
        "file, the statistics mentioned above are simply over the single, per-frame",
        "energy values.[PAR]",

        "The term fluctuation gives the RMSD around the least-squares fit.[PAR]",

        "Some fluctuation-dependent properties can be calculated provided",
        "the correct energy terms are selected, and that the command line option",
        "[TT]-fluct_props[tt] is given. The following properties",
        "will be computed:",
        "",
        "===============================  ===================",
        "Property                         Energy terms needed",
        "===============================  ===================",
        "Heat capacity C[SUB]p[sub] (NPT sims):    Enthalpy, Temp",
        "Heat capacity C[SUB]v[sub] (NVT sims):    Etot, Temp",
        "Thermal expansion coeff. (NPT):  Enthalpy, Vol, Temp",
        "Isothermal compressibility:      Vol, Temp",
        "Adiabatic bulk modulus:          Vol, Temp",
        "===============================  ===================",
        "",
        "You always need to set the number of molecules [TT]-nmol[tt].",
        "The C[SUB]p[sub]/C[SUB]v[sub] computations do [BB]not[bb] include any corrections",
        "for quantum effects. Use the [gmx-dos] program if you need that (and you do).[PAR]",

        "Option [TT]-odh[tt] extracts and plots the free energy data",
        "(Hamiltoian differences and/or the Hamiltonian derivative dhdl)",
        "from the [TT]ener.edr[tt] file.[PAR]",

        "With [TT]-fee[tt] an estimate is calculated for the free-energy",
        "difference with an ideal gas state::",
        "",
        "  [GRK]Delta[grk] A = A(N,V,T) - A[SUB]idealgas[sub](N,V,T) = kT ",
        "  [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln]",
        "  [GRK]Delta[grk] G = G(N,p,T) - G[SUB]idealgas[sub](N,p,T) = kT ",
        "  [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln]",
        "",
        "where k is Boltzmann's constant, T is set by [TT]-fetemp[tt] and",
        "the average is over the ensemble (or time in a trajectory).",
        "Note that this is in principle",
        "only correct when averaging over the whole (Boltzmann) ensemble",
        "and using the potential energy. This also allows for an entropy",
        "estimate using::",
        "",
        "  [GRK]Delta[grk] S(N,V,T) = S(N,V,T) - S[SUB]idealgas[sub](N,V,T) = ",
        "  ([CHEVRON]U[SUB]pot[sub][chevron] - [GRK]Delta[grk] A)/T",
        "  [GRK]Delta[grk] S(N,p,T) = S(N,p,T) - S[SUB]idealgas[sub](N,p,T) = ",
        "  ([CHEVRON]U[SUB]pot[sub][chevron] + pV - [GRK]Delta[grk] G)/T",
        "",

        "When a second energy file is specified ([TT]-f2[tt]), a free energy",
        "difference is calculated::",
        "",
        "  dF = -kT ",
        "  [LN][CHEVRON][EXP]-(E[SUB]B[sub]-E[SUB]A[sub]) / ",
        "  kT[exp][chevron][SUB]A[sub][ln],",
        "",
        "where E[SUB]A[sub] and E[SUB]B[sub] are the energies from the first and second energy",
        "files, and the average is over the ensemble A. The running average",
        "of the free energy difference is printed to a file specified by [TT]-ravg[tt].",
        "[BB]Note[bb] that the energies must both be calculated from the same trajectory."

    };
    static gmx_bool bSum = FALSE, bFee = FALSE, bPrAll = FALSE, bFluct = FALSE, bDriftCorr = FALSE;
    static gmx_bool bDp = FALSE, bMutot = FALSE, bOrinst = FALSE, bOvec = FALSE, bFluctProps = FALSE;
    static int      nmol = 1, nbmin = 5, nbmax = 5;
    static real     reftemp = 300.0, ezero = 0;
    t_pargs         pa[] = {
        { "-fee", FALSE, etBOOL, { &bFee }, "Do a free energy estimate" },
        { "-fetemp",
          FALSE,
          etREAL,
          { &reftemp },
          "Reference temperature for free energy calculation" },
        { "-zero", FALSE, etREAL, { &ezero }, "Subtract a zero-point energy" },
        { "-sum",
          FALSE,
          etBOOL,
          { &bSum },
          "Sum the energy terms selected rather than display them all" },
        { "-dp", FALSE, etBOOL, { &bDp }, "Print energies in high precision" },
        { "-nbmin", FALSE, etINT, { &nbmin }, "Minimum number of blocks for error estimate" },
        { "-nbmax", FALSE, etINT, { &nbmax }, "Maximum number of blocks for error estimate" },
        { "-mutot",
          FALSE,
          etBOOL,
          { &bMutot },
          "Compute the total dipole moment from the components" },
        { "-aver",
          FALSE,
          etBOOL,
          { &bPrAll },
          "Also print the exact average and rmsd stored in the energy frames (only when 1 term is "
          "requested)" },
        { "-nmol",
          FALSE,
          etINT,
          { &nmol },
          "Number of molecules in your sample: the energies are divided by this number" },
        { "-fluct_props",
          FALSE,
          etBOOL,
          { &bFluctProps },
          "Compute properties based on energy fluctuations, like heat capacity" },
        { "-driftcorr",
          FALSE,
          etBOOL,
          { &bDriftCorr },
          "Useful only for calculations of fluctuation properties. The drift in the observables "
          "will be subtracted before computing the fluctuation properties." },
        { "-fluc",
          FALSE,
          etBOOL,
          { &bFluct },
          "Calculate autocorrelation of energy fluctuations rather than energy itself" },
        { "-orinst", FALSE, etBOOL, { &bOrinst }, "Analyse instantaneous orientation data" },
        { "-ovec", FALSE, etBOOL, { &bOvec }, "Also plot the eigenvectors with [TT]-oten[tt]" }
    };
    static const char* setnm[] = { "Pres-XX", "Pres-XY",     "Pres-XZ", "Pres-YX",
                                   "Pres-YY", "Pres-YZ",     "Pres-ZX", "Pres-ZY",
                                   "Pres-ZZ", "Temperature", "Volume",  "Pressure" };

    FILE*        out     = nullptr;
    FILE*        fp_dhdl = nullptr;
    ener_file_t  fp;
    int          timecheck = 0;
    enerdata_t   edat;
    gmx_enxnm_t* enm = nullptr;
    t_enxframe * frame, *fr = nullptr;
    int          cur = 0;
#define NEXT (1 - cur)
    int               nre, nfr;
    int64_t           start_step;
    real              start_t;
    gmx_bool          bDHDL;
    gmx_bool          bFoundStart, bCont, bVisco;
    double            sum, dbl;
    double*           time = nullptr;
    real              Vaver;
    int *             set     = nullptr, i, j, nset, sss;
    gmx_bool*         bIsEner = nullptr;
    char**            leg     = nullptr;
    char              buf[256];
    gmx_output_env_t* oenv;
    int               dh_blocks = 0, dh_hists = 0, dh_samples = 0, dh_lambdas = 0;

    t_filenm fnm[] = {
        { efEDR, "-f", nullptr, ffREAD },        { efEDR, "-f2", nullptr, ffOPTRD },
        { efTPR, "-s", nullptr, ffOPTRD },       { efXVG, "-o", "energy", ffWRITE },
        { efXVG, "-viol", "violaver", ffOPTWR }, { efXVG, "-pairs", "pairs", ffOPTWR },
        { efXVG, "-corr", "enecorr", ffOPTWR },  { efXVG, "-vis", "visco", ffOPTWR },
        { efXVG, "-evisco", "evisco", ffOPTWR }, { efXVG, "-eviscoi", "eviscoi", ffOPTWR },
        { efXVG, "-ravg", "runavgdf", ffOPTWR }, { efXVG, "-odh", "dhdl", ffOPTWR }
    };
#define NFILE asize(fnm)
    int      npargs;
    t_pargs* ppa;

    npargs = asize(pa);
    ppa    = add_acf_pargs(&npargs, pa);
    if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END, NFILE, fnm,
                           npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
    {
        sfree(ppa);
        return 0;
    }

    bDHDL = opt2bSet("-odh", NFILE, fnm);

    nset = 0;

    snew(frame, 2);
    fp = open_enx(ftp2fn(efEDR, NFILE, fnm), "r");
    do_enxnms(fp, &nre, &enm);

    Vaver = -1;

    bVisco = opt2bSet("-vis", NFILE, fnm);

    t_inputrec  irInstance;
    t_inputrec* ir = &irInstance;

    if (!bDHDL)
    {
        if (bVisco)
        {
            nset = asize(setnm);
            snew(set, nset);
            /* This is nasty code... To extract Pres tensor, Volume and Temperature */
            for (j = 0; j < nset; j++)
            {
                for (i = 0; i < nre; i++)
                {
                    if (std::strstr(enm[i].name, setnm[j]))
                    {
                        set[j] = i;
                        break;
                    }
                }
                if (i == nre)
                {
                    if (gmx_strcasecmp(setnm[j], "Volume") == 0)
                    {
                        printf("Enter the box volume (" unit_volume "): ");
                        if (1 != scanf("%lf", &dbl))
                        {
                            gmx_fatal(FARGS, "Error reading user input");
                        }
                        Vaver = dbl;
                    }
                    else
                    {
                        gmx_fatal(FARGS, "Could not find term %s for viscosity calculation", setnm[j]);
                    }
                }
            }
        }
        else
        {
            set = select_by_name(nre, enm, &nset);
        }
        /* Print all the different units once */
        sprintf(buf, "(%s)", enm[set[0]].unit);
        for (i = 1; i < nset; i++)
        {
            for (j = 0; j < i; j++)
            {
                if (std::strcmp(enm[set[i]].unit, enm[set[j]].unit) == 0)
                {
                    break;
                }
            }
            if (j == i)
            {
                std::strcat(buf, ", (");
                std::strcat(buf, enm[set[i]].unit);
                std::strcat(buf, ")");
            }
        }
        out = xvgropen(opt2fn("-o", NFILE, fnm), "GROMACS Energies", "Time (ps)", buf, oenv);

        snew(leg, nset + 1);
        for (i = 0; (i < nset); i++)
        {
            leg[i] = enm[set[i]].name;
        }
        if (bSum)
        {
            leg[nset] = gmx_strdup("Sum");
            xvgr_legend(out, nset + 1, leg, oenv);
        }
        else
        {
            xvgr_legend(out, nset, leg, oenv);
        }

        snew(bIsEner, nset);
        for (i = 0; (i < nset); i++)
        {
            bIsEner[i] = FALSE;
            for (j = 0; (j <= F_ETOT); j++)
            {
                bIsEner[i] = bIsEner[i]
                             || (gmx_strcasecmp(interaction_function[j].longname, leg[i]) == 0);
            }
        }
        if (bPrAll && nset > 1)
        {
            gmx_fatal(FARGS, "Printing averages can only be done when a single set is selected");
        }
    }
    else if (bDHDL)
    {
        get_dhdl_parms(ftp2fn(efTPR, NFILE, fnm), ir);
    }

    /* Initiate energies and set them to zero */
    edat.nsteps    = 0;
    edat.npoints   = 0;
    edat.nframes   = 0;
    edat.step      = nullptr;
    edat.steps     = nullptr;
    edat.points    = nullptr;
    edat.bHaveSums = TRUE;
    snew(edat.s, nset);

    /* Initiate counters */
    bFoundStart = FALSE;
    start_step  = 0;
    start_t     = 0;
    do
    {
        /* This loop searches for the first frame (when -b option is given),
         * or when this has been found it reads just one energy frame
         */
        do
        {
            bCont = do_enx(fp, &(frame[NEXT]));
            if (bCont)
            {
                timecheck = check_times(frame[NEXT].t);
            }
        } while (bCont && (timecheck < 0));

        if ((timecheck == 0) && bCont)
        {
            /* We read a valid frame, so we can use it */
            fr = &(frame[NEXT]);

            if (fr->nre > 0)
            {
                /* The frame contains energies, so update cur */
                cur = NEXT;

                if (edat.nframes % 1000 == 0)
                {
                    srenew(edat.step, edat.nframes + 1000);
                    std::memset(&(edat.step[edat.nframes]), 0, 1000 * sizeof(edat.step[0]));
                    srenew(edat.steps, edat.nframes + 1000);
                    std::memset(&(edat.steps[edat.nframes]), 0, 1000 * sizeof(edat.steps[0]));
                    srenew(edat.points, edat.nframes + 1000);
                    std::memset(&(edat.points[edat.nframes]), 0, 1000 * sizeof(edat.points[0]));

                    for (i = 0; i < nset; i++)
                    {
                        srenew(edat.s[i].ener, edat.nframes + 1000);
                        std::memset(&(edat.s[i].ener[edat.nframes]), 0, 1000 * sizeof(edat.s[i].ener[0]));
                        srenew(edat.s[i].es, edat.nframes + 1000);
                        std::memset(&(edat.s[i].es[edat.nframes]), 0, 1000 * sizeof(edat.s[i].es[0]));
                    }
                }

                nfr            = edat.nframes;
                edat.step[nfr] = fr->step;

                if (!bFoundStart)
                {
                    bFoundStart = TRUE;
                    /* Initiate the previous step data */
                    start_step = fr->step;
                    start_t    = fr->t;
                    /* Initiate the energy sums */
                    edat.steps[nfr]  = 1;
                    edat.points[nfr] = 1;
                    for (i = 0; i < nset; i++)
                    {
                        sss                    = set[i];
                        edat.s[i].es[nfr].sum  = fr->ener[sss].e;
                        edat.s[i].es[nfr].sum2 = 0;
                    }
                    edat.nsteps  = 1;
                    edat.npoints = 1;
                }
                else
                {
                    edat.steps[nfr] = fr->nsteps;

                    if (fr->nsum <= 1)
                    {
                        /* mdrun only calculated the energy at energy output
                         * steps. We don't need to check step intervals.
                         */
                        edat.points[nfr] = 1;
                        for (i = 0; i < nset; i++)
                        {
                            sss                    = set[i];
                            edat.s[i].es[nfr].sum  = fr->ener[sss].e;
                            edat.s[i].es[nfr].sum2 = 0;
                        }
                        edat.npoints += 1;
                        edat.bHaveSums = FALSE;
                    }
                    else if (fr->step - start_step + 1 == edat.nsteps + fr->nsteps)
                    {
                        /* We have statistics  to the previous frame */
                        edat.points[nfr] = fr->nsum;
                        for (i = 0; i < nset; i++)
                        {
                            sss                    = set[i];
                            edat.s[i].es[nfr].sum  = fr->ener[sss].esum;
                            edat.s[i].es[nfr].sum2 = fr->ener[sss].eav;
                        }
                        edat.npoints += fr->nsum;
                    }
                    else
                    {
                        /* The interval does not match fr->nsteps:
                         * can not do exact averages.
                         */
                        edat.bHaveSums = FALSE;
                    }

                    edat.nsteps = fr->step - start_step + 1;
                }
                for (i = 0; i < nset; i++)
                {
                    edat.s[i].ener[nfr] = fr->ener[set[i]].e;
                }
            }
            /*
             * Store energies for analysis afterwards...
             */
            if (!bDHDL && (fr->nre > 0))
            {
                if (edat.nframes % 1000 == 0)
                {
                    srenew(time, edat.nframes + 1000);
                }
                time[edat.nframes] = fr->t;
                edat.nframes++;
            }
            if (bDHDL)
            {
                do_dhdl(fr, ir, &fp_dhdl, opt2fn("-odh", NFILE, fnm), bDp, &dh_blocks, &dh_hists,
                        &dh_samples, &dh_lambdas, oenv);
            }

            /*******************************************
             * E N E R G I E S
             *******************************************/
            else
            {
                if (fr->nre > 0)
                {
                    if (bPrAll)
                    {
                        /* We skip frames with single points (usually only the first frame),
                         * since they would result in an average plot with outliers.
                         */
                        if (fr->nsum > 1)
                        {
                            print_time(out, fr->t);
                            print1(out, bDp, fr->ener[set[0]].e);
                            print1(out, bDp, fr->ener[set[0]].esum / fr->nsum);
                            print1(out, bDp, std::sqrt(fr->ener[set[0]].eav / fr->nsum));
                            fprintf(out, "\n");
                        }
                    }
                    else
                    {
                        print_time(out, fr->t);
                        if (bSum)
                        {
                            sum = 0;
                            for (i = 0; i < nset; i++)
                            {
                                sum += fr->ener[set[i]].e;
                            }
                            print1(out, bDp, sum / nmol - ezero);
                        }
                        else
                        {
                            for (i = 0; (i < nset); i++)
                            {
                                if (bIsEner[i])
                                {
                                    print1(out, bDp, (fr->ener[set[i]].e) / nmol - ezero);
                                }
                                else
                                {
                                    print1(out, bDp, fr->ener[set[i]].e);
                                }
                            }
                        }
                        fprintf(out, "\n");
                    }
                }
            }
        }
    } while (bCont && (timecheck == 0));

    fprintf(stderr, "\n");
    done_ener_file(fp);
    if (out)
    {
        xvgrclose(out);
    }

    if (bDHDL)
    {
        if (fp_dhdl)
        {
            gmx_fio_fclose(fp_dhdl);
            printf("\n\nWrote %d lambda values with %d samples as ", dh_lambdas, dh_samples);
            if (dh_hists > 0)
            {
                printf("%d dH histograms ", dh_hists);
            }
            if (dh_blocks > 0)
            {
                printf("%d dH data blocks ", dh_blocks);
            }
            printf("to %s\n", opt2fn("-odh", NFILE, fnm));
        }
        else
        {
            gmx_fatal(FARGS, "No dH data in %s\n", opt2fn("-f", NFILE, fnm));
        }
    }
    else
    {
        double dt = (frame[cur].t - start_t) / (edat.nframes - 1);
        analyse_ener(opt2bSet("-corr", NFILE, fnm), opt2fn("-corr", NFILE, fnm),
                     opt2fn("-evisco", NFILE, fnm), opt2fn("-eviscoi", NFILE, fnm), bFee, bSum,
                     bFluct, bVisco, opt2fn("-vis", NFILE, fnm), nmol, start_step, start_t,
                     frame[cur].step, frame[cur].t, reftemp, &edat, nset, set, bIsEner, leg, enm,
                     Vaver, ezero, nbmin, nbmax, oenv);
        if (bFluctProps)
        {
            calc_fluctuation_props(stdout, bDriftCorr, dt, nset, nmol, leg, &edat, nbmin, nbmax);
        }
    }
    if (opt2bSet("-f2", NFILE, fnm))
    {
        fec(opt2fn("-f2", NFILE, fnm), opt2fn("-ravg", NFILE, fnm), reftemp, nset, set, leg, &edat,
            time, oenv);
    }
    // Clean up!
    done_enerdata_t(nset, &edat);
    sfree(time);
    free_enxframe(&frame[0]);
    free_enxframe(&frame[1]);
    sfree(frame);
    free_enxnms(nre, enm);
    sfree(ppa);
    sfree(set);
    sfree(leg);
    sfree(bIsEner);
    {
        const char* nxy = "-nxy";

        do_view(oenv, opt2fn("-o", NFILE, fnm), nxy);
        do_view(oenv, opt2fn_null("-ravg", NFILE, fnm), nxy);
        do_view(oenv, opt2fn_null("-odh", NFILE, fnm), nxy);
    }
    output_env_done(oenv);

    return 0;
}
