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[gromacs.git] / src / gromacs / gmxana / gmx_potential.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) 2013,2014,2015,2016,2017 by the GROMACS development team.
 * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
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 * GROMACS is free software; you can redistribute it and/or
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#include "gmxpre.h"

#include <cctype>
#include <cmath>
#include <cstring>

#include "gromacs/commandline/pargs.h"
#include "gromacs/commandline/viewit.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/princ.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/topology/index.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"

#define EPS0 8.85419E-12
#define ELC 1.60219E-19

/****************************************************************************/
/* This program calculates the electrostatic potential across the box by    */
/* determining the charge density in slices of the box and integrating these*/
/* twice.                                                                   */
/* Peter Tieleman, April 1995                                               */
/* It now also calculates electrostatic potential in spherical micelles,    */
/* using \frac{1}{r}\frac{d^2r\Psi}{r^2} = - \frac{\rho}{\epsilon_0}        */
/* This probably sucks but it seems to work.                                */
/****************************************************************************/

static int ce = 0, cb = 0;

/* this routine integrates the array data and returns the resulting array */
/* routine uses simple trapezoid rule                                     */
static void p_integrate(double* result, const double data[], int ndata, double slWidth)
{
    int    i, slice;
    double sum;

    if (ndata <= 2)
    {
        fprintf(stderr,
                "Warning: nr of slices very small. This will result"
                "in nonsense.\n");
    }

    fprintf(stderr, "Integrating from slice %d to slice %d\n", cb, ndata - ce);

    for (slice = cb; slice < (ndata - ce); slice++)
    {
        sum = 0;
        for (i = cb; i < slice; i++)
        {
            sum += slWidth * (data[i] + 0.5 * (data[i + 1] - data[i]));
        }
        result[slice] = sum;
    }
}

static void calc_potential(const char*             fn,
                           int**                   index,
                           int                     gnx[],
                           double***               slPotential,
                           double***               slCharge,
                           double***               slField,
                           int*                    nslices,
                           const t_topology*       top,
                           int                     ePBC,
                           int                     axis,
                           int                     nr_grps,
                           double*                 slWidth,
                           double                  fudge_z,
                           gmx_bool                bSpherical,
                           gmx_bool                bCorrect,
                           const gmx_output_env_t* oenv)
{
    rvec*        x0;     /* coordinates without pbc */
    matrix       box;    /* box (3x3) */
    int          natoms; /* nr. atoms in trj */
    t_trxstatus* status;
    int          i, n,                                   /* loop indices */
            teller = 0, ax1 = 0, ax2 = 0, nr_frames = 0, /* number of frames */
            slice;                                       /* current slice */
    double      slVolume; /* volume of slice for spherical averaging */
    double      qsum, nn;
    real        t;
    double      z;
    rvec        xcm;
    gmx_rmpbc_t gpbc = nullptr;

    switch (axis)
    {
        case 0:
            ax1 = 1;
            ax2 = 2;
            break;
        case 1:
            ax1 = 0;
            ax2 = 2;
            break;
        case 2:
            ax1 = 0;
            ax2 = 1;
            break;
        default: gmx_fatal(FARGS, "Invalid axes. Terminating\n");
    }

    if ((natoms = read_first_x(oenv, &status, fn, &t, &x0, box)) == 0)
    {
        gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
    }

    if (!*nslices)
    {
        *nslices = static_cast<int>(box[axis][axis] * 10.0); /* default value */
    }
    fprintf(stderr, "\nDividing the box in %d slices\n", *nslices);

    snew(*slField, nr_grps);
    snew(*slCharge, nr_grps);
    snew(*slPotential, nr_grps);

    for (i = 0; i < nr_grps; i++)
    {
        snew((*slField)[i], *nslices);
        snew((*slCharge)[i], *nslices);
        snew((*slPotential)[i], *nslices);
    }


    gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);

    /*********** Start processing trajectory ***********/
    do
    {
        *slWidth = box[axis][axis] / static_cast<real>((*nslices));
        teller++;
        gmx_rmpbc(gpbc, natoms, box, x0);

        /* calculate position of center of mass based on group 1 */
        calc_xcm(x0, gnx[0], index[0], top->atoms.atom, xcm, FALSE);
        svmul(-1, xcm, xcm);

        for (n = 0; n < nr_grps; n++)
        {
            /* Check whether we actually have all positions of the requested index
             * group in the trajectory file */
            if (gnx[n] > natoms)
            {
                gmx_fatal(FARGS,
                          "You selected a group with %d atoms, but only %d atoms\n"
                          "were found in the trajectory.\n",
                          gnx[n], natoms);
            }
            for (i = 0; i < gnx[n]; i++) /* loop over all atoms in index file */
            {
                if (bSpherical)
                {
                    rvec_add(x0[index[n][i]], xcm, x0[index[n][i]]);
                    /* only distance from origin counts, not sign */
                    slice = static_cast<int>(norm(x0[index[n][i]]) / (*slWidth));

                    /* this is a nice check for spherical groups but not for
                       all water in a cubic box since a lot will fall outside
                       the sphere
                       if (slice > (*nslices))
                       {
                       fprintf(stderr,"Warning: slice = %d\n",slice);
                       }
                     */
                    (*slCharge)[n][slice] += top->atoms.atom[index[n][i]].q;
                }
                else
                {
                    z = x0[index[n][i]][axis];
                    z = z + fudge_z;
                    if (z < 0)
                    {
                        z += box[axis][axis];
                    }
                    if (z > box[axis][axis])
                    {
                        z -= box[axis][axis];
                    }
                    /* determine which slice atom is in */
                    slice = static_cast<int>((z / (*slWidth)));
                    (*slCharge)[n][slice] += top->atoms.atom[index[n][i]].q;
                }
            }
        }
        nr_frames++;
    } while (read_next_x(oenv, status, &t, x0, box));

    gmx_rmpbc_done(gpbc);

    /*********** done with status file **********/
    close_trx(status);

    /* slCharge now contains the total charge per slice, summed over all
       frames. Now divide by nr_frames and integrate twice
     */


    if (bSpherical)
    {
        fprintf(stderr,
                "\n\nRead %d frames from trajectory. Calculating potential"
                "in spherical coordinates\n",
                nr_frames);
    }
    else
    {
        fprintf(stderr, "\n\nRead %d frames from trajectory. Calculating potential\n", nr_frames);
    }

    for (n = 0; n < nr_grps; n++)
    {
        for (i = 0; i < *nslices; i++)
        {
            if (bSpherical)
            {
                /* charge per volume is now the summed charge, divided by the nr
                   of frames and by the volume of the slice it's in, 4pi r^2 dr
                 */
                slVolume = 4 * M_PI * gmx::square(i) * gmx::square(*slWidth) * *slWidth;
                if (slVolume == 0)
                {
                    (*slCharge)[n][i] = 0;
                }
                else
                {
                    (*slCharge)[n][i] = (*slCharge)[n][i] / (nr_frames * slVolume);
                }
            }
            else
            {
                /* get charge per volume */
                (*slCharge)[n][i] = (*slCharge)[n][i] * (*nslices)
                                    / (static_cast<real>(nr_frames) * box[axis][axis]
                                       * box[ax1][ax1] * box[ax2][ax2]);
            }
        }
        /* Now we have charge densities */
    }

    if (bCorrect && !bSpherical)
    {
        for (n = 0; n < nr_grps; n++)
        {
            nn   = 0;
            qsum = 0;
            for (i = 0; i < *nslices; i++)
            {
                if (std::abs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
                {
                    nn++;
                    qsum += (*slCharge)[n][i];
                }
            }
            qsum /= nn;
            for (i = 0; i < *nslices; i++)
            {
                if (std::abs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
                {
                    (*slCharge)[n][i] -= qsum;
                }
            }
        }
    }

    for (n = 0; n < nr_grps; n++)
    {
        /* integrate twice to get field and potential */
        p_integrate((*slField)[n], (*slCharge)[n], *nslices, *slWidth);
    }


    if (bCorrect && !bSpherical)
    {
        for (n = 0; n < nr_grps; n++)
        {
            nn   = 0;
            qsum = 0;
            for (i = 0; i < *nslices; i++)
            {
                if (std::abs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
                {
                    nn++;
                    qsum += (*slField)[n][i];
                }
            }
            qsum /= nn;
            for (i = 0; i < *nslices; i++)
            {
                if (std::abs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
                {
                    (*slField)[n][i] -= qsum;
                }
            }
        }
    }

    for (n = 0; n < nr_grps; n++)
    {
        p_integrate((*slPotential)[n], (*slField)[n], *nslices, *slWidth);
    }

    /* Now correct for eps0 and in spherical case for r*/
    for (n = 0; n < nr_grps; n++)
    {
        for (i = 0; i < *nslices; i++)
        {
            if (bSpherical)
            {
                (*slPotential)[n][i] = ELC * (*slPotential)[n][i] * -1.0E9 / (EPS0 * i * (*slWidth));
                (*slField)[n][i]     = ELC * (*slField)[n][i] * 1E18 / (EPS0 * i * (*slWidth));
            }
            else
            {
                (*slPotential)[n][i] = ELC * (*slPotential)[n][i] * -1.0E9 / EPS0;
                (*slField)[n][i]     = ELC * (*slField)[n][i] * 1E18 / EPS0;
            }
        }
    }

    sfree(x0); /* free memory used by coordinate array */
}

static void plot_potential(double*                 potential[],
                           double*                 charge[],
                           double*                 field[],
                           const char*             afile,
                           const char*             bfile,
                           const char*             cfile,
                           int                     nslices,
                           int                     nr_grps,
                           const char* const       grpname[],
                           double                  slWidth,
                           const gmx_output_env_t* oenv)
{
    FILE *pot,     /* xvgr file with potential */
            *cha,  /* xvgr file with charges   */
            *fie;  /* xvgr files with fields   */
    char buf[256]; /* for xvgr title */
    int  slice, n;

    sprintf(buf, "Electrostatic Potential");
    pot = xvgropen(afile, buf, "Box (nm)", "Potential (V)", oenv);
    xvgr_legend(pot, nr_grps, grpname, oenv);

    sprintf(buf, "Charge Distribution");
    cha = xvgropen(bfile, buf, "Box (nm)", "Charge density (q/nm\\S3\\N)", oenv);
    xvgr_legend(cha, nr_grps, grpname, oenv);

    sprintf(buf, "Electric Field");
    fie = xvgropen(cfile, buf, "Box (nm)", "Field (V/nm)", oenv);
    xvgr_legend(fie, nr_grps, grpname, oenv);

    for (slice = cb; slice < (nslices - ce); slice++)
    {
        fprintf(pot, "%20.16g  ", slice * slWidth);
        fprintf(cha, "%20.16g  ", slice * slWidth);
        fprintf(fie, "%20.16g  ", slice * slWidth);
        for (n = 0; n < nr_grps; n++)
        {
            fprintf(pot, "   %20.16g", potential[n][slice]);
            fprintf(fie, "   %20.16g", field[n][slice] / 1e9); /* convert to V/nm */
            fprintf(cha, "   %20.16g", charge[n][slice]);
        }
        fprintf(pot, "\n");
        fprintf(cha, "\n");
        fprintf(fie, "\n");
    }

    xvgrclose(pot);
    xvgrclose(cha);
    xvgrclose(fie);
}

int gmx_potential(int argc, char* argv[])
{
    const char* desc[] = {
        "[THISMODULE] computes the electrostatical potential across the box. The potential is",
        "calculated by first summing the charges per slice and then integrating",
        "twice of this charge distribution. Periodic boundaries are not taken",
        "into account. Reference of potential is taken to be the left side of",
        "the box. It is also possible to calculate the potential in spherical",
        "coordinates as function of r by calculating a charge distribution in",
        "spherical slices and twice integrating them. epsilon_r is taken as 1,",
        "but 2 is more appropriate in many cases."
    };
    gmx_output_env_t*  oenv;
    static int         axis       = 2; /* normal to memb. default z  */
    static const char* axtitle    = "Z";
    static int         nslices    = 10; /* nr of slices defined       */
    static int         ngrps      = 1;
    static gmx_bool    bSpherical = FALSE; /* default is bilayer types   */
    static real        fudge_z    = 0;     /* translate coordinates      */
    static gmx_bool    bCorrect   = false;
    t_pargs            pa[]       = {
        { "-d",
          FALSE,
          etSTR,
          { &axtitle },
          "Take the normal on the membrane in direction X, Y or Z." },
        { "-sl",
          FALSE,
          etINT,
          { &nslices },
          "Calculate potential as function of boxlength, dividing the box"
          " in this number of slices." },
        { "-cb",
          FALSE,
          etINT,
          { &cb },
          "Discard this number of  first slices of box for integration" },
        { "-ce",
          FALSE,
          etINT,
          { &ce },
          "Discard this number of last slices of box for integration" },
        { "-tz",
          FALSE,
          etREAL,
          { &fudge_z },
          "Translate all coordinates by this distance in the direction of the box" },
        { "-spherical", FALSE, etBOOL, { &bSpherical }, "Calculate in spherical coordinates" },
        { "-ng", FALSE, etINT, { &ngrps }, "Number of groups to consider" },
        { "-correct",
          FALSE,
          etBOOL,
          { &bCorrect },
          "Assume net zero charge of groups to improve accuracy" }
    };
    const char* bugs[] = { "Discarding slices for integration should not be necessary." };

    double **potential,  /* potential per slice        */
            **charge,    /* total charge per slice     */
            **field,     /* field per slice            */
            slWidth;     /* width of one slice         */
    char**      grpname; /* groupnames                 */
    int*        ngx;     /* sizes of groups            */
    t_topology* top;     /* topology        */
    int         ePBC;
    int**       index; /* indices for all groups     */
    t_filenm    fnm[] = {
        /* files for g_order       */
        { efTRX, "-f", nullptr, ffREAD },      /* trajectory file             */
        { efNDX, nullptr, nullptr, ffREAD },   /* index file          */
        { efTPR, nullptr, nullptr, ffREAD },   /* topology file               */
        { efXVG, "-o", "potential", ffWRITE }, /* xvgr output file    */
        { efXVG, "-oc", "charge", ffWRITE },   /* xvgr output file    */
        { efXVG, "-of", "field", ffWRITE },    /* xvgr output file    */
    };

#define NFILE asize(fnm)

    if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa,
                           asize(desc), desc, asize(bugs), bugs, &oenv))
    {
        return 0;
    }

    /* Calculate axis */
    axis = toupper(axtitle[0]) - 'X';

    top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */

    snew(grpname, ngrps);
    snew(index, ngrps);
    snew(ngx, ngrps);

    rd_index(ftp2fn(efNDX, NFILE, fnm), ngrps, ngx, index, grpname);


    calc_potential(ftp2fn(efTRX, NFILE, fnm), index, ngx, &potential, &charge, &field, &nslices,
                   top, ePBC, axis, ngrps, &slWidth, fudge_z, bSpherical, bCorrect, oenv);

    plot_potential(potential, charge, field, opt2fn("-o", NFILE, fnm), opt2fn("-oc", NFILE, fnm),
                   opt2fn("-of", NFILE, fnm), nslices, ngrps, grpname, slWidth, oenv);

    do_view(oenv, opt2fn("-o", NFILE, fnm), nullptr);  /* view xvgr file */
    do_view(oenv, opt2fn("-oc", NFILE, fnm), nullptr); /* view xvgr file */
    do_view(oenv, opt2fn("-of", NFILE, fnm), nullptr); /* view xvgr file */

    return 0;
}