/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright 1991- The GROMACS Authors
 * and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
 * Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
 *
 * 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,
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 * 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
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 */
#include "gmxpre.h"

#include <cmath>
#include <cstring>

#include "gromacs/commandline/pargs.h"
#include "gromacs/commandline/viewit.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.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/gmxassert.h"
#include "gromacs/utility/smalloc.h"

int gmx_densmap(int argc, char* argv[])
{
    const char* desc[] = {
        "[THISMODULE] computes 2D number-density maps.",
        "It can make planar and axial-radial density maps.",
        "The output [REF].xpm[ref] file can be visualized with for instance xv",
        "and can be converted to postscript with [TT]xpm2ps[tt].",
        "Optionally, output can be in text form to a [REF].dat[ref] file with [TT]-od[tt], ",
        "instead of the usual [REF].xpm[ref] file with [TT]-o[tt].",
        "[PAR]",
        "The default analysis is a 2-D number-density map for a selected",
        "group of atoms in the x-y plane.",
        "The averaging direction can be changed with the option [TT]-aver[tt].",
        "When [TT]-xmin[tt] and/or [TT]-xmax[tt] are set only atoms that are",
        "within the limit(s) in the averaging direction are taken into account.",
        "The grid spacing is set with the option [TT]-bin[tt].",
        "When [TT]-n1[tt] or [TT]-n2[tt] is non-zero, the grid",
        "size is set by this option.",
        "Box size fluctuations are properly taken into account.",
        "[PAR]",
        "When options [TT]-amax[tt] and [TT]-rmax[tt] are set, an axial-radial",
        "number-density map is made. Three groups should be supplied, the centers",
        "of mass of the first two groups define the axis, the third defines the",
        "analysis group. The axial direction goes from -amax to +amax, where",
        "the center is defined as the midpoint between the centers of mass and",
        "the positive direction goes from the first to the second center of mass.",
        "The radial direction goes from 0 to rmax or from -rmax to +rmax",
        "when the [TT]-mirror[tt] option has been set.",
        "[PAR]",
        "The normalization of the output is set with the [TT]-unit[tt] option.",
        "The default produces a true number density. Unit [TT]nm-2[tt] leaves out",
        "the normalization for the averaging or the angular direction.",
        "Option [TT]count[tt] produces the count for each grid cell.",
        "When you do not want the scale in the output to go",
        "from zero to the maximum density, you can set the maximum",
        "with the option [TT]-dmax[tt]."
    };
    static int         n1 = 0, n2 = 0;
    static real        xmin = -1, xmax = -1, bin = 0.02, dmin = 0, dmax = 0, amax = 0, rmax = 0;
    static gmx_bool    bMirror = FALSE, bSums = FALSE;
    static const char* eaver[] = { nullptr, "z", "y", "x", nullptr };
    static const char* eunit[] = { nullptr, "nm-3", "nm-2", "count", nullptr };

    t_pargs pa[] = {
        { "-bin", FALSE, etREAL, { &bin }, "Grid size (nm)" },
        { "-aver", FALSE, etENUM, { eaver }, "The direction to average over" },
        { "-xmin", FALSE, etREAL, { &xmin }, "Minimum coordinate for averaging" },
        { "-xmax", FALSE, etREAL, { &xmax }, "Maximum coordinate for averaging" },
        { "-n1", FALSE, etINT, { &n1 }, "Number of grid cells in the first direction" },
        { "-n2", FALSE, etINT, { &n2 }, "Number of grid cells in the second direction" },
        { "-amax", FALSE, etREAL, { &amax }, "Maximum axial distance from the center" },
        { "-rmax", FALSE, etREAL, { &rmax }, "Maximum radial distance" },
        { "-mirror", FALSE, etBOOL, { &bMirror }, "Add the mirror image below the axial axis" },
        { "-sums", FALSE, etBOOL, { &bSums }, "Print density sums (1D map) to stdout" },
        { "-unit", FALSE, etENUM, { eunit }, "Unit for the output" },
        { "-dmin", FALSE, etREAL, { &dmin }, "Minimum density in output" },
        { "-dmax", FALSE, etREAL, { &dmax }, "Maximum density in output (0 means calculate it)" },
    };
    gmx_bool          bXmin, bXmax, bRadial;
    FILE*             fp;
    t_trxstatus*      status;
    t_topology        top;
    PbcType           pbcType = PbcType::Unset;
    rvec *            x, xcom[2], direction, center, dx;
    matrix            box;
    real              t, m, mtot;
    t_pbc             pbc;
    int               cav = 0, c1 = 0, c2 = 0;
    char **           grpname, buf[STRLEN];
    const char*       unit;
    int               i, j, k, l, ngrps, anagrp, *gnx = nullptr, nindex, nradial = 0, nfr, nmpower;
    int **            ind = nullptr, *index;
    real **           grid, maxgrid, m1, m2, box1, box2, *tickx, *tickz, invcellvol;
    real              invspa = 0, invspz = 0, axial, r, vol_old, vol, rowsum;
    int               nlev = 51;
    t_rgb             rlo = { 1, 1, 1 }, rhi = { 0, 0, 0 };
    gmx_output_env_t* oenv;
    const char*       label[] = { "x (nm)", "y (nm)", "z (nm)" };
    t_filenm          fnm[]   = { { efTRX, "-f", nullptr, ffREAD },
                       { efTPS, nullptr, nullptr, ffOPTRD },
                       { efNDX, nullptr, nullptr, ffOPTRD },
                       { efDAT, "-od", "densmap", ffOPTWR },
                       { efXPM, "-o", "densmap", ffWRITE } };
#define NFILE asize(fnm)
    int npargs;

    npargs = asize(pa);

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

    bXmin   = opt2parg_bSet("-xmin", npargs, pa);
    bXmax   = opt2parg_bSet("-xmax", npargs, pa);
    bRadial = (amax > 0 || rmax > 0);
    if (bRadial)
    {
        if (amax <= 0 || rmax <= 0)
        {
            gmx_fatal(FARGS, "Both amax and rmax should be larger than zero");
        }
    }

    GMX_RELEASE_ASSERT(eunit[0] != nullptr, "Option setting inconsistency; eunit[0] is NULL");

    if (std::strcmp(eunit[0], "nm-3") == 0)
    {
        nmpower = -3;
        unit    = "(nm^-3)";
    }
    else if (std::strcmp(eunit[0], "nm-2") == 0)
    {
        nmpower = -2;
        unit    = "(nm^-2)";
    }
    else
    {
        nmpower = 0;
        unit    = "count";
    }

    if (ftp2bSet(efTPS, NFILE, fnm) || !ftp2bSet(efNDX, NFILE, fnm))
    {
        read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &pbcType, &x, nullptr, box, bRadial);
    }
    if (!bRadial)
    {
        ngrps = 1;
        fprintf(stderr, "\nSelect an analysis group\n");
    }
    else
    {
        ngrps = 3;
        fprintf(stderr, "\nSelect two groups to define the axis and an analysis group\n");
    }
    snew(gnx, ngrps);
    snew(grpname, ngrps);
    snew(ind, ngrps);
    get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), ngrps, gnx, ind, grpname);
    anagrp = ngrps - 1;
    nindex = gnx[anagrp];
    index  = ind[anagrp];
    if (bRadial)
    {
        if ((gnx[0] > 1 || gnx[1] > 1) && !ftp2bSet(efTPS, NFILE, fnm))
        {
            gmx_fatal(FARGS,
                      "No run input file was supplied (option -s), this is required for the center "
                      "of mass calculation");
        }
    }

    GMX_RELEASE_ASSERT(eaver[0] != nullptr, "Option setting inconsistency; eaver[0] is NULL");

    switch (eaver[0][0])
    {
        case 'x':
            cav = XX;
            c1  = YY;
            c2  = ZZ;
            break;
        case 'y':
            cav = YY;
            c1  = XX;
            c2  = ZZ;
            break;
        case 'z':
            cav = ZZ;
            c1  = XX;
            c2  = YY;
            break;
    }

    read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);

    if (!bRadial)
    {
        if (n1 == 0)
        {
            n1 = gmx::roundToInt(box[c1][c1] / bin);
        }
        if (n2 == 0)
        {
            n2 = gmx::roundToInt(box[c2][c2] / bin);
        }
    }
    else
    {
        n1      = gmx::roundToInt(2 * amax / bin);
        nradial = gmx::roundToInt(rmax / bin);
        invspa  = n1 / (2 * amax);
        invspz  = nradial / rmax;
        if (bMirror)
        {
            n2 = 2 * nradial;
        }
        else
        {
            n2 = nradial;
        }
    }

    snew(grid, n1);
    for (i = 0; i < n1; i++)
    {
        snew(grid[i], n2);
    }

    box1 = 0;
    box2 = 0;
    nfr  = 0;
    do
    {
        if (!bRadial)
        {
            box1 += box[c1][c1];
            box2 += box[c2][c2];
            invcellvol = n1 * n2;
            if (nmpower == -3)
            {
                invcellvol /= det(box);
            }
            else if (nmpower == -2)
            {
                invcellvol /= box[c1][c1] * box[c2][c2];
            }
            for (i = 0; i < nindex; i++)
            {
                j = index[i];
                if ((!bXmin || x[j][cav] >= xmin) && (!bXmax || x[j][cav] <= xmax))
                {
                    m1 = x[j][c1] / box[c1][c1];
                    if (m1 >= 1)
                    {
                        m1 -= 1;
                    }
                    if (m1 < 0)
                    {
                        m1 += 1;
                    }
                    m2 = x[j][c2] / box[c2][c2];
                    if (m2 >= 1)
                    {
                        m2 -= 1;
                    }
                    if (m2 < 0)
                    {
                        m2 += 1;
                    }
                    grid[static_cast<int>(m1 * n1)][static_cast<int>(m2 * n2)] += invcellvol;
                }
            }
        }
        else
        {
            set_pbc(&pbc, pbcType, box);
            for (i = 0; i < 2; i++)
            {
                if (gnx[i] == 1)
                {
                    /* One atom, just copy the coordinates */
                    copy_rvec(x[ind[i][0]], xcom[i]);
                }
                else
                {
                    /* Calculate the center of mass */
                    clear_rvec(xcom[i]);
                    mtot = 0;
                    for (j = 0; j < gnx[i]; j++)
                    {
                        k = ind[i][j];
                        m = top.atoms.atom[k].m;
                        for (l = 0; l < DIM; l++)
                        {
                            xcom[i][l] += m * x[k][l];
                        }
                        mtot += m;
                    }
                    svmul(1 / mtot, xcom[i], xcom[i]);
                }
            }
            pbc_dx(&pbc, xcom[1], xcom[0], direction);
            for (i = 0; i < DIM; i++)
            {
                center[i] = xcom[0][i] + 0.5 * direction[i];
            }
            unitv(direction, direction);
            for (i = 0; i < nindex; i++)
            {
                j = index[i];
                pbc_dx(&pbc, x[j], center, dx);
                axial = iprod(dx, direction);
                r     = std::sqrt(norm2(dx) - axial * axial);
                if (axial >= -amax && axial < amax && r < rmax)
                {
                    if (bMirror)
                    {
                        r += rmax;
                    }
                    grid[static_cast<int>((axial + amax) * invspa)][static_cast<int>(r * invspz)] += 1;
                }
            }
        }
        nfr++;
    } while (read_next_x(oenv, status, &t, x, box));
    close_trx(status);

    /* normalize gridpoints */
    maxgrid = 0;
    if (!bRadial)
    {
        for (i = 0; i < n1; i++)
        {
            for (j = 0; j < n2; j++)
            {
                grid[i][j] /= nfr;
                if (grid[i][j] > maxgrid)
                {
                    maxgrid = grid[i][j];
                }
            }
        }
    }
    else
    {
        for (i = 0; i < n1; i++)
        {
            vol_old = 0;
            for (j = 0; j < nradial; j++)
            {
                switch (nmpower)
                {
                    case -3: vol = M_PI * (j + 1) * (j + 1) / (invspz * invspz * invspa); break;
                    case -2: vol = (j + 1) / (invspz * invspa); break;
                    default: vol = j + 1; break;
                }
                if (bMirror)
                {
                    k = j + nradial;
                }
                else
                {
                    k = j;
                }
                grid[i][k] /= nfr * (vol - vol_old);
                if (bMirror)
                {
                    grid[i][nradial - 1 - j] = grid[i][k];
                }
                vol_old = vol;
                if (grid[i][k] > maxgrid)
                {
                    maxgrid = grid[i][k];
                }
            }
        }
    }
    fprintf(stdout, "\n  The maximum density is %f %s\n", maxgrid, unit);
    if (dmax > 0)
    {
        maxgrid = dmax;
    }

    snew(tickx, n1 + 1);
    snew(tickz, n2 + 1);
    if (!bRadial)
    {
        /* normalize box-axes */
        box1 /= nfr;
        box2 /= nfr;
        for (i = 0; i <= n1; i++)
        {
            tickx[i] = i * box1 / n1;
        }
        for (i = 0; i <= n2; i++)
        {
            tickz[i] = i * box2 / n2;
        }
    }
    else
    {
        for (i = 0; i <= n1; i++)
        {
            tickx[i] = i / invspa - amax;
        }
        if (bMirror)
        {
            for (i = 0; i <= n2; i++)
            {
                tickz[i] = i / invspz - rmax;
            }
        }
        else
        {
            for (i = 0; i <= n2; i++)
            {
                tickz[i] = i / invspz;
            }
        }
    }

    if (bSums)
    {
        for (i = 0; i < n1; ++i)
        {
            fprintf(stdout, "Density sums:\n");
            rowsum = 0;
            for (j = 0; j < n2; ++j)
            {
                rowsum += grid[i][j];
            }
            fprintf(stdout, "%g\t", rowsum);
        }
        fprintf(stdout, "\n");
    }

    sprintf(buf, "%s number density", grpname[anagrp]);
    if (!bRadial && (bXmin || bXmax))
    {
        if (!bXmax)
        {
            sprintf(buf + std::strlen(buf), ", %c > %g nm", eaver[0][0], xmin);
        }
        else if (!bXmin)
        {
            sprintf(buf + std::strlen(buf), ", %c < %g nm", eaver[0][0], xmax);
        }
        else
        {
            sprintf(buf + std::strlen(buf), ", %c: %g - %g nm", eaver[0][0], xmin, xmax);
        }
    }
    if (ftp2bSet(efDAT, NFILE, fnm))
    {
        fp = gmx_ffopen(ftp2fn(efDAT, NFILE, fnm), "w");
        /*optional text form output:  first row is tickz; first col is tickx */
        fprintf(fp, "0\t");
        for (j = 0; j < n2; ++j)
        {
            fprintf(fp, "%g\t", tickz[j]);
        }
        fprintf(fp, "\n");

        for (i = 0; i < n1; ++i)
        {
            fprintf(fp, "%g\t", tickx[i]);
            for (j = 0; j < n2; ++j)
            {
                fprintf(fp, "%g\t", grid[i][j]);
            }
            fprintf(fp, "\n");
        }
        gmx_ffclose(fp);
    }
    else
    {
        fp = gmx_ffopen(ftp2fn(efXPM, NFILE, fnm), "w");
        write_xpm(fp,
                  MAT_SPATIAL_X | MAT_SPATIAL_Y,
                  buf,
                  unit,
                  bRadial ? "axial (nm)" : label[c1],
                  bRadial ? "r (nm)" : label[c2],
                  n1,
                  n2,
                  tickx,
                  tickz,
                  grid,
                  dmin,
                  maxgrid,
                  rlo,
                  rhi,
                  &nlev);
        gmx_ffclose(fp);
    }

    do_view(oenv, opt2fn("-o", NFILE, fnm), nullptr);

    return 0;
}
