Moved domdec structures out of commrec.h.

[gromacs.git] / src / gromacs / mdlib / update.cpp

/*
 * 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, 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.
 *
 * 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
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 *
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 */
#include "gmxpre.h"

#include "update.h"

#include <math.h>
#include <stdio.h>

#include <algorithm>

#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/txtdump.h"
#include "gromacs/gmxlib/disre.h"
#include "gromacs/gmxlib/gmx_omp_nthreads.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/gmxlib/orires.h"
#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdlib/tgroup.h"
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/boxutilities.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/random/random.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxomp.h"
#include "gromacs/utility/smalloc.h"

/*For debugging, start at v(-dt/2) for velolcity verlet -- uncomment next line */
/*#define STARTFROMDT2*/

typedef struct {
    double gdt;
    double eph;
    double emh;
    double em;
    double b;
    double c;
    double d;
} gmx_sd_const_t;

typedef struct {
    real V;
    real X;
    real Yv;
    real Yx;
} gmx_sd_sigma_t;

typedef struct {
    /* BD stuff */
    real           *bd_rf;
    /* SD stuff */
    gmx_sd_const_t *sdc;
    gmx_sd_sigma_t *sdsig;
    rvec           *sd_V;
    int             sd_V_nalloc;
    /* andersen temperature control stuff */
    gmx_bool       *randomize_group;
    real           *boltzfac;
} gmx_stochd_t;

typedef struct gmx_update
{
    gmx_stochd_t *sd;
    /* xprime for constraint algorithms */
    rvec         *xp;
    int           xp_nalloc;

    /* Variables for the deform algorithm */
    gmx_int64_t     deformref_step;
    matrix          deformref_box;
} t_gmx_update;


static void do_update_md(int start, int nrend, double dt,
                         t_grp_tcstat *tcstat,
                         double nh_vxi[],
                         gmx_bool bNEMD, t_grp_acc *gstat, rvec accel[],
                         ivec nFreeze[],
                         real invmass[],
                         unsigned short ptype[], unsigned short cFREEZE[],
                         unsigned short cACC[], unsigned short cTC[],
                         rvec x[], rvec xprime[], rvec v[],
                         rvec f[], matrix M,
                         gmx_bool bNH, gmx_bool bPR)
{
    double imass, w_dt;
    int    gf = 0, ga = 0, gt = 0;
    rvec   vrel;
    real   vn, vv, va, vb, vnrel;
    real   lg, vxi = 0, u;
    int    n, d;

    if (bNH || bPR)
    {
        /* Update with coupling to extended ensembles, used for
         * Nose-Hoover and Parrinello-Rahman coupling
         * Nose-Hoover uses the reversible leap-frog integrator from
         * Holian et al. Phys Rev E 52(3) : 2338, 1995
         */
        for (n = start; n < nrend; n++)
        {
            imass = invmass[n];
            if (cFREEZE)
            {
                gf   = cFREEZE[n];
            }
            if (cACC)
            {
                ga   = cACC[n];
            }
            if (cTC)
            {
                gt   = cTC[n];
            }
            lg   = tcstat[gt].lambda;
            if (bNH)
            {
                vxi   = nh_vxi[gt];
            }
            rvec_sub(v[n], gstat[ga].u, vrel);

            for (d = 0; d < DIM; d++)
            {
                if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
                {
                    vnrel = (lg*vrel[d] + dt*(imass*f[n][d] - 0.5*vxi*vrel[d]
                                              - iprod(M[d], vrel)))/(1 + 0.5*vxi*dt);
                    /* do not scale the mean velocities u */
                    vn             = gstat[ga].u[d] + accel[ga][d]*dt + vnrel;
                    v[n][d]        = vn;
                    xprime[n][d]   = x[n][d]+vn*dt;
                }
                else
                {
                    v[n][d]        = 0.0;
                    xprime[n][d]   = x[n][d];
                }
            }
        }
    }
    else if (cFREEZE != NULL ||
             nFreeze[0][XX] || nFreeze[0][YY] || nFreeze[0][ZZ] ||
             bNEMD)
    {
        /* Update with Berendsen/v-rescale coupling and freeze or NEMD */
        for (n = start; n < nrend; n++)
        {
            w_dt = invmass[n]*dt;
            if (cFREEZE)
            {
                gf   = cFREEZE[n];
            }
            if (cACC)
            {
                ga   = cACC[n];
            }
            if (cTC)
            {
                gt   = cTC[n];
            }
            lg   = tcstat[gt].lambda;

            for (d = 0; d < DIM; d++)
            {
                vn             = v[n][d];
                if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
                {
                    vv             = lg*vn + f[n][d]*w_dt;

                    /* do not scale the mean velocities u */
                    u              = gstat[ga].u[d];
                    va             = vv + accel[ga][d]*dt;
                    vb             = va + (1.0-lg)*u;
                    v[n][d]        = vb;
                    xprime[n][d]   = x[n][d]+vb*dt;
                }
                else
                {
                    v[n][d]        = 0.0;
                    xprime[n][d]   = x[n][d];
                }
            }
        }
    }
    else
    {
        /* Plain update with Berendsen/v-rescale coupling */
        for (n = start; n < nrend; n++)
        {
            if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
            {
                w_dt = invmass[n]*dt;
                if (cTC)
                {
                    gt = cTC[n];
                }
                lg = tcstat[gt].lambda;

                for (d = 0; d < DIM; d++)
                {
                    vn           = lg*v[n][d] + f[n][d]*w_dt;
                    v[n][d]      = vn;
                    xprime[n][d] = x[n][d] + vn*dt;
                }
            }
            else
            {
                for (d = 0; d < DIM; d++)
                {
                    v[n][d]        = 0.0;
                    xprime[n][d]   = x[n][d];
                }
            }
        }
    }
}

static void do_update_vv_vel(int start, int nrend, double dt,
                             rvec accel[], ivec nFreeze[], real invmass[],
                             unsigned short ptype[], unsigned short cFREEZE[],
                             unsigned short cACC[], rvec v[], rvec f[],
                             gmx_bool bExtended, real veta, real alpha)
{
    double w_dt;
    int    gf = 0, ga = 0;
    int    n, d;
    double g, mv1, mv2;

    if (bExtended)
    {
        g        = 0.25*dt*veta*alpha;
        mv1      = exp(-g);
        mv2      = series_sinhx(g);
    }
    else
    {
        mv1      = 1.0;
        mv2      = 1.0;
    }
    for (n = start; n < nrend; n++)
    {
        w_dt = invmass[n]*dt;
        if (cFREEZE)
        {
            gf   = cFREEZE[n];
        }
        if (cACC)
        {
            ga   = cACC[n];
        }

        for (d = 0; d < DIM; d++)
        {
            if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
            {
                v[n][d]             = mv1*(mv1*v[n][d] + 0.5*(w_dt*mv2*f[n][d]))+0.5*accel[ga][d]*dt;
            }
            else
            {
                v[n][d]        = 0.0;
            }
        }
    }
} /* do_update_vv_vel */

static void do_update_vv_pos(int start, int nrend, double dt,
                             ivec nFreeze[],
                             unsigned short ptype[], unsigned short cFREEZE[],
                             rvec x[], rvec xprime[], rvec v[],
                             gmx_bool bExtended, real veta)
{
    int    gf = 0;
    int    n, d;
    double g, mr1, mr2;

    /* Would it make more sense if Parrinello-Rahman was put here? */
    if (bExtended)
    {
        g        = 0.5*dt*veta;
        mr1      = exp(g);
        mr2      = series_sinhx(g);
    }
    else
    {
        mr1      = 1.0;
        mr2      = 1.0;
    }

    for (n = start; n < nrend; n++)
    {

        if (cFREEZE)
        {
            gf   = cFREEZE[n];
        }

        for (d = 0; d < DIM; d++)
        {
            if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
            {
                xprime[n][d]   = mr1*(mr1*x[n][d]+mr2*dt*v[n][d]);
            }
            else
            {
                xprime[n][d]   = x[n][d];
            }
        }
    }
} /* do_update_vv_pos */

static void do_update_visc(int start, int nrend, double dt,
                           t_grp_tcstat *tcstat,
                           double nh_vxi[],
                           real invmass[],
                           unsigned short ptype[], unsigned short cTC[],
                           rvec x[], rvec xprime[], rvec v[],
                           rvec f[], matrix M, matrix box, real
                           cos_accel, real vcos,
                           gmx_bool bNH, gmx_bool bPR)
{
    double imass, w_dt;
    int    gt = 0;
    real   vn, vc;
    real   lg, vxi = 0, vv;
    real   fac, cosz;
    rvec   vrel;
    int    n, d;

    fac = 2*M_PI/(box[ZZ][ZZ]);

    if (bNH || bPR)
    {
        /* Update with coupling to extended ensembles, used for
         * Nose-Hoover and Parrinello-Rahman coupling
         */
        for (n = start; n < nrend; n++)
        {
            imass = invmass[n];
            if (cTC)
            {
                gt   = cTC[n];
            }
            lg   = tcstat[gt].lambda;
            cosz = cos(fac*x[n][ZZ]);

            copy_rvec(v[n], vrel);

            vc            = cosz*vcos;
            vrel[XX]     -= vc;
            if (bNH)
            {
                vxi        = nh_vxi[gt];
            }
            for (d = 0; d < DIM; d++)
            {
                if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
                {
                    vn  = (lg*vrel[d] + dt*(imass*f[n][d] - 0.5*vxi*vrel[d]
                                            - iprod(M[d], vrel)))/(1 + 0.5*vxi*dt);
                    if (d == XX)
                    {
                        vn += vc + dt*cosz*cos_accel;
                    }
                    v[n][d]        = vn;
                    xprime[n][d]   = x[n][d]+vn*dt;
                }
                else
                {
                    xprime[n][d]   = x[n][d];
                }
            }
        }
    }
    else
    {
        /* Classic version of update, used with berendsen coupling */
        for (n = start; n < nrend; n++)
        {
            w_dt = invmass[n]*dt;
            if (cTC)
            {
                gt   = cTC[n];
            }
            lg   = tcstat[gt].lambda;
            cosz = cos(fac*x[n][ZZ]);

            for (d = 0; d < DIM; d++)
            {
                vn             = v[n][d];

                if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
                {
                    if (d == XX)
                    {
                        vc           = cosz*vcos;
                        /* Do not scale the cosine velocity profile */
                        vv           = vc + lg*(vn - vc + f[n][d]*w_dt);
                        /* Add the cosine accelaration profile */
                        vv          += dt*cosz*cos_accel;
                    }
                    else
                    {
                        vv           = lg*(vn + f[n][d]*w_dt);
                    }
                    v[n][d]        = vv;
                    xprime[n][d]   = x[n][d]+vv*dt;
                }
                else
                {
                    v[n][d]        = 0.0;
                    xprime[n][d]   = x[n][d];
                }
            }
        }
    }
}

static gmx_stochd_t *init_stochd(t_inputrec *ir)
{
    gmx_stochd_t   *sd;
    gmx_sd_const_t *sdc;
    int             ngtc, n;
    real            y;

    snew(sd, 1);

    ngtc = ir->opts.ngtc;

    if (ir->eI == eiBD)
    {
        snew(sd->bd_rf, ngtc);
    }
    else if (EI_SD(ir->eI))
    {
        snew(sd->sdc, ngtc);
        snew(sd->sdsig, ngtc);

        sdc = sd->sdc;
        for (n = 0; n < ngtc; n++)
        {
            if (ir->opts.tau_t[n] > 0)
            {
                sdc[n].gdt = ir->delta_t/ir->opts.tau_t[n];
                sdc[n].eph = exp(sdc[n].gdt/2);
                sdc[n].emh = exp(-sdc[n].gdt/2);
                sdc[n].em  = exp(-sdc[n].gdt);
            }
            else
            {
                /* No friction and noise on this group */
                sdc[n].gdt = 0;
                sdc[n].eph = 1;
                sdc[n].emh = 1;
                sdc[n].em  = 1;
            }
            if (sdc[n].gdt >= 0.05)
            {
                sdc[n].b = sdc[n].gdt*(sdc[n].eph*sdc[n].eph - 1)
                    - 4*(sdc[n].eph - 1)*(sdc[n].eph - 1);
                sdc[n].c = sdc[n].gdt - 3 + 4*sdc[n].emh - sdc[n].em;
                sdc[n].d = 2 - sdc[n].eph - sdc[n].emh;
            }
            else
            {
                y = sdc[n].gdt/2;
                /* Seventh order expansions for small y */
                sdc[n].b = y*y*y*y*(1/3.0+y*(1/3.0+y*(17/90.0+y*7/9.0)));
                sdc[n].c = y*y*y*(2/3.0+y*(-1/2.0+y*(7/30.0+y*(-1/12.0+y*31/1260.0))));
                sdc[n].d = y*y*(-1+y*y*(-1/12.0-y*y/360.0));
            }
            if (debug)
            {
                fprintf(debug, "SD const tc-grp %d: b %g  c %g  d %g\n",
                        n, sdc[n].b, sdc[n].c, sdc[n].d);
            }
        }
    }
    else if (ETC_ANDERSEN(ir->etc))
    {
        int        ngtc;
        t_grpopts *opts;
        real       reft;

        opts = &ir->opts;
        ngtc = opts->ngtc;

        snew(sd->randomize_group, ngtc);
        snew(sd->boltzfac, ngtc);

        /* for now, assume that all groups, if randomized, are randomized at the same rate, i.e. tau_t is the same. */
        /* since constraint groups don't necessarily match up with temperature groups! This is checked in readir.c */

        for (n = 0; n < ngtc; n++)
        {
            reft = std::max<real>(0, opts->ref_t[n]);
            if ((opts->tau_t[n] > 0) && (reft > 0))  /* tau_t or ref_t = 0 means that no randomization is done */
            {
                sd->randomize_group[n] = TRUE;
                sd->boltzfac[n]        = BOLTZ*opts->ref_t[n];
            }
            else
            {
                sd->randomize_group[n] = FALSE;
            }
        }
    }
    return sd;
}

gmx_update_t init_update(t_inputrec *ir)
{
    t_gmx_update *upd;

    snew(upd, 1);

    if (ir->eI == eiBD || EI_SD(ir->eI) || ir->etc == etcVRESCALE || ETC_ANDERSEN(ir->etc))
    {
        upd->sd    = init_stochd(ir);
    }

    upd->xp        = NULL;
    upd->xp_nalloc = 0;

    return upd;
}

static void do_update_sd1(gmx_stochd_t *sd,
                          int start, int nrend, double dt,
                          rvec accel[], ivec nFreeze[],
                          real invmass[], unsigned short ptype[],
                          unsigned short cFREEZE[], unsigned short cACC[],
                          unsigned short cTC[],
                          rvec x[], rvec xprime[], rvec v[], rvec f[],
                          int ngtc, real ref_t[],
                          gmx_bool bDoConstr,
                          gmx_bool bFirstHalfConstr,
                          gmx_int64_t step, int seed, int* gatindex)
{
    gmx_sd_const_t *sdc;
    gmx_sd_sigma_t *sig;
    real            kT;
    int             gf = 0, ga = 0, gt = 0;
    real            ism;
    int             n, d;

    sdc = sd->sdc;
    sig = sd->sdsig;

    for (n = 0; n < ngtc; n++)
    {
        kT = BOLTZ*ref_t[n];
        /* The mass is encounted for later, since this differs per atom */
        sig[n].V  = sqrt(kT*(1 - sdc[n].em*sdc[n].em));
    }

    if (!bDoConstr)
    {
        for (n = start; n < nrend; n++)
        {
            real rnd[3];
            int  ng = gatindex ? gatindex[n] : n;

            ism = sqrt(invmass[n]);
            if (cFREEZE)
            {
                gf  = cFREEZE[n];
            }
            if (cACC)
            {
                ga  = cACC[n];
            }
            if (cTC)
            {
                gt  = cTC[n];
            }

            gmx_rng_cycle_3gaussian_table(step, ng, seed, RND_SEED_UPDATE, rnd);

            for (d = 0; d < DIM; d++)
            {
                if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
                {
                    real sd_V, vn;

                    sd_V         = ism*sig[gt].V*rnd[d];
                    vn           = v[n][d] + (invmass[n]*f[n][d] + accel[ga][d])*dt;
                    v[n][d]      = vn*sdc[gt].em + sd_V;
                    /* Here we include half of the friction+noise
                     * update of v into the integration of x.
                     */
                    xprime[n][d] = x[n][d] + 0.5*(vn + v[n][d])*dt;
                }
                else
                {
                    v[n][d]      = 0.0;
                    xprime[n][d] = x[n][d];
                }
            }
        }
    }
    else
    {
        /* We do have constraints */
        if (bFirstHalfConstr)
        {
            /* First update without friction and noise */
            real im;

            for (n = start; n < nrend; n++)
            {
                im = invmass[n];

                if (cFREEZE)
                {
                    gf  = cFREEZE[n];
                }
                if (cACC)
                {
                    ga  = cACC[n];
                }

                for (d = 0; d < DIM; d++)
                {
                    if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
                    {
                        v[n][d]      = v[n][d] + (im*f[n][d] + accel[ga][d])*dt;
                        xprime[n][d] = x[n][d] +  v[n][d]*dt;
                    }
                    else
                    {
                        v[n][d]      = 0.0;
                        xprime[n][d] = x[n][d];
                    }
                }
            }
        }
        else
        {
            /* Update friction and noise only */
            for (n = start; n < nrend; n++)
            {
                real rnd[3];
                int  ng = gatindex ? gatindex[n] : n;

                ism = sqrt(invmass[n]);
                if (cFREEZE)
                {
                    gf  = cFREEZE[n];
                }
                if (cTC)
                {
                    gt  = cTC[n];
                }

                gmx_rng_cycle_3gaussian_table(step, ng, seed, RND_SEED_UPDATE, rnd);

                for (d = 0; d < DIM; d++)
                {
                    if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
                    {
                        real sd_V, vn;

                        sd_V         = ism*sig[gt].V*rnd[d];
                        vn           = v[n][d];
                        v[n][d]      = vn*sdc[gt].em + sd_V;
                        /* Add the friction and noise contribution only */
                        xprime[n][d] = xprime[n][d] + 0.5*(v[n][d] - vn)*dt;
                    }
                }
            }
        }
    }
}

static void check_sd2_work_data_allocation(gmx_stochd_t *sd, int nrend)
{
    if (nrend > sd->sd_V_nalloc)
    {
        sd->sd_V_nalloc = over_alloc_dd(nrend);
        srenew(sd->sd_V, sd->sd_V_nalloc);
    }
}

static void do_update_sd2_Tconsts(gmx_stochd_t *sd,
                                  int           ngtc,
                                  const real    tau_t[],
                                  const real    ref_t[])
{
    /* This is separated from the update below, because it is single threaded */
    gmx_sd_const_t *sdc;
    gmx_sd_sigma_t *sig;
    int             gt;
    real            kT;

    sdc = sd->sdc;
    sig = sd->sdsig;

    for (gt = 0; gt < ngtc; gt++)
    {
        kT = BOLTZ*ref_t[gt];
        /* The mass is encounted for later, since this differs per atom */
        sig[gt].V  = sqrt(kT*(1-sdc[gt].em));
        sig[gt].X  = sqrt(kT*sqr(tau_t[gt])*sdc[gt].c);
        sig[gt].Yv = sqrt(kT*sdc[gt].b/sdc[gt].c);
        sig[gt].Yx = sqrt(kT*sqr(tau_t[gt])*sdc[gt].b/(1-sdc[gt].em));
    }
}

static void do_update_sd2(gmx_stochd_t *sd,
                          gmx_bool bInitStep,
                          int start, int nrend,
                          rvec accel[], ivec nFreeze[],
                          real invmass[], unsigned short ptype[],
                          unsigned short cFREEZE[], unsigned short cACC[],
                          unsigned short cTC[],
                          rvec x[], rvec xprime[], rvec v[], rvec f[],
                          rvec sd_X[],
                          const real tau_t[],
                          gmx_bool bFirstHalf, gmx_int64_t step, int seed,
                          int* gatindex)
{
    gmx_sd_const_t *sdc;
    gmx_sd_sigma_t *sig;
    /* The random part of the velocity update, generated in the first
     * half of the update, needs to be remembered for the second half.
     */
    rvec  *sd_V;
    int    gf = 0, ga = 0, gt = 0;
    real   vn = 0, Vmh, Xmh;
    real   ism;
    int    n, d, ng;

    sdc  = sd->sdc;
    sig  = sd->sdsig;
    sd_V = sd->sd_V;

    for (n = start; n < nrend; n++)
    {
        real rnd[6], rndi[3];
        ng  = gatindex ? gatindex[n] : n;
        ism = sqrt(invmass[n]);
        if (cFREEZE)
        {
            gf  = cFREEZE[n];
        }
        if (cACC)
        {
            ga  = cACC[n];
        }
        if (cTC)
        {
            gt  = cTC[n];
        }

        gmx_rng_cycle_6gaussian_table(step*2+(bFirstHalf ? 1 : 2), ng, seed, RND_SEED_UPDATE, rnd);
        if (bInitStep)
        {
            gmx_rng_cycle_3gaussian_table(step*2, ng, seed, RND_SEED_UPDATE, rndi);
        }
        for (d = 0; d < DIM; d++)
        {
            if (bFirstHalf)
            {
                vn             = v[n][d];
            }
            if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
            {
                if (bFirstHalf)
                {
                    if (bInitStep)
                    {
                        sd_X[n][d] = ism*sig[gt].X*rndi[d];
                    }
                    Vmh = sd_X[n][d]*sdc[gt].d/(tau_t[gt]*sdc[gt].c)
                        + ism*sig[gt].Yv*rnd[d*2];
                    sd_V[n][d] = ism*sig[gt].V*rnd[d*2+1];

                    v[n][d] = vn*sdc[gt].em
                        + (invmass[n]*f[n][d] + accel[ga][d])*tau_t[gt]*(1 - sdc[gt].em)
                        + sd_V[n][d] - sdc[gt].em*Vmh;

                    xprime[n][d] = x[n][d] + v[n][d]*tau_t[gt]*(sdc[gt].eph - sdc[gt].emh);
                }
                else
                {
                    /* Correct the velocities for the constraints.
                     * This operation introduces some inaccuracy,
                     * since the velocity is determined from differences in coordinates.
                     */
                    v[n][d] =
                        (xprime[n][d] - x[n][d])/(tau_t[gt]*(sdc[gt].eph - sdc[gt].emh));

                    Xmh = sd_V[n][d]*tau_t[gt]*sdc[gt].d/(sdc[gt].em-1)
                        + ism*sig[gt].Yx*rnd[d*2];
                    sd_X[n][d] = ism*sig[gt].X*rnd[d*2+1];

                    xprime[n][d] += sd_X[n][d] - Xmh;

                }
            }
            else
            {
                if (bFirstHalf)
                {
                    v[n][d]        = 0.0;
                    xprime[n][d]   = x[n][d];
                }
            }
        }
    }
}

static void do_update_bd_Tconsts(double dt, real friction_coefficient,
                                 int ngtc, const real ref_t[],
                                 real *rf)
{
    /* This is separated from the update below, because it is single threaded */
    int gt;

    if (friction_coefficient != 0)
    {
        for (gt = 0; gt < ngtc; gt++)
        {
            rf[gt] = sqrt(2.0*BOLTZ*ref_t[gt]/(friction_coefficient*dt));
        }
    }
    else
    {
        for (gt = 0; gt < ngtc; gt++)
        {
            rf[gt] = sqrt(2.0*BOLTZ*ref_t[gt]);
        }
    }
}

static void do_update_bd(int start, int nrend, double dt,
                         ivec nFreeze[],
                         real invmass[], unsigned short ptype[],
                         unsigned short cFREEZE[], unsigned short cTC[],
                         rvec x[], rvec xprime[], rvec v[],
                         rvec f[], real friction_coefficient,
                         real *rf, gmx_int64_t step, int seed,
                         int* gatindex)
{
    /* note -- these appear to be full step velocities . . .  */
    int    gf = 0, gt = 0;
    real   vn;
    real   invfr = 0;
    int    n, d;

    if (friction_coefficient != 0)
    {
        invfr = 1.0/friction_coefficient;
    }

    for (n = start; (n < nrend); n++)
    {
        real rnd[3];
        int  ng  = gatindex ? gatindex[n] : n;

        if (cFREEZE)
        {
            gf = cFREEZE[n];
        }
        if (cTC)
        {
            gt = cTC[n];
        }
        gmx_rng_cycle_3gaussian_table(step, ng, seed, RND_SEED_UPDATE, rnd);
        for (d = 0; (d < DIM); d++)
        {
            if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
            {
                if (friction_coefficient != 0)
                {
                    vn = invfr*f[n][d] + rf[gt]*rnd[d];
                }
                else
                {
                    /* NOTE: invmass = 2/(mass*friction_constant*dt) */
                    vn = 0.5*invmass[n]*f[n][d]*dt
                        + sqrt(0.5*invmass[n])*rf[gt]*rnd[d];
                }

                v[n][d]      = vn;
                xprime[n][d] = x[n][d]+vn*dt;
            }
            else
            {
                v[n][d]      = 0.0;
                xprime[n][d] = x[n][d];
            }
        }
    }
}

static void dump_it_all(FILE gmx_unused *fp, const char gmx_unused *title,
                        int gmx_unused natoms, rvec gmx_unused x[], rvec gmx_unused xp[],
                        rvec gmx_unused v[], rvec gmx_unused f[])
{
#ifdef DEBUG
    if (fp)
    {
        fprintf(fp, "%s\n", title);
        pr_rvecs(fp, 0, "x", x, natoms);
        pr_rvecs(fp, 0, "xp", xp, natoms);
        pr_rvecs(fp, 0, "v", v, natoms);
        pr_rvecs(fp, 0, "f", f, natoms);
    }
#endif
}

static void calc_ke_part_normal(rvec v[], t_grpopts *opts, t_mdatoms *md,
                                gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel)
{
    int           g;
    t_grp_tcstat *tcstat  = ekind->tcstat;
    t_grp_acc    *grpstat = ekind->grpstat;
    int           nthread, thread;

    /* three main: VV with AveVel, vv with AveEkin, leap with AveEkin.  Leap with AveVel is also
       an option, but not supported now.
       bEkinAveVel: If TRUE, we sum into ekin, if FALSE, into ekinh.
     */

    /* group velocities are calculated in update_ekindata and
     * accumulated in acumulate_groups.
     * Now the partial global and groups ekin.
     */
    for (g = 0; (g < opts->ngtc); g++)
    {
        copy_mat(tcstat[g].ekinh, tcstat[g].ekinh_old);
        if (bEkinAveVel)
        {
            clear_mat(tcstat[g].ekinf);
            tcstat[g].ekinscalef_nhc = 1.0;   /* need to clear this -- logic is complicated! */
        }
        else
        {
            clear_mat(tcstat[g].ekinh);
        }
    }
    ekind->dekindl_old = ekind->dekindl;
    nthread            = gmx_omp_nthreads_get(emntUpdate);

#pragma omp parallel for num_threads(nthread) schedule(static)
    for (thread = 0; thread < nthread; thread++)
    {
        // This OpenMP only loops over arrays and does not call any functions
        // or memory allocation. It should not be able to throw, so for now
        // we do not need a try/catch wrapper.
        int     start_t, end_t, n;
        int     ga, gt;
        rvec    v_corrt;
        real    hm;
        int     d, m;
        matrix *ekin_sum;
        real   *dekindl_sum;

        start_t = ((thread+0)*md->homenr)/nthread;
        end_t   = ((thread+1)*md->homenr)/nthread;

        ekin_sum    = ekind->ekin_work[thread];
        dekindl_sum = ekind->dekindl_work[thread];

        for (gt = 0; gt < opts->ngtc; gt++)
        {
            clear_mat(ekin_sum[gt]);
        }
        *dekindl_sum = 0.0;

        ga = 0;
        gt = 0;
        for (n = start_t; n < end_t; n++)
        {
            if (md->cACC)
            {
                ga = md->cACC[n];
            }
            if (md->cTC)
            {
                gt = md->cTC[n];
            }
            hm   = 0.5*md->massT[n];

            for (d = 0; (d < DIM); d++)
            {
                v_corrt[d]  = v[n][d]  - grpstat[ga].u[d];
            }
            for (d = 0; (d < DIM); d++)
            {
                for (m = 0; (m < DIM); m++)
                {
                    /* if we're computing a full step velocity, v_corrt[d] has v(t).  Otherwise, v(t+dt/2) */
                    ekin_sum[gt][m][d] += hm*v_corrt[m]*v_corrt[d];
                }
            }
            if (md->nMassPerturbed && md->bPerturbed[n])
            {
                *dekindl_sum +=
                    0.5*(md->massB[n] - md->massA[n])*iprod(v_corrt, v_corrt);
            }
        }
    }

    ekind->dekindl = 0;
    for (thread = 0; thread < nthread; thread++)
    {
        for (g = 0; g < opts->ngtc; g++)
        {
            if (bEkinAveVel)
            {
                m_add(tcstat[g].ekinf, ekind->ekin_work[thread][g],
                      tcstat[g].ekinf);
            }
            else
            {
                m_add(tcstat[g].ekinh, ekind->ekin_work[thread][g],
                      tcstat[g].ekinh);
            }
        }

        ekind->dekindl += *ekind->dekindl_work[thread];
    }

    inc_nrnb(nrnb, eNR_EKIN, md->homenr);
}

static void calc_ke_part_visc(matrix box, rvec x[], rvec v[],
                              t_grpopts *opts, t_mdatoms *md,
                              gmx_ekindata_t *ekind,
                              t_nrnb *nrnb, gmx_bool bEkinAveVel)
{
    int           start = 0, homenr = md->homenr;
    int           g, d, n, m, gt = 0;
    rvec          v_corrt;
    real          hm;
    t_grp_tcstat *tcstat = ekind->tcstat;
    t_cos_acc    *cosacc = &(ekind->cosacc);
    real          dekindl;
    real          fac, cosz;
    double        mvcos;

    for (g = 0; g < opts->ngtc; g++)
    {
        copy_mat(ekind->tcstat[g].ekinh, ekind->tcstat[g].ekinh_old);
        clear_mat(ekind->tcstat[g].ekinh);
    }
    ekind->dekindl_old = ekind->dekindl;

    fac     = 2*M_PI/box[ZZ][ZZ];
    mvcos   = 0;
    dekindl = 0;
    for (n = start; n < start+homenr; n++)
    {
        if (md->cTC)
        {
            gt = md->cTC[n];
        }
        hm   = 0.5*md->massT[n];

        /* Note that the times of x and v differ by half a step */
        /* MRS -- would have to be changed for VV */
        cosz         = cos(fac*x[n][ZZ]);
        /* Calculate the amplitude of the new velocity profile */
        mvcos       += 2*cosz*md->massT[n]*v[n][XX];

        copy_rvec(v[n], v_corrt);
        /* Subtract the profile for the kinetic energy */
        v_corrt[XX] -= cosz*cosacc->vcos;
        for (d = 0; (d < DIM); d++)
        {
            for (m = 0; (m < DIM); m++)
            {
                /* if we're computing a full step velocity, v_corrt[d] has v(t).  Otherwise, v(t+dt/2) */
                if (bEkinAveVel)
                {
                    tcstat[gt].ekinf[m][d] += hm*v_corrt[m]*v_corrt[d];
                }
                else
                {
                    tcstat[gt].ekinh[m][d] += hm*v_corrt[m]*v_corrt[d];
                }
            }
        }
        if (md->nPerturbed && md->bPerturbed[n])
        {
            /* The minus sign here might be confusing.
             * The kinetic contribution from dH/dl doesn't come from
             * d m(l)/2 v^2 / dl, but rather from d p^2/2m(l) / dl,
             * where p are the momenta. The difference is only a minus sign.
             */
            dekindl -= 0.5*(md->massB[n] - md->massA[n])*iprod(v_corrt, v_corrt);
        }
    }
    ekind->dekindl = dekindl;
    cosacc->mvcos  = mvcos;

    inc_nrnb(nrnb, eNR_EKIN, homenr);
}

void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md,
                  gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel)
{
    if (ekind->cosacc.cos_accel == 0)
    {
        calc_ke_part_normal(state->v, opts, md, ekind, nrnb, bEkinAveVel);
    }
    else
    {
        calc_ke_part_visc(state->box, state->x, state->v, opts, md, ekind, nrnb, bEkinAveVel);
    }
}

extern void init_ekinstate(ekinstate_t *ekinstate, const t_inputrec *ir)
{
    ekinstate->ekin_n = ir->opts.ngtc;
    snew(ekinstate->ekinh, ekinstate->ekin_n);
    snew(ekinstate->ekinf, ekinstate->ekin_n);
    snew(ekinstate->ekinh_old, ekinstate->ekin_n);
    snew(ekinstate->ekinscalef_nhc, ekinstate->ekin_n);
    snew(ekinstate->ekinscaleh_nhc, ekinstate->ekin_n);
    snew(ekinstate->vscale_nhc, ekinstate->ekin_n);
    ekinstate->dekindl = 0;
    ekinstate->mvcos   = 0;
}

void update_ekinstate(ekinstate_t *ekinstate, gmx_ekindata_t *ekind)
{
    int i;

    for (i = 0; i < ekinstate->ekin_n; i++)
    {
        copy_mat(ekind->tcstat[i].ekinh, ekinstate->ekinh[i]);
        copy_mat(ekind->tcstat[i].ekinf, ekinstate->ekinf[i]);
        copy_mat(ekind->tcstat[i].ekinh_old, ekinstate->ekinh_old[i]);
        ekinstate->ekinscalef_nhc[i] = ekind->tcstat[i].ekinscalef_nhc;
        ekinstate->ekinscaleh_nhc[i] = ekind->tcstat[i].ekinscaleh_nhc;
        ekinstate->vscale_nhc[i]     = ekind->tcstat[i].vscale_nhc;
    }

    copy_mat(ekind->ekin, ekinstate->ekin_total);
    ekinstate->dekindl = ekind->dekindl;
    ekinstate->mvcos   = ekind->cosacc.mvcos;

}

void restore_ekinstate_from_state(t_commrec *cr,
                                  gmx_ekindata_t *ekind, const ekinstate_t *ekinstate)
{
    int i, n;

    if (MASTER(cr))
    {
        for (i = 0; i < ekinstate->ekin_n; i++)
        {
            copy_mat(ekinstate->ekinh[i], ekind->tcstat[i].ekinh);
            copy_mat(ekinstate->ekinf[i], ekind->tcstat[i].ekinf);
            copy_mat(ekinstate->ekinh_old[i], ekind->tcstat[i].ekinh_old);
            ekind->tcstat[i].ekinscalef_nhc = ekinstate->ekinscalef_nhc[i];
            ekind->tcstat[i].ekinscaleh_nhc = ekinstate->ekinscaleh_nhc[i];
            ekind->tcstat[i].vscale_nhc     = ekinstate->vscale_nhc[i];
        }

        copy_mat(ekinstate->ekin_total, ekind->ekin);

        ekind->dekindl      = ekinstate->dekindl;
        ekind->cosacc.mvcos = ekinstate->mvcos;
        n                   = ekinstate->ekin_n;
    }

    if (PAR(cr))
    {
        gmx_bcast(sizeof(n), &n, cr);
        for (i = 0; i < n; i++)
        {
            gmx_bcast(DIM*DIM*sizeof(ekind->tcstat[i].ekinh[0][0]),
                      ekind->tcstat[i].ekinh[0], cr);
            gmx_bcast(DIM*DIM*sizeof(ekind->tcstat[i].ekinf[0][0]),
                      ekind->tcstat[i].ekinf[0], cr);
            gmx_bcast(DIM*DIM*sizeof(ekind->tcstat[i].ekinh_old[0][0]),
                      ekind->tcstat[i].ekinh_old[0], cr);

            gmx_bcast(sizeof(ekind->tcstat[i].ekinscalef_nhc),
                      &(ekind->tcstat[i].ekinscalef_nhc), cr);
            gmx_bcast(sizeof(ekind->tcstat[i].ekinscaleh_nhc),
                      &(ekind->tcstat[i].ekinscaleh_nhc), cr);
            gmx_bcast(sizeof(ekind->tcstat[i].vscale_nhc),
                      &(ekind->tcstat[i].vscale_nhc), cr);
        }
        gmx_bcast(DIM*DIM*sizeof(ekind->ekin[0][0]),
                  ekind->ekin[0], cr);

        gmx_bcast(sizeof(ekind->dekindl), &ekind->dekindl, cr);
        gmx_bcast(sizeof(ekind->cosacc.mvcos), &ekind->cosacc.mvcos, cr);
    }
}

void set_deform_reference_box(gmx_update_t upd, gmx_int64_t step, matrix box)
{
    upd->deformref_step = step;
    copy_mat(box, upd->deformref_box);
}

static void deform(gmx_update_t upd,
                   int start, int homenr, rvec x[], matrix box,
                   const t_inputrec *ir, gmx_int64_t step)
{
    matrix bnew, invbox, mu;
    real   elapsed_time;
    int    i, j;

    elapsed_time = (step + 1 - upd->deformref_step)*ir->delta_t;
    copy_mat(box, bnew);
    for (i = 0; i < DIM; i++)
    {
        for (j = 0; j < DIM; j++)
        {
            if (ir->deform[i][j] != 0)
            {
                bnew[i][j] =
                    upd->deformref_box[i][j] + elapsed_time*ir->deform[i][j];
            }
        }
    }
    /* We correct the off-diagonal elements,
     * which can grow indefinitely during shearing,
     * so the shifts do not get messed up.
     */
    for (i = 1; i < DIM; i++)
    {
        for (j = i-1; j >= 0; j--)
        {
            while (bnew[i][j] - box[i][j] > 0.5*bnew[j][j])
            {
                rvec_dec(bnew[i], bnew[j]);
            }
            while (bnew[i][j] - box[i][j] < -0.5*bnew[j][j])
            {
                rvec_inc(bnew[i], bnew[j]);
            }
        }
    }
    m_inv_ur0(box, invbox);
    copy_mat(bnew, box);
    mmul_ur0(box, invbox, mu);

    for (i = start; i < start+homenr; i++)
    {
        x[i][XX] = mu[XX][XX]*x[i][XX]+mu[YY][XX]*x[i][YY]+mu[ZZ][XX]*x[i][ZZ];
        x[i][YY] = mu[YY][YY]*x[i][YY]+mu[ZZ][YY]*x[i][ZZ];
        x[i][ZZ] = mu[ZZ][ZZ]*x[i][ZZ];
    }
}

void update_tcouple(gmx_int64_t       step,
                    t_inputrec       *inputrec,
                    t_state          *state,
                    gmx_ekindata_t   *ekind,
                    t_extmass        *MassQ,
                    t_mdatoms        *md)

{
    gmx_bool   bTCouple = FALSE;
    real       dttc;
    int        i, offset;

    /* if using vv with trotter decomposition methods, we do this elsewhere in the code */
    if (inputrec->etc != etcNO &&
        !(inputrecNvtTrotter(inputrec) || inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec)))
    {
        /* We should only couple after a step where energies were determined (for leapfrog versions)
           or the step energies are determined, for velocity verlet versions */

        if (EI_VV(inputrec->eI))
        {
            offset = 0;
        }
        else
        {
            offset = 1;
        }
        bTCouple = (inputrec->nsttcouple == 1 ||
                    do_per_step(step+inputrec->nsttcouple-offset,
                                inputrec->nsttcouple));
    }

    if (bTCouple)
    {
        dttc = inputrec->nsttcouple*inputrec->delta_t;

        switch (inputrec->etc)
        {
            case etcNO:
                break;
            case etcBERENDSEN:
                berendsen_tcoupl(inputrec, ekind, dttc);
                break;
            case etcNOSEHOOVER:
                nosehoover_tcoupl(&(inputrec->opts), ekind, dttc,
                                  state->nosehoover_xi, state->nosehoover_vxi, MassQ);
                break;
            case etcVRESCALE:
                vrescale_tcoupl(inputrec, step, ekind, dttc,
                                state->therm_integral);
                break;
        }
        /* rescale in place here */
        if (EI_VV(inputrec->eI))
        {
            rescale_velocities(ekind, md, 0, md->homenr, state->v);
        }
    }
    else
    {
        /* Set the T scaling lambda to 1 to have no scaling */
        for (i = 0; (i < inputrec->opts.ngtc); i++)
        {
            ekind->tcstat[i].lambda = 1.0;
        }
    }
}

void update_pcouple(FILE             *fplog,
                    gmx_int64_t       step,
                    t_inputrec       *inputrec,
                    t_state          *state,
                    matrix            pcoupl_mu,
                    matrix            M,
                    gmx_bool          bInitStep)
{
    gmx_bool   bPCouple = FALSE;
    real       dtpc     = 0;
    int        i;

    /* if using Trotter pressure, we do this in coupling.c, so we leave it false. */
    if (inputrec->epc != epcNO && (!(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec))))
    {
        /* We should only couple after a step where energies were determined */
        bPCouple = (inputrec->nstpcouple == 1 ||
                    do_per_step(step+inputrec->nstpcouple-1,
                                inputrec->nstpcouple));
    }

    clear_mat(pcoupl_mu);
    for (i = 0; i < DIM; i++)
    {
        pcoupl_mu[i][i] = 1.0;
    }

    clear_mat(M);

    if (bPCouple)
    {
        dtpc = inputrec->nstpcouple*inputrec->delta_t;

        switch (inputrec->epc)
        {
            /* We can always pcoupl, even if we did not sum the energies
             * the previous step, since state->pres_prev is only updated
             * when the energies have been summed.
             */
            case (epcNO):
                break;
            case (epcBERENDSEN):
                if (!bInitStep)
                {
                    berendsen_pcoupl(fplog, step, inputrec, dtpc, state->pres_prev, state->box,
                                     pcoupl_mu);
                }
                break;
            case (epcPARRINELLORAHMAN):
                parrinellorahman_pcoupl(fplog, step, inputrec, dtpc, state->pres_prev,
                                        state->box, state->box_rel, state->boxv,
                                        M, pcoupl_mu, bInitStep);
                break;
            default:
                break;
        }
    }
}

static rvec *get_xprime(const t_state *state, gmx_update_t upd)
{
    if (state->nalloc > upd->xp_nalloc)
    {
        upd->xp_nalloc = state->nalloc;
        srenew(upd->xp, upd->xp_nalloc);
    }

    return upd->xp;
}

static void combine_forces(gmx_update_t upd,
                           int nstcalclr,
                           gmx_constr_t constr,
                           t_inputrec *ir, t_mdatoms *md, t_idef *idef,
                           t_commrec *cr,
                           gmx_int64_t step,
                           t_state *state, gmx_bool bMolPBC,
                           int start, int nrend,
                           rvec f[], rvec f_lr[],
                           tensor *vir_lr_constr,
                           t_nrnb *nrnb)
{
    int  i, d;

    /* f contains the short-range forces + the long range forces
     * which are stored separately in f_lr.
     */

    if (constr != NULL && vir_lr_constr != NULL &&
        !(ir->eConstrAlg == econtSHAKE && ir->epc == epcNO))
    {
        /* We need to constrain the LR forces separately,
         * because due to the different pre-factor for the SR and LR
         * forces in the update algorithm, we have to correct
         * the constraint virial for the nstcalclr-1 extra f_lr.
         * Constrain only the additional LR part of the force.
         */
        rvec *xp;
        real  fac;
        int   gf = 0;

        xp  = get_xprime(state, upd);

        fac = (nstcalclr - 1)*ir->delta_t*ir->delta_t;

        for (i = 0; i < md->homenr; i++)
        {
            if (md->cFREEZE != NULL)
            {
                gf = md->cFREEZE[i];
            }
            for (d = 0; d < DIM; d++)
            {
                if ((md->ptype[i] != eptVSite) &&
                    (md->ptype[i] != eptShell) &&
                    !ir->opts.nFreeze[gf][d])
                {
                    xp[i][d] = state->x[i][d] + fac*f_lr[i][d]*md->invmass[i];
                }
                else
                {
                    xp[i][d] = state->x[i][d];
                }
            }
        }
        constrain(NULL, FALSE, FALSE, constr, idef, ir, cr, step, 0, 1.0, md,
                  state->x, xp, xp, bMolPBC, state->box, state->lambda[efptBONDED], NULL,
                  NULL, vir_lr_constr, nrnb, econqForce);
    }

    /* Add nstcalclr-1 times the LR force to the sum of both forces
     * and store the result in forces_lr.
     */
    for (i = start; i < nrend; i++)
    {
        for (d = 0; d < DIM; d++)
        {
            f_lr[i][d] = f[i][d] + (nstcalclr - 1)*f_lr[i][d];
        }
    }
}

void update_constraints(FILE             *fplog,
                        gmx_int64_t       step,
                        real             *dvdlambda, /* the contribution to be added to the bonded interactions */
                        t_inputrec       *inputrec,  /* input record and box stuff      */
                        t_mdatoms        *md,
                        t_state          *state,
                        gmx_bool          bMolPBC,
                        t_graph          *graph,
                        rvec              force[],   /* forces on home particles */
                        t_idef           *idef,
                        tensor            vir_part,
                        t_commrec        *cr,
                        t_nrnb           *nrnb,
                        gmx_wallcycle_t   wcycle,
                        gmx_update_t      upd,
                        gmx_constr_t      constr,
                        gmx_bool          bFirstHalf,
                        gmx_bool          bCalcVir)
{
    gmx_bool             bLastStep, bLog = FALSE, bEner = FALSE, bDoConstr = FALSE;
    double               dt;
    int                  start, homenr, nrend, i, m;
    tensor               vir_con;
    rvec                *xprime = NULL;
    int                  nth, th;

    if (constr)
    {
        bDoConstr = TRUE;
    }
    if (bFirstHalf && !EI_VV(inputrec->eI))
    {
        bDoConstr = FALSE;
    }

    /* for now, SD update is here -- though it really seems like it
       should be reformulated as a velocity verlet method, since it has two parts */

    start  = 0;
    homenr = md->homenr;
    nrend  = start+homenr;

    dt   = inputrec->delta_t;

    /*
     *  Steps (7C, 8C)
     *  APPLY CONSTRAINTS:
     *  BLOCK SHAKE

     * When doing PR pressure coupling we have to constrain the
     * bonds in each iteration. If we are only using Nose-Hoover tcoupling
     * it is enough to do this once though, since the relative velocities
     * after this will be normal to the bond vector
     */

    if (bDoConstr)
    {
        /* clear out constraints before applying */
        clear_mat(vir_part);

        xprime = get_xprime(state, upd);

        bLastStep = (step == inputrec->init_step+inputrec->nsteps);
        bLog      = (do_per_step(step, inputrec->nstlog) || bLastStep || (step < 0));
        bEner     = (do_per_step(step, inputrec->nstenergy) || bLastStep);
        /* Constrain the coordinates xprime */
        wallcycle_start(wcycle, ewcCONSTR);
        if (EI_VV(inputrec->eI) && bFirstHalf)
        {
            constrain(NULL, bLog, bEner, constr, idef,
                      inputrec, cr, step, 1, 1.0, md,
                      state->x, state->v, state->v,
                      bMolPBC, state->box,
                      state->lambda[efptBONDED], dvdlambda,
                      NULL, bCalcVir ? &vir_con : NULL, nrnb, econqVeloc);
        }
        else
        {
            constrain(NULL, bLog, bEner, constr, idef,
                      inputrec, cr, step, 1, 1.0, md,
                      state->x, xprime, NULL,
                      bMolPBC, state->box,
                      state->lambda[efptBONDED], dvdlambda,
                      state->v, bCalcVir ? &vir_con : NULL, nrnb, econqCoord);
        }
        wallcycle_stop(wcycle, ewcCONSTR);

        where();

        dump_it_all(fplog, "After Shake",
                    state->natoms, state->x, xprime, state->v, force);

        if (bCalcVir)
        {
            if (inputrec->eI == eiSD2)
            {
                /* A correction factor eph is needed for the SD constraint force */
                /* Here we can, unfortunately, not have proper corrections
                 * for different friction constants, so we use the first one.
                 */
                for (i = 0; i < DIM; i++)
                {
                    for (m = 0; m < DIM; m++)
                    {
                        vir_part[i][m] += upd->sd->sdc[0].eph*vir_con[i][m];
                    }
                }
            }
            else
            {
                m_add(vir_part, vir_con, vir_part);
            }
            if (debug)
            {
                pr_rvecs(debug, 0, "constraint virial", vir_part, DIM);
            }
        }
    }

    where();

    if (inputrec->eI == eiSD1 && bDoConstr && !bFirstHalf)
    {
        wallcycle_start(wcycle, ewcUPDATE);
        xprime = get_xprime(state, upd);

        nth = gmx_omp_nthreads_get(emntUpdate);

#pragma omp parallel for num_threads(nth) schedule(static)
        for (th = 0; th < nth; th++)
        {
            try
            {
                int start_th, end_th;

                start_th = start + ((nrend-start)* th   )/nth;
                end_th   = start + ((nrend-start)*(th+1))/nth;

                /* The second part of the SD integration */
                do_update_sd1(upd->sd,
                              start_th, end_th, dt,
                              inputrec->opts.acc, inputrec->opts.nFreeze,
                              md->invmass, md->ptype,
                              md->cFREEZE, md->cACC, md->cTC,
                              state->x, xprime, state->v, force,
                              inputrec->opts.ngtc, inputrec->opts.ref_t,
                              bDoConstr, FALSE,
                              step, inputrec->ld_seed,
                              DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
            }
            GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
        }
        inc_nrnb(nrnb, eNR_UPDATE, homenr);
        wallcycle_stop(wcycle, ewcUPDATE);

        if (bDoConstr)
        {
            /* Constrain the coordinates xprime for half a time step */
            wallcycle_start(wcycle, ewcCONSTR);

            constrain(NULL, bLog, bEner, constr, idef,
                      inputrec, cr, step, 1, 0.5, md,
                      state->x, xprime, NULL,
                      bMolPBC, state->box,
                      state->lambda[efptBONDED], dvdlambda,
                      state->v, NULL, nrnb, econqCoord);

            wallcycle_stop(wcycle, ewcCONSTR);
        }
    }

    if ((inputrec->eI == eiSD2) && !(bFirstHalf))
    {
        wallcycle_start(wcycle, ewcUPDATE);
        xprime = get_xprime(state, upd);

        nth = gmx_omp_nthreads_get(emntUpdate);

#pragma omp parallel for num_threads(nth) schedule(static)
        for (th = 0; th < nth; th++)
        {
            try
            {
                int start_th, end_th;

                start_th = start + ((nrend-start)* th   )/nth;
                end_th   = start + ((nrend-start)*(th+1))/nth;

                /* The second part of the SD integration */
                do_update_sd2(upd->sd,
                              FALSE, start_th, end_th,
                              inputrec->opts.acc, inputrec->opts.nFreeze,
                              md->invmass, md->ptype,
                              md->cFREEZE, md->cACC, md->cTC,
                              state->x, xprime, state->v, force, state->sd_X,
                              inputrec->opts.tau_t,
                              FALSE, step, inputrec->ld_seed,
                              DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
            }
            GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
        }
        inc_nrnb(nrnb, eNR_UPDATE, homenr);
        wallcycle_stop(wcycle, ewcUPDATE);

        if (bDoConstr)
        {
            /* Constrain the coordinates xprime */
            wallcycle_start(wcycle, ewcCONSTR);
            constrain(NULL, bLog, bEner, constr, idef,
                      inputrec, cr, step, 1, 1.0, md,
                      state->x, xprime, NULL,
                      bMolPBC, state->box,
                      state->lambda[efptBONDED], dvdlambda,
                      NULL, NULL, nrnb, econqCoord);
            wallcycle_stop(wcycle, ewcCONSTR);
        }
    }


    /* We must always unshift after updating coordinates; if we did not shake
       x was shifted in do_force */

    if (!(bFirstHalf)) /* in the first half of vv, no shift. */
    {
        /* NOTE This part of the update actually does not belong with
         * the constraints, since we also call it without constraints.
         * But currently we always integrate to a temporary buffer and
         * then copy the results back here.
         */
        wallcycle_start_nocount(wcycle, ewcUPDATE);

        if (graph && (graph->nnodes > 0))
        {
            unshift_x(graph, state->box, state->x, upd->xp);
            if (TRICLINIC(state->box))
            {
                inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
            }
            else
            {
                inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
            }
        }
        else
        {
#ifndef __clang_analyzer__
            // cppcheck-suppress unreadVariable
            nth = gmx_omp_nthreads_get(emntUpdate);
#endif
#pragma omp parallel for num_threads(nth) schedule(static)
            for (i = start; i < nrend; i++)
            {
                // Trivial statement, does not throw
                copy_rvec(upd->xp[i], state->x[i]);
            }
        }
        wallcycle_stop(wcycle, ewcUPDATE);

        dump_it_all(fplog, "After unshift",
                    state->natoms, state->x, upd->xp, state->v, force);
    }
/* ############# END the update of velocities and positions ######### */
}

void update_box(FILE             *fplog,
                gmx_int64_t       step,
                t_inputrec       *inputrec,  /* input record and box stuff      */
                t_mdatoms        *md,
                t_state          *state,
                rvec              force[],   /* forces on home particles */
                matrix            pcoupl_mu,
                t_nrnb           *nrnb,
                gmx_update_t      upd)
{
    double               dt;
    int                  start, homenr, i, n, m;

    start  = 0;
    homenr = md->homenr;

    dt = inputrec->delta_t;

    where();

    /* now update boxes */
    switch (inputrec->epc)
    {
        case (epcNO):
            break;
        case (epcBERENDSEN):
            /* We should only scale after a step where the pressure (kinetic
             * energy and virial) was calculated. This happens after the
             * coordinate update, whereas the current routine is called before
             * that, so we scale when step % nstpcouple = 1 instead of 0.
             */
            if (inputrec->nstpcouple == 1 || (step % inputrec->nstpcouple == 1))
            {
                berendsen_pscale(inputrec, pcoupl_mu, state->box, state->box_rel,
                                 start, homenr, state->x, md->cFREEZE, nrnb);
            }
            break;
        case (epcPARRINELLORAHMAN):
            /* The box velocities were updated in do_pr_pcoupl in the update
             * iteration, but we dont change the box vectors until we get here
             * since we need to be able to shift/unshift above.
             */
            for (i = 0; i < DIM; i++)
            {
                for (m = 0; m <= i; m++)
                {
                    state->box[i][m] += dt*state->boxv[i][m];
                }
            }
            preserve_box_shape(inputrec, state->box_rel, state->box);

            /* Scale the coordinates */
            for (n = start; (n < start+homenr); n++)
            {
                tmvmul_ur0(pcoupl_mu, state->x[n], state->x[n]);
            }
            break;
        case (epcMTTK):
            switch (inputrec->epct)
            {
                case (epctISOTROPIC):
                    /* DIM * eta = ln V.  so DIM*eta_new = DIM*eta_old + DIM*dt*veta =>
                       ln V_new = ln V_old + 3*dt*veta => V_new = V_old*exp(3*dt*veta) =>
                       Side length scales as exp(veta*dt) */

                    msmul(state->box, exp(state->veta*dt), state->box);

                    /* Relate veta to boxv.  veta = d(eta)/dT = (1/DIM)*1/V dV/dT.
                       o               If we assume isotropic scaling, and box length scaling
                       factor L, then V = L^DIM (det(M)).  So dV/dt = DIM
                       L^(DIM-1) dL/dt det(M), and veta = (1/L) dL/dt.  The
                       determinant of B is L^DIM det(M), and the determinant
                       of dB/dt is (dL/dT)^DIM det (M).  veta will be
                       (det(dB/dT)/det(B))^(1/3).  Then since M =
                       B_new*(vol_new)^(1/3), dB/dT_new = (veta_new)*B(new). */

                    msmul(state->box, state->veta, state->boxv);
                    break;
                default:
                    break;
            }
            break;
        default:
            break;
    }

    if (inputrecDeform(inputrec))
    {
        deform(upd, start, homenr, state->x, state->box, inputrec, step);
    }
    where();
    dump_it_all(fplog, "After update",
                state->natoms, state->x, upd->xp, state->v, force);
}

void update_coords(FILE             *fplog,
                   gmx_int64_t       step,
                   t_inputrec       *inputrec,  /* input record and box stuff   */
                   t_mdatoms        *md,
                   t_state          *state,
                   gmx_bool          bMolPBC,
                   rvec             *f,    /* forces on home particles */
                   gmx_bool          bDoLR,
                   rvec             *f_lr,
                   tensor           *vir_lr_constr,
                   t_fcdata         *fcd,
                   gmx_ekindata_t   *ekind,
                   matrix            M,
                   gmx_update_t      upd,
                   gmx_bool          bInitStep,
                   int               UpdatePart,
                   t_commrec        *cr, /* these shouldn't be here -- need to think about it */
                   t_nrnb           *nrnb,
                   gmx_constr_t      constr,
                   t_idef           *idef)
{
    gmx_bool          bNH, bPR, bDoConstr = FALSE;
    double            dt, alpha;
    rvec             *force;
    int               start, homenr, nrend;
    rvec             *xprime;
    int               nth, th;

    bDoConstr = (NULL != constr);

    /* Running the velocity half does nothing except for velocity verlet */
    if ((UpdatePart == etrtVELOCITY1 || UpdatePart == etrtVELOCITY2) &&
        !EI_VV(inputrec->eI))
    {
        gmx_incons("update_coords called for velocity without VV integrator");
    }

    start  = 0;
    homenr = md->homenr;
    nrend  = start+homenr;

    xprime = get_xprime(state, upd);

    dt   = inputrec->delta_t;

    /* We need to update the NMR restraint history when time averaging is used */
    if (state->flags & (1<<estDISRE_RM3TAV))
    {
        update_disres_history(fcd, &state->hist);
    }
    if (state->flags & (1<<estORIRE_DTAV))
    {
        update_orires_history(fcd, &state->hist);
    }


    bNH = inputrec->etc == etcNOSEHOOVER;
    bPR = ((inputrec->epc == epcPARRINELLORAHMAN) || (inputrec->epc == epcMTTK));

    if (bDoLR && inputrec->nstcalclr > 1)
    {
        GMX_RELEASE_ASSERT(!EI_VV(inputrec->eI), "The twin-range setup is not supported by velocity-Verlet integrators");
        /* Store the total force + nstcalclr-1 times the LR force
         * in forces_lr, so it can be used in a normal update algorithm
         * to produce twin time stepping.
         */
        combine_forces(upd,
                       inputrec->nstcalclr, constr, inputrec, md, idef, cr,
                       step, state, bMolPBC,
                       start, nrend, f, f_lr, vir_lr_constr, nrnb);
        force = f_lr;
    }
    else
    {
        force = f;
    }

    /* ############# START The update of velocities and positions ######### */
    where();
    dump_it_all(fplog, "Before update",
                state->natoms, state->x, xprime, state->v, force);

    if (inputrec->eI == eiSD2)
    {
        check_sd2_work_data_allocation(upd->sd, nrend);

        do_update_sd2_Tconsts(upd->sd,
                              inputrec->opts.ngtc,
                              inputrec->opts.tau_t,
                              inputrec->opts.ref_t);
    }
    if (inputrec->eI == eiBD)
    {
        do_update_bd_Tconsts(dt, inputrec->bd_fric,
                             inputrec->opts.ngtc, inputrec->opts.ref_t,
                             upd->sd->bd_rf);
    }

    nth = gmx_omp_nthreads_get(emntUpdate);

#pragma omp parallel for num_threads(nth) schedule(static) private(alpha)
    for (th = 0; th < nth; th++)
    {
        try
        {
            int start_th, end_th;

            start_th = start + ((nrend-start)* th   )/nth;
            end_th   = start + ((nrend-start)*(th+1))/nth;

            switch (inputrec->eI)
            {
                case (eiMD):
                    if (ekind->cosacc.cos_accel == 0)
                    {
                        do_update_md(start_th, end_th, dt,
                                     ekind->tcstat, state->nosehoover_vxi,
                                     ekind->bNEMD, ekind->grpstat, inputrec->opts.acc,
                                     inputrec->opts.nFreeze,
                                     md->invmass, md->ptype,
                                     md->cFREEZE, md->cACC, md->cTC,
                                     state->x, xprime, state->v, force, M,
                                     bNH, bPR);
                    }
                    else
                    {
                        do_update_visc(start_th, end_th, dt,
                                       ekind->tcstat, state->nosehoover_vxi,
                                       md->invmass, md->ptype,
                                       md->cTC, state->x, xprime, state->v, force, M,
                                       state->box,
                                       ekind->cosacc.cos_accel,
                                       ekind->cosacc.vcos,
                                       bNH, bPR);
                    }
                    break;
                case (eiSD1):
                    /* With constraints, the SD1 update is done in 2 parts */
                    do_update_sd1(upd->sd,
                                  start_th, end_th, dt,
                                  inputrec->opts.acc, inputrec->opts.nFreeze,
                                  md->invmass, md->ptype,
                                  md->cFREEZE, md->cACC, md->cTC,
                                  state->x, xprime, state->v, force,
                                  inputrec->opts.ngtc, inputrec->opts.ref_t,
                                  bDoConstr, TRUE,
                                  step, inputrec->ld_seed, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
                    break;
                case (eiSD2):
                    /* The SD2 update is always done in 2 parts,
                     * because an extra constraint step is needed
                     */
                    do_update_sd2(upd->sd,
                                  bInitStep, start_th, end_th,
                                  inputrec->opts.acc, inputrec->opts.nFreeze,
                                  md->invmass, md->ptype,
                                  md->cFREEZE, md->cACC, md->cTC,
                                  state->x, xprime, state->v, force, state->sd_X,
                                  inputrec->opts.tau_t,
                                  TRUE, step, inputrec->ld_seed,
                                  DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
                    break;
                case (eiBD):
                    do_update_bd(start_th, end_th, dt,
                                 inputrec->opts.nFreeze, md->invmass, md->ptype,
                                 md->cFREEZE, md->cTC,
                                 state->x, xprime, state->v, force,
                                 inputrec->bd_fric,
                                 upd->sd->bd_rf,
                                 step, inputrec->ld_seed, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
                    break;
                case (eiVV):
                case (eiVVAK):
                    alpha = 1.0 + DIM/((double)inputrec->opts.nrdf[0]); /* assuming barostat coupled to group 0. */
                    switch (UpdatePart)
                    {
                        case etrtVELOCITY1:
                        case etrtVELOCITY2:
                            do_update_vv_vel(start_th, end_th, dt,
                                             inputrec->opts.acc, inputrec->opts.nFreeze,
                                             md->invmass, md->ptype,
                                             md->cFREEZE, md->cACC,
                                             state->v, force,
                                             (bNH || bPR), state->veta, alpha);
                            break;
                        case etrtPOSITION:
                            do_update_vv_pos(start_th, end_th, dt,
                                             inputrec->opts.nFreeze,
                                             md->ptype, md->cFREEZE,
                                             state->x, xprime, state->v,
                                             (bNH || bPR), state->veta);
                            break;
                    }
                    break;
                default:
                    gmx_fatal(FARGS, "Don't know how to update coordinates");
                    break;
            }
        }
        GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
    }

}


void correct_ekin(FILE *log, int start, int end, rvec v[], rvec vcm, real mass[],
                  real tmass, tensor ekin)
{
    /*
     * This is a debugging routine. It should not be called for production code
     *
     * The kinetic energy should calculated according to:
     *   Ekin = 1/2 m (v-vcm)^2
     * However the correction is not always applied, since vcm may not be
     * known in time and we compute
     *   Ekin' = 1/2 m v^2 instead
     * This can be corrected afterwards by computing
     *   Ekin = Ekin' + 1/2 m ( -2 v vcm + vcm^2)
     * or in hsorthand:
     *   Ekin = Ekin' - m v vcm + 1/2 m vcm^2
     */
    int    i, j, k;
    real   m, tm;
    rvec   hvcm, mv;
    tensor dekin;

    /* Local particles */
    clear_rvec(mv);

    /* Processor dependent part. */
    tm = 0;
    for (i = start; (i < end); i++)
    {
        m      = mass[i];
        tm    += m;
        for (j = 0; (j < DIM); j++)
        {
            mv[j] += m*v[i][j];
        }
    }
    /* Shortcut */
    svmul(1/tmass, vcm, vcm);
    svmul(0.5, vcm, hvcm);
    clear_mat(dekin);
    for (j = 0; (j < DIM); j++)
    {
        for (k = 0; (k < DIM); k++)
        {
            dekin[j][k] += vcm[k]*(tm*hvcm[j]-mv[j]);
        }
    }
    pr_rvecs(log, 0, "dekin", dekin, DIM);
    pr_rvecs(log, 0, " ekin", ekin, DIM);
    fprintf(log, "dekin = %g, ekin = %g  vcm = (%8.4f %8.4f %8.4f)\n",
            trace(dekin), trace(ekin), vcm[XX], vcm[YY], vcm[ZZ]);
    fprintf(log, "mv = (%8.4f %8.4f %8.4f)\n",
            mv[XX], mv[YY], mv[ZZ]);
}

extern gmx_bool update_randomize_velocities(t_inputrec *ir, gmx_int64_t step, const t_commrec *cr,
                                            t_mdatoms *md, t_state *state, gmx_update_t upd, gmx_constr_t constr)
{

    real rate = (ir->delta_t)/ir->opts.tau_t[0];

    if (ir->etc == etcANDERSEN && constr != NULL)
    {
        /* Currently, Andersen thermostat does not support constrained
           systems. Functionality exists in the andersen_tcoupl
           function in GROMACS 4.5.7 to allow this combination. That
           code could be ported to the current random-number
           generation approach, but has not yet been done because of
           lack of time and resources. */
        gmx_fatal(FARGS, "Normal Andersen is currently not supported with constraints, use massive Andersen instead");
    }

    /* proceed with andersen if 1) it's fixed probability per
       particle andersen or 2) it's massive andersen and it's tau_t/dt */
    if ((ir->etc == etcANDERSEN) || do_per_step(step, (int)(1.0/rate)))
    {
        andersen_tcoupl(ir, step, cr, md, state, rate,
                        upd->sd->randomize_group, upd->sd->boltzfac);
        return TRUE;
    }
    return FALSE;
}