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[gromacs.git] / src / gromacs / ewald / ewald.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) 2013,2014,2015,2017,2018 by the GROMACS development team.
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 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
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/*! \internal \file
 *
 * \brief This file contains function definitions necessary for
 * computing energies and forces for the plain-Ewald long-ranged part,
 * and the correction for overall system charge for all Ewald-family
 * methods.
 *
 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
 * \author Mark Abraham <mark.j.abraham@gmail.com>
 * \ingroup module_ewald
 */
#include "gmxpre.h"

#include "ewald.h"

#include <cmath>
#include <cstdio>
#include <cstdlib>

#include <algorithm>

#include "gromacs/ewald/ewald_utils.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/gmxcomplex.h"
#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"

struct gmx_ewald_tab_t
{
    int        nx, ny, nz, kmax;
    cvec**     eir;
    t_complex *tab_xy, *tab_qxyz;
};

void init_ewald_tab(struct gmx_ewald_tab_t** et, const t_inputrec* ir, FILE* fp)
{
    snew(*et, 1);
    if (fp)
    {
        fprintf(fp, "Will do ordinary reciprocal space Ewald sum.\n");
    }

    (*et)->nx       = ir->nkx + 1;
    (*et)->ny       = ir->nky + 1;
    (*et)->nz       = ir->nkz + 1;
    (*et)->kmax     = std::max((*et)->nx, std::max((*et)->ny, (*et)->nz));
    (*et)->eir      = nullptr;
    (*et)->tab_xy   = nullptr;
    (*et)->tab_qxyz = nullptr;
}

//! Calculates wave vectors.
static void calc_lll(const rvec box, rvec lll)
{
    lll[XX] = 2.0 * M_PI / box[XX];
    lll[YY] = 2.0 * M_PI / box[YY];
    lll[ZZ] = 2.0 * M_PI / box[ZZ];
}

//! Make tables for the structure factor parts
static void tabulateStructureFactors(int natom, const rvec x[], int kmax, cvec** eir, const rvec lll)
{
    int i, j, m;

    if (kmax < 1)
    {
        printf("Go away! kmax = %d\n", kmax);
        exit(1);
    }

    for (i = 0; (i < natom); i++)
    {
        for (m = 0; (m < 3); m++)
        {
            eir[0][i][m].re = 1;
            eir[0][i][m].im = 0;
        }

        for (m = 0; (m < 3); m++)
        {
            eir[1][i][m].re = std::cos(x[i][m] * lll[m]);
            eir[1][i][m].im = std::sin(x[i][m] * lll[m]);
        }
        for (j = 2; (j < kmax); j++)
        {
            for (m = 0; (m < 3); m++)
            {
                eir[j][i][m] = cmul(eir[j - 1][i][m], eir[1][i][m]);
            }
        }
    }
}

real do_ewald(const t_inputrec* ir,
              const rvec        x[],
              rvec              f[],
              const real        chargeA[],
              const real        chargeB[],
              const matrix      box,
              const t_commrec*  cr,
              int               natoms,
              matrix            lrvir,
              real              ewaldcoeff,
              real              lambda,
              real*             dvdlambda,
              gmx_ewald_tab_t*  et)
{
    real        factor = -1.0 / (4 * ewaldcoeff * ewaldcoeff);
    const real* charge;
    real        energy_AB[2], energy;
    rvec        lll;
    int         lowiy, lowiz, ix, iy, iz, n, q;
    real        tmp, cs, ss, ak, akv, mx, my, mz, m2, scale;
    gmx_bool    bFreeEnergy;

    if (cr != nullptr)
    {
        if (PAR(cr))
        {
            gmx_fatal(FARGS, "No parallel Ewald. Use PME instead.\n");
        }
    }

    /* Scale box with Ewald wall factor */
    matrix          scaledBox;
    EwaldBoxZScaler boxScaler(*ir);
    boxScaler.scaleBox(box, scaledBox);

    rvec boxDiag;
    for (int i = 0; (i < DIM); i++)
    {
        boxDiag[i] = scaledBox[i][i];
    }

    /* 1/(Vol*e0) */
    real scaleRecip = 4.0 * M_PI / (boxDiag[XX] * boxDiag[YY] * boxDiag[ZZ]) * ONE_4PI_EPS0 / ir->epsilon_r;

    if (!et->eir) /* allocate if we need to */
    {
        snew(et->eir, et->kmax);
        for (n = 0; n < et->kmax; n++)
        {
            snew(et->eir[n], natoms);
        }
        snew(et->tab_xy, natoms);
        snew(et->tab_qxyz, natoms);
    }

    bFreeEnergy = (ir->efep != efepNO);

    clear_mat(lrvir);

    calc_lll(boxDiag, lll);
    tabulateStructureFactors(natoms, x, et->kmax, et->eir, lll);

    for (q = 0; q < (bFreeEnergy ? 2 : 1); q++)
    {
        if (!bFreeEnergy)
        {
            charge = chargeA;
            scale  = 1.0;
        }
        else if (q == 0)
        {
            charge = chargeA;
            scale  = 1.0 - lambda;
        }
        else
        {
            charge = chargeB;
            scale  = lambda;
        }
        lowiy        = 0;
        lowiz        = 1;
        energy_AB[q] = 0;
        for (ix = 0; ix < et->nx; ix++)
        {
            mx = ix * lll[XX];
            for (iy = lowiy; iy < et->ny; iy++)
            {
                my = iy * lll[YY];
                if (iy >= 0)
                {
                    for (n = 0; n < natoms; n++)
                    {
                        et->tab_xy[n] = cmul(et->eir[ix][n][XX], et->eir[iy][n][YY]);
                    }
                }
                else
                {
                    for (n = 0; n < natoms; n++)
                    {
                        et->tab_xy[n] = cmul(et->eir[ix][n][XX], conjugate(et->eir[-iy][n][YY]));
                    }
                }
                for (iz = lowiz; iz < et->nz; iz++)
                {
                    mz  = iz * lll[ZZ];
                    m2  = mx * mx + my * my + mz * mz;
                    ak  = std::exp(m2 * factor) / m2;
                    akv = 2.0 * ak * (1.0 / m2 - factor);
                    if (iz >= 0)
                    {
                        for (n = 0; n < natoms; n++)
                        {
                            et->tab_qxyz[n] = rcmul(charge[n], cmul(et->tab_xy[n], et->eir[iz][n][ZZ]));
                        }
                    }
                    else
                    {
                        for (n = 0; n < natoms; n++)
                        {
                            et->tab_qxyz[n] = rcmul(
                                    charge[n], cmul(et->tab_xy[n], conjugate(et->eir[-iz][n][ZZ])));
                        }
                    }

                    cs = ss = 0;
                    for (n = 0; n < natoms; n++)
                    {
                        cs += et->tab_qxyz[n].re;
                        ss += et->tab_qxyz[n].im;
                    }
                    energy_AB[q] += ak * (cs * cs + ss * ss);
                    tmp = scale * akv * (cs * cs + ss * ss);
                    lrvir[XX][XX] -= tmp * mx * mx;
                    lrvir[XX][YY] -= tmp * mx * my;
                    lrvir[XX][ZZ] -= tmp * mx * mz;
                    lrvir[YY][YY] -= tmp * my * my;
                    lrvir[YY][ZZ] -= tmp * my * mz;
                    lrvir[ZZ][ZZ] -= tmp * mz * mz;
                    for (n = 0; n < natoms; n++)
                    {
                        /*tmp=scale*ak*(cs*tab_qxyz[n].im-ss*tab_qxyz[n].re);*/
                        tmp = scale * ak * (cs * et->tab_qxyz[n].im - ss * et->tab_qxyz[n].re);
                        f[n][XX] += tmp * mx * 2 * scaleRecip;
                        f[n][YY] += tmp * my * 2 * scaleRecip;
                        f[n][ZZ] += tmp * mz * 2 * scaleRecip;
#if 0
                        f[n][XX] += tmp*mx;
                        f[n][YY] += tmp*my;
                        f[n][ZZ] += tmp*mz;
#endif
                    }
                    lowiz = 1 - et->nz;
                }
                lowiy = 1 - et->ny;
            }
        }
    }

    if (!bFreeEnergy)
    {
        energy = energy_AB[0];
    }
    else
    {
        energy = (1.0 - lambda) * energy_AB[0] + lambda * energy_AB[1];
        *dvdlambda += scaleRecip * (energy_AB[1] - energy_AB[0]);
    }

    lrvir[XX][XX] = -0.5 * scaleRecip * (lrvir[XX][XX] + energy);
    lrvir[XX][YY] = -0.5 * scaleRecip * (lrvir[XX][YY]);
    lrvir[XX][ZZ] = -0.5 * scaleRecip * (lrvir[XX][ZZ]);
    lrvir[YY][YY] = -0.5 * scaleRecip * (lrvir[YY][YY] + energy);
    lrvir[YY][ZZ] = -0.5 * scaleRecip * (lrvir[YY][ZZ]);
    lrvir[ZZ][ZZ] = -0.5 * scaleRecip * (lrvir[ZZ][ZZ] + energy);

    lrvir[YY][XX] = lrvir[XX][YY];
    lrvir[ZZ][XX] = lrvir[XX][ZZ];
    lrvir[ZZ][YY] = lrvir[YY][ZZ];

    energy *= scaleRecip;

    return energy;
}

real ewald_charge_correction(const t_commrec*  cr,
                             const t_forcerec* fr,
                             const real        lambda,
                             const matrix      box,
                             real*             dvdlambda,
                             tensor            vir)

{
    real vol, fac, qs2A, qs2B, vc, enercorr;
    int  d;

    if (MASTER(cr))
    {
        /* Apply charge correction */
        vol = box[XX][XX] * box[YY][YY] * box[ZZ][ZZ];

        fac = M_PI * ONE_4PI_EPS0
              / (fr->ic->epsilon_r * 2.0 * vol * vol * gmx::square(fr->ic->ewaldcoeff_q));

        qs2A = fr->qsum[0] * fr->qsum[0];
        qs2B = fr->qsum[1] * fr->qsum[1];

        vc = (qs2A * (1 - lambda) + qs2B * lambda) * fac;

        enercorr = -vol * vc;

        *dvdlambda += -vol * (qs2B - qs2A) * fac;

        for (d = 0; d < DIM; d++)
        {
            vir[d][d] += vc;
        }

        if (debug)
        {
            fprintf(debug, "Total charge correction: Vcharge=%g\n", enercorr);
        }
    }
    else
    {
        enercorr = 0;
    }

    return enercorr;
}