[alexxy/gromacs.git] / src / gromacs / mdlib / nsgrid.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) 2013,2014,2015,2017,2018,2019, 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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 */
/* This file is completely threadsafe - keep it that way! */
#include "gmxpre.h"

#include "nsgrid.h"

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

#include <algorithm>

#include "gromacs/domdec/dlb.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"

/***********************************
 *         Grid Routines
 ***********************************/

static const char* range_warn =
        "Explanation: During neighborsearching, we assign each particle to a grid\n"
        "based on its coordinates. If your system contains collisions or parameter\n"
        "errors that give particles very high velocities you might end up with some\n"
        "coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot\n"
        "put these on a grid, so this is usually where we detect those errors.\n"
        "Make sure your system is properly energy-minimized and that the potential\n"
        "energy seems reasonable before trying again.";

static void calc_x_av_stddev(int n, rvec* x, rvec av, rvec stddev)
{
    dvec s1, s2;
    int  i, d;

    clear_dvec(s1);
    clear_dvec(s2);

    for (i = 0; i < n; i++)
    {
        for (d = 0; d < DIM; d++)
        {
            s1[d] += x[i][d];
            s2[d] += x[i][d] * x[i][d];
        }
    }

    dsvmul(1.0 / n, s1, s1);
    dsvmul(1.0 / n, s2, s2);

    for (d = 0; d < DIM; d++)
    {
        av[d]     = s1[d];
        stddev[d] = std::sqrt(s2[d] - s1[d] * s1[d]);
    }
}

static void get_nsgrid_boundaries_vac(real av, real stddev, real* bound0, real* bound1, real* bdens0, real* bdens1)
{
    /* Set the grid to 2 times the standard deviation of
     * the charge group centers in both directions.
     * For a uniform bounded distribution the width is sqrt(3)*stddev,
     * so all charge groups fall within the width.
     * For a sphere stddev is r/sqrt(5): 99.2% falls within the width.
     * For a Gaussian distribution 98% fall within the width.
     */
    *bound0 = av - NSGRID_STDDEV_FAC * stddev;
    *bound1 = av + NSGRID_STDDEV_FAC * stddev;

    *bdens0 = av - GRID_STDDEV_FAC * stddev;
    *bdens1 = av + GRID_STDDEV_FAC * stddev;
}

static void dd_box_bounds_to_ns_bounds(real box0, real box_size, real* gr0, real* gr1)
{
    real av, stddev;

    /* Redetermine av and stddev from the DD box boundaries */
    av     = box0 + 0.5 * box_size;
    stddev = 0.5 * box_size / GRID_STDDEV_FAC;

    *gr0 = av - NSGRID_STDDEV_FAC * stddev;
    *gr1 = av + NSGRID_STDDEV_FAC * stddev;
}

void get_nsgrid_boundaries(int           nboundeddim,
                           matrix        box,
                           gmx_domdec_t* dd,
                           gmx_ddbox_t*  ddbox,
                           rvec*         gr0,
                           rvec*         gr1,
                           int           ncg,
                           rvec*         cgcm,
                           rvec          grid_x0,
                           rvec          grid_x1,
                           real*         grid_density)
{
    rvec av, stddev;
    real vol, bdens0, bdens1;
    int  d;

    if (nboundeddim < DIM)
    {
        calc_x_av_stddev(ncg, cgcm, av, stddev);
    }

    vol = 1;
    for (d = 0; d < DIM; d++)
    {
        if (d < nboundeddim)
        {
            grid_x0[d] = (gr0 != nullptr ? (*gr0)[d] : 0);
            grid_x1[d] = (gr1 != nullptr ? (*gr1)[d] : box[d][d]);
            vol *= (grid_x1[d] - grid_x0[d]);
        }
        else
        {
            if (ddbox == nullptr)
            {
                get_nsgrid_boundaries_vac(av[d], stddev[d], &grid_x0[d], &grid_x1[d], &bdens0, &bdens1);
            }
            else
            {
                /* Temporary fix which uses global ddbox boundaries
                 * for unbounded dimensions.
                 * Should be replaced by local boundaries, which makes
                 * the ns grid smaller and does not require global comm.
                 */
                dd_box_bounds_to_ns_bounds(ddbox->box0[d], ddbox->box_size[d], &grid_x0[d], &grid_x1[d]);
                bdens0 = grid_x0[d];
                bdens1 = grid_x1[d];
            }
            /* Check for a DD cell not at a lower edge */
            if (dd != nullptr && gr0 != nullptr && dd->ci[d] > 0)
            {
                grid_x0[d] = (*gr0)[d];
                bdens0     = (*gr0)[d];
            }
            /* Check for a DD cell not at a higher edge */
            if (dd != nullptr && gr1 != nullptr && dd->ci[d] < dd->nc[d] - 1)
            {
                grid_x1[d] = (*gr1)[d];
                bdens1     = (*gr1)[d];
            }
            vol *= (bdens1 - bdens0);
        }

        if (debug)
        {
            fprintf(debug, "Set grid boundaries dim %d: %f %f\n", d, grid_x0[d], grid_x1[d]);
        }
    }

    *grid_density = ncg / vol;
}

static void set_grid_sizes(matrix              box,
                           rvec                izones_x0,
                           rvec                izones_x1,
                           real                rlist,
                           const gmx_domdec_t* dd,
                           const gmx_ddbox_t*  ddbox,
                           t_grid*             grid,
                           real                grid_density)
{
    int      i, j;
    gmx_bool bDD, bDDRect;
    rvec     izones_size;
    real     inv_r_ideal, size, add_tric, radd;

    for (i = 0; (i < DIM); i++)
    {
        if (debug)
        {
            fprintf(debug, "set_grid_sizes, i-zone bounds for dim %d: %6.3f %6.3f\n", i,
                    izones_x0[i], izones_x1[i]);
        }
        izones_size[i] = izones_x1[i] - izones_x0[i];
    }

    /* Use the ideal number of cg's per cell to set the ideal cell size */
    inv_r_ideal = std::cbrt(grid_density / grid->ncg_ideal);
    if (rlist > 0 && inv_r_ideal * rlist < 1)
    {
        inv_r_ideal = 1 / rlist;
    }
    if (debug)
    {
        fprintf(debug, "CG density %f ideal ns cell size %f\n", grid_density, 1 / inv_r_ideal);
    }

    clear_rvec(grid->cell_offset);
    for (i = 0; (i < DIM); i++)
    {
        /* Initial settings, for DD might change below */
        grid->cell_offset[i] = izones_x0[i];
        size                 = izones_size[i];

        bDD = (dd != nullptr) && (dd->nc[i] > 1);
        if (!bDD)
        {
            bDDRect = FALSE;
        }
        else
        {
            /* With DD grid cell jumps only the first decomposition
             * direction has uniform DD cell boundaries.
             */
            bDDRect = !((ddbox->tric_dir[i] != 0) || (dd_dlb_is_on(dd) && i != dd->dim[0]));

            radd = rlist;
            if (i >= ddbox->npbcdim
                && (rlist == 0 || izones_x1[i] + radd > ddbox->box0[i] + ddbox->box_size[i]))
            {
                radd = ddbox->box0[i] + ddbox->box_size[i] - izones_x1[i];
                if (radd < 0)
                {
                    radd = 0;
                }
            }

            /* With DD we only need a grid of one DD cell size + rlist */
            if (bDDRect)
            {
                size += radd;
            }
            else
            {
                size += radd / ddbox->skew_fac[i];
            }

            /* Check if the cell boundary in this direction is
             * perpendicular to the Cartesian axis.
             * Since grid->npbcdim isan integer that in principle can take
             * any value, we help the compiler avoid warnings and potentially
             * optimize by ensuring that j < DIM here.
             */
            for (j = i + 1; j < grid->npbcdim && j < DIM; j++)
            {
                if (box[j][i] != 0)
                {
                    /* Correct the offset for the home cell location */
                    grid->cell_offset[i] += izones_x0[j] * box[j][i] / box[j][j];

                    /* Correct the offset and size for the off-diagonal
                     * displacement of opposing DD cell corners.
                     */
                    /* Without rouding we would need to add:
                     * box[j][i]*rlist/(dd->skew_fac[i]*box[j][j])
                     */
                    /* Determine the shift for the corners of the triclinic box */
                    add_tric = izones_size[j] * box[j][i] / box[j][j];
                    if (dd->ndim == 1 && j == ZZ)
                    {
                        /* With 1D domain decomposition the cg's are not in
                         * the triclinic box, but trilinic x-y and rectangular y-z.
                         * Therefore we need to add the shift from the trilinic
                         * corner to the corner at y=0.
                         */
                        add_tric += -box[YY][XX] * box[ZZ][YY] / box[YY][YY];
                    }
                    if (box[j][i] < 0)
                    {
                        grid->cell_offset[i] += add_tric;
                        size -= add_tric;
                    }
                    else
                    {
                        size += add_tric;
                    }
                }
            }
        }
        if (!bDDRect)
        {
            /* No DD or the box is triclinic is this direction:
             * we will use the normal grid ns that checks all cells
             * that are within cut-off distance of the i-particle.
             */
            grid->n[i] = gmx::roundToInt(size * inv_r_ideal);
            if (grid->n[i] < 2)
            {
                grid->n[i] = 2;
            }
            grid->cell_size[i] = size / grid->n[i];
            grid->ncpddc[i]    = 0;
        }
        else
        {
            /* We use grid->ncpddc[i] such that all particles
             * in one ns cell belong to a single DD cell only.
             * We can then beforehand exclude certain ns grid cells
             * for non-home i-particles.
             */
            grid->ncpddc[i] = gmx::roundToInt(izones_size[i] * inv_r_ideal);
            if (grid->ncpddc[i] < 2)
            {
                grid->ncpddc[i] = 2;
            }
            grid->cell_size[i] = izones_size[i] / grid->ncpddc[i];
            grid->n[i]         = grid->ncpddc[i] + static_cast<int>(radd / grid->cell_size[i]) + 1;
        }
        if (debug)
        {
            fprintf(debug, "grid dim %d size %d x %f: %f - %f\n", i, grid->n[i], grid->cell_size[i],
                    grid->cell_offset[i], grid->cell_offset[i] + grid->n[i] * grid->cell_size[i]);
        }
    }

    if (debug)
    {
        fprintf(debug, "CG ncg ideal %d, actual density %.1f\n", grid->ncg_ideal,
                grid_density * grid->cell_size[XX] * grid->cell_size[YY] * grid->cell_size[ZZ]);
    }
}

t_grid* init_grid(FILE* fplog, t_forcerec* fr)
{
    char*   ptr;
    t_grid* grid;

    snew(grid, 1);

    grid->npbcdim = ePBC2npbcdim(fr->ePBC);

    if (fr->ePBC == epbcXY && fr->nwall == 2)
    {
        grid->nboundeddim = 3;
    }
    else
    {
        grid->nboundeddim = grid->npbcdim;
    }

    if (debug)
    {
        fprintf(debug, "The coordinates are bounded in %d dimensions\n", grid->nboundeddim);
    }

    /* The ideal number of cg's per ns grid cell seems to be 10 */
    grid->ncg_ideal = 10;
    ptr             = getenv("GMX_NSCELL_NCG");
    if (ptr)
    {
        sscanf(ptr, "%d", &grid->ncg_ideal);
        if (fplog)
        {
            fprintf(fplog, "Set ncg_ideal to %d\n", grid->ncg_ideal);
        }
        if (grid->ncg_ideal <= 0)
        {
            gmx_fatal(FARGS, "The number of cg's per cell should be > 0");
        }
    }
    if (debug)
    {
        fprintf(debug, "Set ncg_ideal to %d\n", grid->ncg_ideal);
    }

    return grid;
}

void done_grid(t_grid* grid)
{
    if (grid == nullptr)
    {
        return;
    }
    grid->nr = 0;
    clear_ivec(grid->n);
    grid->ncells = 0;
    sfree(grid->cell_index);
    sfree(grid->a);
    sfree(grid->index);
    sfree(grid->nra);
    grid->cells_nalloc = 0;
    sfree(grid->dcx2);
    sfree(grid->dcy2);
    sfree(grid->dcz2);
    grid->dc_nalloc = 0;

    if (debug)
    {
        fprintf(debug, "Successfully freed memory for grid pointers.");
    }
    sfree(grid);
}

int xyz2ci_(int nry, int nrz, int x, int y, int z)
/* Return the cell index */
{
    return (nry * nrz * x + nrz * y + z);
}

void ci2xyz(t_grid* grid, int i, int* x, int* y, int* z)
/* Return x,y and z from the cell index */
{
    int ci;

    range_check_mesg(i, 0, grid->nr, range_warn);

    ci = grid->cell_index[i];
    *x = ci / (grid->n[YY] * grid->n[ZZ]);
    ci -= (*x) * grid->n[YY] * grid->n[ZZ];
    *y = ci / grid->n[ZZ];
    ci -= (*y) * grid->n[ZZ];
    *z = ci;
}

static int ci_not_used(const ivec n)
{
    /* Return an improbable value */
    return xyz2ci(n[YY], n[ZZ], 3 * n[XX], 3 * n[YY], 3 * n[ZZ]);
}

static void set_grid_ncg(t_grid* grid, int ncg)
{
    int nr_old, i;

    grid->nr = ncg;
    if (grid->nr + 1 > grid->nr_alloc)
    {
        nr_old         = grid->nr_alloc;
        grid->nr_alloc = over_alloc_dd(grid->nr) + 1;
        srenew(grid->cell_index, grid->nr_alloc);
        for (i = nr_old; i < grid->nr_alloc; i++)
        {
            grid->cell_index[i] = 0;
        }
        srenew(grid->a, grid->nr_alloc);
    }
}

void grid_first(FILE*              fplog,
                t_grid*            grid,
                gmx_domdec_t*      dd,
                const gmx_ddbox_t* ddbox,
                matrix             box,
                rvec               izones_x0,
                rvec               izones_x1,
                real               rlist,
                real               grid_density)
{
    int i, m;

    set_grid_sizes(box, izones_x0, izones_x1, rlist, dd, ddbox, grid, grid_density);

    grid->ncells = grid->n[XX] * grid->n[YY] * grid->n[ZZ];

    if (grid->ncells + 1 > grid->cells_nalloc)
    {
        /* Allocate double the size so we have some headroom */
        grid->cells_nalloc = 2 * grid->ncells;
        srenew(grid->nra, grid->cells_nalloc + 1);
        srenew(grid->index, grid->cells_nalloc + 1);

        if (fplog)
        {
            fprintf(fplog, "Grid: %d x %d x %d cells\n", grid->n[XX], grid->n[YY], grid->n[ZZ]);
        }
    }

    m = std::max(grid->n[XX], std::max(grid->n[YY], grid->n[ZZ]));
    if (m > grid->dc_nalloc)
    {
        /* Allocate with double the initial size for box scaling */
        grid->dc_nalloc = 2 * m;
        srenew(grid->dcx2, grid->dc_nalloc);
        srenew(grid->dcy2, grid->dc_nalloc);
        srenew(grid->dcz2, grid->dc_nalloc);
    }

    grid->nr = 0;
    for (i = 0; (i < grid->ncells); i++)
    {
        grid->nra[i] = 0;
    }
}

static void calc_bor(int cg0, int cg1, int ncg, int CG0[2], int CG1[2])
{
    if (cg1 > ncg)
    {
        CG0[0] = cg0;
        CG1[0] = ncg;
        CG0[1] = 0;
        CG1[1] = cg1 - ncg;
    }
    else
    {
        CG0[0] = cg0;
        CG1[0] = cg1;
        CG0[1] = 0;
        CG1[1] = 0;
    }
    if (debug)
    {
        int m;

        fprintf(debug, "calc_bor: cg0=%d, cg1=%d, ncg=%d\n", cg0, cg1, ncg);
        for (m = 0; (m < 2); m++)
        {
            fprintf(debug, "CG0[%d]=%d, CG1[%d]=%d\n", m, CG0[m], m, CG1[m]);
        }
    }
}

void calc_elemnr(t_grid* grid, int cg0, int cg1, int ncg)
{
    int  CG0[2], CG1[2];
    int* cell_index = grid->cell_index;
    int* nra        = grid->nra;
    int  i, m, ncells;
    int  ci, not_used;

    ncells = grid->ncells;
    if (ncells <= 0)
    {
        gmx_fatal(FARGS, "Number of grid cells is zero. Probably the system and box collapsed.\n");
    }

    not_used = ci_not_used(grid->n);

    calc_bor(cg0, cg1, ncg, CG0, CG1);
    for (m = 0; (m < 2); m++)
    {
        for (i = CG0[m]; (i < CG1[m]); i++)
        {
            ci = cell_index[i];
            if (ci != not_used)
            {
                range_check_mesg(ci, 0, ncells, range_warn);
                nra[ci]++;
            }
        }
    }
}

void calc_ptrs(t_grid* grid)
{
    int* index = grid->index;
    int* nra   = grid->nra;
    int  ix, iy, iz, ci, nr;
    int  nnra, ncells;

    ncells = grid->ncells;
    if (ncells <= 0)
    {
        gmx_fatal(FARGS, "Number of grid cells is zero. Probably the system and box collapsed.\n");
    }

    ci = nr = 0;
    for (ix = 0; (ix < grid->n[XX]); ix++)
    {
        for (iy = 0; (iy < grid->n[YY]); iy++)
        {
            for (iz = 0; (iz < grid->n[ZZ]); iz++, ci++)
            {
                range_check_mesg(ci, 0, ncells, range_warn);
                index[ci] = nr;
                nnra      = nra[ci];
                nr += nnra;
                nra[ci] = 0;
            }
        }
    }
}

void grid_last(t_grid* grid, int cg0, int cg1, int ncg)
{
    int  CG0[2], CG1[2];
    int  i, m;
    int  ci, not_used, ind, ncells;
    int* cell_index = grid->cell_index;
    int* nra        = grid->nra;
    int* index      = grid->index;
    int* a          = grid->a;

    ncells = grid->ncells;
    if (ncells <= 0)
    {
        gmx_fatal(FARGS, "Number of grid cells is zero. Probably the system and box collapsed.\n");
    }

    not_used = ci_not_used(grid->n);

    calc_bor(cg0, cg1, ncg, CG0, CG1);
    for (m = 0; (m < 2); m++)
    {
        for (i = CG0[m]; (i < CG1[m]); i++)
        {
            ci = cell_index[i];
            if (ci != not_used)
            {
                range_check_mesg(ci, 0, ncells, range_warn);
                ind = index[ci] + nra[ci]++;
                range_check_mesg(ind, 0, grid->nr, range_warn);
                a[ind] = i;
            }
        }
    }
}

void fill_grid(gmx_domdec_zones_t* dd_zones, t_grid* grid, int ncg_tot, int cg0, int cg1, rvec cg_cm[])
{
    int*     cell_index;
    int      nry, nrz;
    rvec     n_box, offset;
    int      zone, ccg0, ccg1, cg, d, not_used;
    ivec     shift0, useall, b0, b1, ind;
    gmx_bool bUse;

    if (cg0 == -1)
    {
        /* We have already filled the grid up to grid->ncg,
         * continue from there.
         */
        cg0 = grid->nr;
    }

    set_grid_ncg(grid, ncg_tot);

    cell_index = grid->cell_index;

    /* Initiate cell borders */
    nry = grid->n[YY];
    nrz = grid->n[ZZ];
    for (d = 0; d < DIM; d++)
    {
        if (grid->cell_size[d] > 0)
        {
            n_box[d] = 1 / grid->cell_size[d];
        }
        else
        {
            n_box[d] = 0;
        }
    }
    copy_rvec(grid->cell_offset, offset);

    if (debug)
    {
        fprintf(debug, "Filling grid from %d to %d\n", cg0, cg1);
    }

    if (dd_zones == nullptr)
    {
        for (cg = cg0; cg < cg1; cg++)
        {
            for (d = 0; d < DIM; d++)
            {
                ind[d] = static_cast<int>((cg_cm[cg][d] - offset[d]) * n_box[d]);
                /* With pbc we should be done here.
                 * Without pbc cg's outside the grid
                 * should be assigned to the closest grid cell.
                 */
                if (ind[d] < 0)
                {
                    ind[d] = 0;
                }
                else if (ind[d] >= grid->n[d])
                {
                    ind[d] = grid->n[d] - 1;
                }
            }
            cell_index[cg] = xyz2ci(nry, nrz, ind[XX], ind[YY], ind[ZZ]);
        }
    }
    else
    {
        for (zone = 0; zone < dd_zones->n; zone++)
        {
            ccg0 = dd_zones->cg_range[zone];
            ccg1 = dd_zones->cg_range[zone + 1];
            if (ccg1 <= cg0 || ccg0 >= cg1)
            {
                continue;
            }

            /* Determine the ns grid cell limits for this DD zone */
            for (d = 0; d < DIM; d++)
            {
                shift0[d] = dd_zones->shift[zone][d];
                useall[d] = static_cast<int>(shift0[d] == 0 || d >= grid->npbcdim);
                /* Check if we need to do normal or optimized grid assignments.
                 * Normal is required for dims without DD or triclinic dims.
                 * DD edge cell on dims without pbc will be automatically
                 * be correct, since the shift=0 zones with have b0 and b1
                 * set to the grid boundaries and there are no shift=1 zones.
                 */
                if (grid->ncpddc[d] == 0)
                {
                    b0[d] = 0;
                    b1[d] = grid->n[d];
                }
                else
                {
                    if (shift0[d] == 0)
                    {
                        b0[d] = 0;
                        b1[d] = grid->ncpddc[d];
                    }
                    else
                    {
                        /* shift = 1 */
                        b0[d] = grid->ncpddc[d];
                        b1[d] = grid->n[d];
                    }
                }
            }

            not_used = ci_not_used(grid->n);

            /* Put all the charge groups of this DD zone on the grid */
            for (cg = ccg0; cg < ccg1; cg++)
            {
                if (cell_index[cg] == -1)
                {
                    /* This cg has moved to another node */
                    cell_index[cg] = NSGRID_SIGNAL_MOVED_FAC * grid->ncells;
                    continue;
                }

                bUse = TRUE;
                for (d = 0; d < DIM; d++)
                {
                    ind[d] = static_cast<int>((cg_cm[cg][d] - offset[d]) * n_box[d]);
                    /* Here we have to correct for rounding problems,
                     * as this cg_cm to cell index operation is not necessarily
                     * binary identical to the operation for the DD zone assignment
                     * and therefore a cg could end up in an unused grid cell.
                     * For dimensions without pbc we need to check
                     * for cells on the edge if charge groups are beyond
                     * the grid and if so, store them in the closest cell.
                     */
                    if (ind[d] < b0[d])
                    {
                        ind[d] = b0[d];
                    }
                    else if (ind[d] >= b1[d])
                    {
                        if (useall[d])
                        {
                            ind[d] = b1[d] - 1;
                        }
                        else
                        {
                            /* Charge groups in this DD zone further away than the cut-off
                             * in direction do not participate in non-bonded interactions.
                             */
                            bUse = FALSE;
                        }
                    }
                }
                if (cg > grid->nr_alloc)
                {
                    fprintf(stderr, "WARNING: nra_alloc %d cg0 %d cg1 %d cg %d\n", grid->nr_alloc,
                            cg0, cg1, cg);
                }
                if (bUse)
                {
                    cell_index[cg] = xyz2ci(nry, nrz, ind[XX], ind[YY], ind[ZZ]);
                }
                else
                {
                    cell_index[cg] = not_used;
                }
            }
        }
    }
}

void check_grid(t_grid* grid)
{
    int ix, iy, iz, ci, cci, nra;

    if (grid->ncells <= 0)
    {
        gmx_fatal(FARGS, "Number of grid cells is zero. Probably the system and box collapsed.\n");
    }

    ci  = 0;
    cci = 0;
    for (ix = 0; (ix < grid->n[XX]); ix++)
    {
        for (iy = 0; (iy < grid->n[YY]); iy++)
        {
            for (iz = 0; (iz < grid->n[ZZ]); iz++, ci++)
            {
                if (ci > 0)
                {
                    nra = grid->index[ci] - grid->index[cci];
                    if (nra != grid->nra[cci])
                    {
                        gmx_fatal(FARGS, "nra=%d, grid->nra=%d, cci=%d", nra, grid->nra[cci], cci);
                    }
                }
                cci = xyz2ci(grid->n[YY], grid->n[ZZ], ix, iy, iz);
                range_check_mesg(cci, 0, grid->ncells, range_warn);

                if (cci != ci)
                {
                    gmx_fatal(FARGS, "ci = %d, cci = %d", ci, cci);
                }
            }
        }
    }
}

void print_grid(FILE* log, t_grid* grid)
{
    int i, nra, index;
    int ix, iy, iz, ci;

    fprintf(log, "nr:        %d\n", grid->nr);
    fprintf(log, "nrx:       %d\n", grid->n[XX]);
    fprintf(log, "nry:       %d\n", grid->n[YY]);
    fprintf(log, "nrz:       %d\n", grid->n[ZZ]);
    fprintf(log, "ncg_ideal: %d\n", grid->ncg_ideal);
    fprintf(log, "    i  cell_index\n");
    for (i = 0; (i < grid->nr); i++)
    {
        fprintf(log, "%5d  %5d\n", i, grid->cell_index[i]);
    }
    fprintf(log, "cells\n");
    fprintf(log, " ix iy iz   nr  index  cgs...\n");
    ci = 0;
    for (ix = 0; (ix < grid->n[XX]); ix++)
    {
        for (iy = 0; (iy < grid->n[YY]); iy++)
        {
            for (iz = 0; (iz < grid->n[ZZ]); iz++, ci++)
            {
                index = grid->index[ci];
                nra   = grid->nra[ci];
                fprintf(log, "%3d%3d%3d%5d%5d", ix, iy, iz, nra, index);
                for (i = 0; (i < nra); i++)
                {
                    fprintf(log, "%5d", grid->a[index + i]);
                }
                fprintf(log, "\n");
            }
        }
    }
    fflush(log);
}