Fixed bug in gmx disres indexing arrays.

[gromacs.git] / src / gromacs / listed-forces / position-restraints.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2014,2015,2016,2017, 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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/*! \internal \file
 *
 * \brief This file defines low-level functions necessary for
 * computing energies and forces for position restraints.
 *
 * \author Mark Abraham <mark.j.abraham@gmail.com>
 *
 * \ingroup module_listed-forces
 */

#include "gmxpre.h"

#include "position-restraints.h"

#include <assert.h>

#include <cmath>

#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/idef.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/fatalerror.h"

struct gmx_wallcycle;

namespace
{

/*! \brief returns dx, rdist, and dpdl for functions posres() and fbposres()
 */
void posres_dx(const rvec x, const rvec pos0A, const rvec pos0B,
               const rvec comA_sc, const rvec comB_sc,
               real lambda,
               const t_pbc *pbc, int refcoord_scaling, int npbcdim,
               rvec dx, rvec rdist, rvec dpdl)
{
    int  m, d;
    real posA, posB, L1, ref = 0.;
    rvec pos;

    L1 = 1.0-lambda;

    for (m = 0; m < DIM; m++)
    {
        posA = pos0A[m];
        posB = pos0B[m];
        if (m < npbcdim)
        {
            switch (refcoord_scaling)
            {
                case erscNO:
                    ref      = 0;
                    rdist[m] = L1*posA + lambda*posB;
                    dpdl[m]  = posB - posA;
                    break;
                case erscALL:
                    /* Box relative coordinates are stored for dimensions with pbc */
                    posA *= pbc->box[m][m];
                    posB *= pbc->box[m][m];
                    assert(npbcdim <= DIM);
                    for (d = m+1; d < npbcdim; d++)
                    {
                        posA += pos0A[d]*pbc->box[d][m];
                        posB += pos0B[d]*pbc->box[d][m];
                    }
                    ref      = L1*posA + lambda*posB;
                    rdist[m] = 0;
                    dpdl[m]  = posB - posA;
                    break;
                case erscCOM:
                    ref      = L1*comA_sc[m] + lambda*comB_sc[m];
                    rdist[m] = L1*posA       + lambda*posB;
                    dpdl[m]  = comB_sc[m] - comA_sc[m] + posB - posA;
                    break;
                default:
                    gmx_fatal(FARGS, "No such scaling method implemented");
            }
        }
        else
        {
            ref      = L1*posA + lambda*posB;
            rdist[m] = 0;
            dpdl[m]  = posB - posA;
        }

        /* We do pbc_dx with ref+rdist,
         * since with only ref we can be up to half a box vector wrong.
         */
        pos[m] = ref + rdist[m];
    }

    if (pbc)
    {
        pbc_dx(pbc, x, pos, dx);
    }
    else
    {
        rvec_sub(x, pos, dx);
    }
}

/*! \brief Computes forces and potential for flat-bottom cylindrical restraints.
 *         Returns the flat-bottom potential. */
real do_fbposres_cylinder(int fbdim, rvec fm, rvec dx, real rfb, real kk, gmx_bool bInvert)
{
    int     d;
    real    dr, dr2, invdr, v, rfb2;

    dr2  = 0.0;
    rfb2 = gmx::square(rfb);
    v    = 0.0;

    for (d = 0; d < DIM; d++)
    {
        if (d != fbdim)
        {
            dr2 += gmx::square(dx[d]);
        }
    }

    if  (dr2 > 0.0 &&
         ( (dr2 > rfb2 && bInvert == FALSE ) || (dr2 < rfb2 && bInvert == TRUE ) )
         )
    {
        dr     = std::sqrt(dr2);
        invdr  = 1./dr;
        v      = 0.5*kk*gmx::square(dr - rfb);
        for (d = 0; d < DIM; d++)
        {
            if (d != fbdim)
            {
                fm[d] = -kk*(dr-rfb)*dx[d]*invdr; /* Force pointing to the center */
            }
        }
    }

    return v;
}

/*! \brief Adds forces of flat-bottomed positions restraints to f[]
 *         and fixes vir_diag.
 *
 * Returns the flat-bottomed potential. Same PBC treatment as in
 * normal position restraints */
real fbposres(int nbonds,
              const t_iatom forceatoms[], const t_iparams forceparams[],
              const rvec x[], rvec f[], rvec vir_diag,
              const t_pbc *pbc,
              int refcoord_scaling, int ePBC, rvec com)
/* compute flat-bottomed positions restraints */
{
    int              i, ai, m, d, type, npbcdim = 0, fbdim;
    const t_iparams *pr;
    real             vtot, kk, v;
    real             dr, dr2, rfb, rfb2, fact;
    rvec             com_sc, rdist, dx, dpdl, fm;
    gmx_bool         bInvert;

    npbcdim = ePBC2npbcdim(ePBC);

    if (refcoord_scaling == erscCOM)
    {
        clear_rvec(com_sc);
        for (m = 0; m < npbcdim; m++)
        {
            assert(npbcdim <= DIM);
            for (d = m; d < npbcdim; d++)
            {
                com_sc[m] += com[d]*pbc->box[d][m];
            }
        }
    }

    vtot = 0.0;
    for (i = 0; (i < nbonds); )
    {
        type = forceatoms[i++];
        ai   = forceatoms[i++];
        pr   = &forceparams[type];

        /* same calculation as for normal posres, but with identical A and B states, and lambda==0 */
        posres_dx(x[ai], forceparams[type].fbposres.pos0, forceparams[type].fbposres.pos0,
                  com_sc, com_sc, 0.0,
                  pbc, refcoord_scaling, npbcdim,
                  dx, rdist, dpdl);

        clear_rvec(fm);
        v = 0.0;

        kk   = pr->fbposres.k;
        rfb  = pr->fbposres.r;
        rfb2 = gmx::square(rfb);

        /* with rfb<0, push particle out of the sphere/cylinder/layer */
        bInvert = FALSE;
        if (rfb < 0.)
        {
            bInvert = TRUE;
            rfb     = -rfb;
        }

        switch (pr->fbposres.geom)
        {
            case efbposresSPHERE:
                /* spherical flat-bottom posres */
                dr2 = norm2(dx);
                if (dr2 > 0.0 &&
                    ( (dr2 > rfb2 && bInvert == FALSE ) || (dr2 < rfb2 && bInvert == TRUE ) )
                    )
                {
                    dr   = std::sqrt(dr2);
                    v    = 0.5*kk*gmx::square(dr - rfb);
                    fact = -kk*(dr-rfb)/dr; /* Force pointing to the center pos0 */
                    svmul(fact, dx, fm);
                }
                break;
            case efbposresCYLINDERX:
                /* cylindrical flat-bottom posres in y-z plane. fm[XX] = 0. */
                fbdim = XX;
                v     = do_fbposres_cylinder(fbdim, fm, dx, rfb, kk, bInvert);
                break;
            case efbposresCYLINDERY:
                /* cylindrical flat-bottom posres in x-z plane. fm[YY] = 0. */
                fbdim = YY;
                v     = do_fbposres_cylinder(fbdim, fm, dx, rfb, kk, bInvert);
                break;
            case efbposresCYLINDER:
            /* equivalent to efbposresCYLINDERZ for backwards compatibility */
            case efbposresCYLINDERZ:
                /* cylindrical flat-bottom posres in x-y plane. fm[ZZ] = 0. */
                fbdim = ZZ;
                v     = do_fbposres_cylinder(fbdim, fm, dx, rfb, kk, bInvert);
                break;
            case efbposresX: /* fbdim=XX */
            case efbposresY: /* fbdim=YY */
            case efbposresZ: /* fbdim=ZZ */
                /* 1D flat-bottom potential */
                fbdim = pr->fbposres.geom - efbposresX;
                dr    = dx[fbdim];
                if ( ( dr > rfb && bInvert == FALSE ) || ( 0 < dr && dr < rfb && bInvert == TRUE )  )
                {
                    v         = 0.5*kk*gmx::square(dr - rfb);
                    fm[fbdim] = -kk*(dr - rfb);
                }
                else if ( (dr < (-rfb) && bInvert == FALSE ) || ( (-rfb) < dr && dr < 0 && bInvert == TRUE ))
                {
                    v         = 0.5*kk*gmx::square(dr + rfb);
                    fm[fbdim] = -kk*(dr + rfb);
                }
                break;
        }

        vtot += v;

        for (m = 0; (m < DIM); m++)
        {
            f[ai][m]   += fm[m];
            /* Here we correct for the pbc_dx which included rdist */
            vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm[m];
        }
    }

    return vtot;
}


/*! \brief Compute energies and forces for position restraints
 *
 * Note that position restraints require a different pbc treatment
 * from other bondeds */
real posres(int nbonds,
            const t_iatom forceatoms[], const t_iparams forceparams[],
            const rvec x[], rvec f[], rvec vir_diag,
            const struct t_pbc *pbc,
            real lambda, real *dvdlambda,
            int refcoord_scaling, int ePBC, rvec comA, rvec comB)
{
    int              i, ai, m, d, type, npbcdim = 0;
    const t_iparams *pr;
    real             L1;
    real             vtot, kk, fm;
    rvec             comA_sc, comB_sc, rdist, dpdl, dx;
    gmx_bool         bForceValid = TRUE;

    if ((f == nullptr) || (vir_diag == nullptr))    /* should both be null together! */
    {
        bForceValid = FALSE;
    }

    npbcdim = ePBC2npbcdim(ePBC);

    if (refcoord_scaling == erscCOM)
    {
        clear_rvec(comA_sc);
        clear_rvec(comB_sc);
        for (m = 0; m < npbcdim; m++)
        {
            assert(npbcdim <= DIM);
            for (d = m; d < npbcdim; d++)
            {
                comA_sc[m] += comA[d]*pbc->box[d][m];
                comB_sc[m] += comB[d]*pbc->box[d][m];
            }
        }
    }

    L1 = 1.0 - lambda;

    vtot = 0.0;
    for (i = 0; (i < nbonds); )
    {
        type = forceatoms[i++];
        ai   = forceatoms[i++];
        pr   = &forceparams[type];

        /* return dx, rdist, and dpdl */
        posres_dx(x[ai], forceparams[type].posres.pos0A, forceparams[type].posres.pos0B,
                  comA_sc, comB_sc, lambda,
                  pbc, refcoord_scaling, npbcdim,
                  dx, rdist, dpdl);

        for (m = 0; (m < DIM); m++)
        {
            kk          = L1*pr->posres.fcA[m] + lambda*pr->posres.fcB[m];
            fm          = -kk*dx[m];
            vtot       += 0.5*kk*dx[m]*dx[m];
            *dvdlambda +=
                0.5*(pr->posres.fcB[m] - pr->posres.fcA[m])*dx[m]*dx[m]
                + fm*dpdl[m];

            /* Here we correct for the pbc_dx which included rdist */
            if (bForceValid)
            {
                f[ai][m]    += fm;
                vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm;
            }
        }
    }

    return vtot;
}

} // namespace

void
posres_wrapper(t_nrnb             *nrnb,
               const t_idef       *idef,
               const struct t_pbc *pbc,
               const rvec          x[],
               gmx_enerdata_t     *enerd,
               real               *lambda,
               t_forcerec         *fr)
{
    real  v, dvdl;

    dvdl = 0;
    v    = posres(idef->il[F_POSRES].nr, idef->il[F_POSRES].iatoms,
                  idef->iparams_posres,
                  x, as_rvec_array(fr->f_novirsum->data()), fr->vir_diag_posres,
                  fr->ePBC == epbcNONE ? nullptr : pbc,
                  lambda[efptRESTRAINT], &dvdl,
                  fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
    enerd->term[F_POSRES] += v;
    /* If just the force constant changes, the FEP term is linear,
     * but if k changes, it is not.
     */
    enerd->dvdl_nonlin[efptRESTRAINT] += dvdl;
    inc_nrnb(nrnb, eNR_POSRES, idef->il[F_POSRES].nr/2);
}

void
posres_wrapper_lambda(struct gmx_wallcycle *wcycle,
                      const t_lambda       *fepvals,
                      const t_idef         *idef,
                      const struct t_pbc   *pbc,
                      const rvec            x[],
                      gmx_enerdata_t       *enerd,
                      real                 *lambda,
                      t_forcerec           *fr)
{
    real  v;
    int   i;

    if (0 == idef->il[F_POSRES].nr)
    {
        return;
    }

    wallcycle_sub_start_nocount(wcycle, ewcsRESTRAINTS);
    for (i = 0; i < enerd->n_lambda; i++)
    {
        real dvdl_dum = 0, lambda_dum;

        lambda_dum = (i == 0 ? lambda[efptRESTRAINT] : fepvals->all_lambda[efptRESTRAINT][i-1]);
        v          = posres(idef->il[F_POSRES].nr, idef->il[F_POSRES].iatoms,
                            idef->iparams_posres,
                            x, nullptr, nullptr,
                            fr->ePBC == epbcNONE ? nullptr : pbc, lambda_dum, &dvdl_dum,
                            fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
        enerd->enerpart_lambda[i] += v;
    }
    wallcycle_sub_stop(wcycle, ewcsRESTRAINTS);
}

/*! \brief Helper function that wraps calls to fbposres for
    free-energy perturbation */
void fbposres_wrapper(t_nrnb             *nrnb,
                      const t_idef       *idef,
                      const struct t_pbc *pbc,
                      const rvec          x[],
                      gmx_enerdata_t     *enerd,
                      t_forcerec         *fr)
{
    real  v;

    v = fbposres(idef->il[F_FBPOSRES].nr, idef->il[F_FBPOSRES].iatoms,
                 idef->iparams_fbposres,
                 x, as_rvec_array(fr->f_novirsum->data()), fr->vir_diag_posres,
                 fr->ePBC == epbcNONE ? nullptr : pbc,
                 fr->rc_scaling, fr->ePBC, fr->posres_com);
    enerd->term[F_FBPOSRES] += v;
    inc_nrnb(nrnb, eNR_FBPOSRES, idef->il[F_FBPOSRES].nr/2);
}