N_les_assemble.c

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/*****************************************************************************
*
* MODULE:       Grass PDE Numerical Library
* AUTHOR(S):    Soeren Gebbert, Berlin (GER) Dec 2006
*               soerengebbert <at> gmx <dot> de
*               
* PURPOSE:      functions to assemble a linear equation system
*               part of the gpde library
*               
* COPYRIGHT:    (C) 2000 by the GRASS Development Team
*
*               This program is free software under the GNU General Public
*               License (>=v2). Read the file COPYING that comes with GRASS
*               for details.
*
*****************************************************************************/


#include <math.h>
#include "grass/N_pde.h"

/* local protos */
static int make_les_entry_2d(int i, int j, int offset_i, int offset_j,
                             int count, int pos, N_les * les,
                             G_math_spvector * spvect,
                             N_array_2d * cell_count, N_array_2d * status,
                             N_array_2d * start_val, double entry,
                             int cell_type);

static int make_les_entry_3d(int i, int j, int k, int offset_i, int offset_j,
                             int offset_k, int count, int pos, N_les * les,
                             G_math_spvector * spvect,
                             N_array_3d * cell_count, N_array_3d * status,
                             N_array_3d * start_val, double entry,
                             int cell_type);

/* *************************************************************** * 
 * ********************** N_alloc_5star ************************** * 
 * *************************************************************** */
N_data_star *N_alloc_5star(void)
{
    N_data_star *star = (N_data_star *) G_calloc(1, sizeof(N_data_star));

    star->type = N_5_POINT_STAR;
    star->count = 5;
    return star;
}

/* *************************************************************** * 
 * ********************* N_alloc_7star *************************** * 
 * *************************************************************** */
N_data_star *N_alloc_7star(void)
{
    N_data_star *star = (N_data_star *) G_calloc(1, sizeof(N_data_star));

    star->type = N_7_POINT_STAR;
    star->count = 7;
    return star;
}

/* *************************************************************** * 
 * ********************* N_alloc_9star *************************** * 
 * *************************************************************** */
N_data_star *N_alloc_9star(void)
{
    N_data_star *star = (N_data_star *) G_calloc(1, sizeof(N_data_star));

    star->type = N_9_POINT_STAR;
    star->count = 9;
    return star;
}

/* *************************************************************** * 
 * ********************* N_alloc_27star ************************** * 
 * *************************************************************** */
N_data_star *N_alloc_27star(void)
{
    N_data_star *star = (N_data_star *) G_calloc(1, sizeof(N_data_star));

    star->type = N_27_POINT_STAR;
    star->count = 27;
    return star;
}

/* *************************************************************** * 
 * ********************** N_create_5star ************************* * 
 * *************************************************************** */
N_data_star *N_create_5star(double C, double W, double E, double N,
                            double S, double V)
{
    N_data_star *star = N_alloc_5star();

    star->C = C;
    star->W = W;
    star->E = E;
    star->N = N;
    star->S = S;

    star->V = V;

    G_debug(5, "N_create_5star:  w %g e %g n %g s %g c %g v %g\n", star->W,
            star->E, star->N, star->S, star->C, star->V);

    return star;
}

/* *************************************************************** * 
 * ************************* N_create_7star ********************** * 
 * *************************************************************** */
N_data_star *N_create_7star(double C, double W, double E, double N,
                            double S, double T, double B, double V)
{
    N_data_star *star = N_alloc_7star();

    star->C = C;
    star->W = W;
    star->E = E;
    star->N = N;
    star->S = S;

    star->T = T;
    star->B = B;

    star->V = V;

    G_debug(5, "N_create_7star:  w %g e %g n %g s %g t %g b %g c %g v %g\n",
            star->W, star->E, star->N, star->S, star->T, star->B, star->C,
            star->V);

    return star;
}

/* *************************************************************** * 
 * ************************ N_create_9star *********************** * 
 * *************************************************************** */
N_data_star *N_create_9star(double C, double W, double E, double N,
                            double S, double NW, double SW, double NE,
                            double SE, double V)
{
    N_data_star *star = N_alloc_9star();

    star->C = C;
    star->W = W;
    star->E = E;
    star->N = N;
    star->S = S;

    star->NW = NW;
    star->SW = SW;
    star->NE = NE;
    star->SE = SE;

    star->V = V;

    G_debug(5,
            "N_create_9star:  w %g e %g n %g s %g nw %g sw %g ne %g se %g c %g v %g\n",
            star->W, star->E, star->N, star->S, star->NW, star->SW, star->NE,
            star->SE, star->C, star->V);

    return star;
}

/* *************************************************************** * 
 * ************************ N_create_27star *********************** * 
 * *************************************************************** */
N_data_star *N_create_27star(double C, double W, double E, double N, double S,
                             double NW, double SW, double NE, double SE,
                             double T, double W_T, double E_T, double N_T,
                             double S_T, double NW_T, double SW_T,
                             double NE_T, double SE_T, double B, double W_B,
                             double E_B, double N_B, double S_B, double NW_B,
                             double SW_B, double NE_B, double SE_B, double V)
{
    N_data_star *star = N_alloc_27star();

    star->C = C;
    star->W = W;
    star->E = E;
    star->N = N;
    star->S = S;

    star->NW = NW;
    star->SW = SW;
    star->NE = NE;
    star->SE = SE;

    star->T = T;
    star->W_T = W_T;
    star->E_T = E_T;
    star->N_T = N_T;
    star->S_T = S_T;

    star->NW_T = NW_T;
    star->SW_T = SW_T;
    star->NE_T = NE_T;
    star->SE_T = SE_T;

    star->B = B;
    star->W_B = W_B;
    star->E_B = E_B;
    star->N_B = N_B;
    star->S_B = S_B;

    star->NW_B = NW_B;
    star->SW_B = SW_B;
    star->NE_B = NE_B;
    star->SE_B = SE_B;

    star->V = V;

    G_debug(5,
            "N_create_27star:  w %g e %g n %g s %g nw %g sw %g ne %g se %g c %g v %g\n",
            star->W, star->E, star->N, star->S, star->NW, star->SW, star->NE,
            star->SE, star->C, star->V);

    G_debug(5,
            "N_create_27star:  w_t %g e_t %g n_t %g s_t %g nw_t %g sw_t %g ne_t %g se_t %g t %g \n",
            star->W_T, star->E_T, star->N_T, star->S_T, star->NW_T,
            star->SW_T, star->NE_T, star->SE_T, star->T);

    G_debug(5,
            "N_create_27star:  w_b %g e_b %g n_b %g s_b %g nw_b %g sw_b %g ne_b %g se_B %g b %g\n",
            star->W_B, star->E_B, star->N_B, star->S_B, star->NW_B,
            star->SW_B, star->NE_B, star->SE_B, star->B);



    return star;
}


/* *************************************************************** * 
 * ****************** N_set_les_callback_3d_func ***************** * 
 * *************************************************************** */
void
N_set_les_callback_3d_func(N_les_callback_3d * data,
                           N_data_star * (*callback_func_3d) ())
{
    data->callback = callback_func_3d;
}

/* *************************************************************** * 
 * *************** N_set_les_callback_2d_func ******************** * 
 * *************************************************************** */
void
N_set_les_callback_2d_func(N_les_callback_2d * data,
                           N_data_star * (*callback_func_2d) ())
{
    data->callback = callback_func_2d;
}

/* *************************************************************** * 
 * ************** N_alloc_les_callback_3d ************************ * 
 * *************************************************************** */
N_les_callback_3d *N_alloc_les_callback_3d(void)
{
    N_les_callback_3d *call;

    call = (N_les_callback_3d *) G_calloc(1, sizeof(N_les_callback_3d *));
    call->callback = N_callback_template_3d;

    return call;
}

/* *************************************************************** * 
 * *************** N_alloc_les_callback_2d *********************** * 
 * *************************************************************** */
N_les_callback_2d *N_alloc_les_callback_2d(void)
{
    N_les_callback_2d *call;

    call = (N_les_callback_2d *) G_calloc(1, sizeof(N_les_callback_2d *));
    call->callback = N_callback_template_2d;

    return call;
}

/* *************************************************************** * 
 * ******************** N_callback_template_3d ******************* * 
 * *************************************************************** */
N_data_star *N_callback_template_3d(void *data, N_geom_data * geom, int col,
                                    int row, int depth)
{
    N_data_star *star = N_alloc_7star();

    star->E = 1 / geom->dx;
    star->W = 1 / geom->dx;
    star->N = 1 / geom->dy;
    star->S = 1 / geom->dy;
    star->T = 1 / geom->dz;
    star->B = 1 / geom->dz;
    star->C = -1 * (2 / geom->dx + 2 / geom->dy + 2 / geom->dz);
    star->V = -1;

    G_debug(5,
            "N_callback_template_3d:  w %g e %g n %g s %g t %g b %g c %g v %g\n",
            star->W, star->E, star->N, star->S, star->T, star->B, star->C,
            star->V);


    return star;
}

/* *************************************************************** * 
 * ********************* N_callback_template_2d ****************** * 
 * *************************************************************** */
N_data_star *N_callback_template_2d(void *data, N_geom_data * geom, int col,
                                    int row)
{
    N_data_star *star = N_alloc_9star();

    star->E = 1 / geom->dx;
    star->NE = 1 / sqrt(geom->dx * geom->dx + geom->dy * geom->dy);
    star->SE = 1 / sqrt(geom->dx * geom->dx + geom->dy * geom->dy);
    star->W = 1 / geom->dx;
    star->NW = 1 / sqrt(geom->dx * geom->dx + geom->dy * geom->dy);
    star->SW = 1 / sqrt(geom->dx * geom->dx + geom->dy * geom->dy);
    star->N = 1 / geom->dy;
    star->S = 1 / geom->dy;
    star->C =
        -1 * (star->E + star->NE + star->SE + star->W + star->NW + star->SW +
              star->N + star->S);
    star->V = 0;

    return star;
}

/* *************************************************************** * 
 * ******************** N_assemble_les_2d ************************ * 
 * *************************************************************** */
N_les *N_assemble_les_2d(int les_type, N_geom_data * geom,
                         N_array_2d * status, N_array_2d * start_val,
                         void *data, N_les_callback_2d * call)
{
    return N_assemble_les_2d_param(les_type, geom, status, start_val, data,
                                   call, N_CELL_ACTIVE);
}

N_les *N_assemble_les_2d_active(int les_type, N_geom_data * geom,
                                N_array_2d * status, N_array_2d * start_val,
                                void *data, N_les_callback_2d * call)
{
    return N_assemble_les_2d_param(les_type, geom, status, start_val, data,
                                   call, N_CELL_ACTIVE);
}

N_les *N_assemble_les_2d_dirichlet(int les_type, N_geom_data * geom,
                                   N_array_2d * status,
                                   N_array_2d * start_val, void *data,
                                   N_les_callback_2d * call)
{
    return N_assemble_les_2d_param(les_type, geom, status, start_val, data,
                                   call, N_CELL_DIRICHLET);
}

N_les *N_assemble_les_2d_param(int les_type, N_geom_data * geom,
                               N_array_2d * status, N_array_2d * start_val,
                               void *data, N_les_callback_2d * call,
                               int cell_type)
{
    int i, j, count = 0, pos = 0;

    int cell_type_count = 0;

    int **index_ij;

    N_array_2d *cell_count;

    N_les *les = NULL;

    G_debug(2,
            "N_assemble_les_2d: starting to assemble the linear equation system");

    /* At first count the number of valid cells and save the 
     * each number in a new 2d array. Those numbers are used 
     * to create the linear equation system.
     * */

    cell_count = N_alloc_array_2d(geom->cols, geom->rows, 1, CELL_TYPE);

    /* include dirichlet cells in the les */
    if (cell_type == N_CELL_DIRICHLET) {
        for (j = 0; j < geom->rows; j++) {
            for (i = 0; i < geom->cols; i++) {
                /*use all non-inactive cells for les creation */
                if (N_CELL_INACTIVE < N_get_array_2d_c_value(status, i, j) &&
                    N_get_array_2d_c_value(status, i, j) < N_MAX_CELL_STATE)
                    cell_type_count++;
            }
        }
    }
    /*use only active cell in the les */
    if (cell_type == N_CELL_ACTIVE) {
        for (j = 0; j < geom->rows; j++) {
            for (i = 0; i < geom->cols; i++) {
                /*count only active cells */
                if (N_CELL_ACTIVE == N_get_array_2d_d_value(status, i, j))
                    cell_type_count++;
            }
        }
    }

    G_debug(2, "N_assemble_les_2d: number of used cells %i\n",
            cell_type_count);

    if (cell_type_count == 0)
        G_fatal_error
            ("Not enough cells [%i] to create the linear equation system. Check the cell status. Only active cells (value = 1) are used to create the equation system.",
             cell_type_count);

    /* Then allocate the memory for the linear equation system (les). 
     * Only valid cells are used to create the les. */
    index_ij = (int **)G_calloc(cell_type_count, sizeof(int *));
    for (i = 0; i < cell_type_count; i++)
        index_ij[i] = (int *)G_calloc(2, sizeof(int));

    les = N_alloc_les_Ax_b(cell_type_count, les_type);

    count = 0;

    /*count the number of cells which should be used to create the linear equation system */
    /*save the i and j indices and create a ordered numbering */
    for (j = 0; j < geom->rows; j++) {
        for (i = 0; i < geom->cols; i++) {
            /*count every non-inactive cell */
            if (cell_type == N_CELL_DIRICHLET) {
                if (N_CELL_INACTIVE < N_get_array_2d_c_value(status, i, j) &&
                    N_get_array_2d_c_value(status, i, j) < N_MAX_CELL_STATE) {
                    N_put_array_2d_c_value(cell_count, i, j, count);
                    index_ij[count][0] = i;
                    index_ij[count][1] = j;
                    count++;
                    G_debug(5,
                            "N_assemble_les_2d: non-inactive cells count %i at pos x[%i] y[%i]\n",
                            count, i, j);
                }
                /*count every active cell */
            }
            else if (N_CELL_ACTIVE == N_get_array_2d_c_value(status, i, j)) {
                N_put_array_2d_c_value(cell_count, i, j, count);
                index_ij[count][0] = i;
                index_ij[count][1] = j;
                count++;
                G_debug(5,
                        "N_assemble_les_2d: active cells count %i at pos x[%i] y[%i]\n",
                        count, i, j);
            }
        }
    }

    G_debug(2, "N_assemble_les_2d: starting the parallel assemble loop");

    /* Assemble the matrix in parallel */
#pragma omp parallel for private(i, j, pos, count) schedule(static)
    for (count = 0; count < cell_type_count; count++) {
        i = index_ij[count][0];
        j = index_ij[count][1];

        /*create the entries for the */
        N_data_star *items = call->callback(data, geom, i, j);

        /* we need a sparse vector pointer anytime */
        G_math_spvector *spvect = NULL;

        /*allocate a sprase vector */
        if (les_type == N_SPARSE_LES) {
            spvect = G_math_alloc_spvector(items->count);
        }
        /* initial conditions */
        les->x[count] = N_get_array_2d_d_value(start_val, i, j);

        /* the entry in the vector b */
        les->b[count] = items->V;

        /* pos describes the position in the sparse vector.
         * the first entry is always the diagonal entry of the matrix*/
        pos = 0;

        if (les_type == N_SPARSE_LES) {
            spvect->index[pos] = count;
            spvect->values[pos] = items->C;
        }
        else {
            les->A[count][count] = items->C;
        }
        /* western neighbour, entry is col - 1 */
        if (i > 0) {
            pos = make_les_entry_2d(i, j, -1, 0, count, pos, les, spvect,
                                    cell_count, status, start_val, items->W,
                                    cell_type);
        }
        /* eastern neighbour, entry col + 1 */
        if (i < geom->cols - 1) {
            pos = make_les_entry_2d(i, j, 1, 0, count, pos, les, spvect,
                                    cell_count, status, start_val, items->E,
                                    cell_type);
        }
        /* northern neighbour, entry row - 1 */
        if (j > 0) {
            pos =
                make_les_entry_2d(i, j, 0, -1, count, pos, les, spvect,
                                  cell_count, status, start_val, items->N,
                                  cell_type);
        }
        /* southern neighbour, entry row + 1 */
        if (j < geom->rows - 1) {
            pos = make_les_entry_2d(i, j, 0, 1, count, pos, les, spvect,
                                    cell_count, status, start_val, items->S,
                                    cell_type);
        }
        /*in case of a nine point star, we have additional entries */
        if (items->type == N_9_POINT_STAR) {
            /* north-western neighbour, entry is col - 1 row - 1 */
            if (i > 0 && j > 0) {
                pos = make_les_entry_2d(i, j, -1, -1, count, pos, les, spvect,
                                        cell_count, status, start_val,
                                        items->NW, cell_type);
            }
            /* north-eastern neighbour, entry col + 1 row - 1 */
            if (i < geom->cols - 1 && j > 0) {
                pos = make_les_entry_2d(i, j, 1, -1, count, pos, les, spvect,
                                        cell_count, status, start_val,
                                        items->NE, cell_type);
            }
            /* south-western neighbour, entry is col - 1 row + 1 */
            if (i > 0 && j < geom->rows - 1) {
                pos = make_les_entry_2d(i, j, -1, 1, count, pos, les, spvect,
                                        cell_count, status, start_val,
                                        items->SW, cell_type);
            }
            /* south-eastern neighbour, entry col + 1 row + 1 */
            if (i < geom->cols - 1 && j < geom->rows - 1) {
                pos = make_les_entry_2d(i, j, 1, 1, count, pos, les, spvect,
                                        cell_count, status, start_val,
                                        items->SE, cell_type);
            }
        }

        /*How many entries in the les */
        if (les->type == N_SPARSE_LES) {
            spvect->cols = pos + 1;
            G_math_add_spvector(les->Asp, spvect, count);
        }

        if (items)
            G_free(items);
    }

    /*release memory */
    N_free_array_2d(cell_count);

    for (i = 0; i < cell_type_count; i++)
        G_free(index_ij[i]);

    G_free(index_ij);

    return les;
}

int N_les_integrate_dirichlet_2d(N_les * les, N_geom_data * geom,
                                 N_array_2d * status, N_array_2d * start_val)
{
    int rows, cols;

    int count = 0;

    int i, j, x, y, stat;

    double *dvect1;

    double *dvect2;

    G_debug(2,
            "N_les_integrate_dirichlet_2d: integrating the dirichlet boundary condition");

    rows = geom->rows;
    cols = geom->cols;

    /*we nned to additional vectors */
    dvect1 = (double *)G_calloc(les->cols, sizeof(double));
    dvect2 = (double *)G_calloc(les->cols, sizeof(double));

    /*fill the first one with the x vector data of Dirichlet cells */
    count = 0;
    for (y = 0; y < rows; y++) {
        for (x = 0; x < cols; x++) {
            stat = N_get_array_2d_c_value(status, x, y);
            if (stat > N_CELL_ACTIVE && stat < N_MAX_CELL_STATE) {
                dvect1[count] = N_get_array_2d_d_value(start_val, x, y);
                count++;
            }
            else if (stat == N_CELL_ACTIVE) {
                dvect1[count] = 0.0;
                count++;
            }
        }
    }

#pragma omp parallel default(shared)
    {
        /*performe the matrix vector product and */
        if (les->type == N_SPARSE_LES)
            G_math_Ax_sparse(les->Asp, dvect1, dvect2, les->rows);
        else
            G_math_d_Ax(les->A, dvect1, dvect2, les->rows, les->cols);
#pragma omp for schedule (static) private(i)
        for (i = 0; i < les->cols; i++)
            les->b[i] = les->b[i] - dvect2[i];
    }

    /*now set the Dirichlet cell rows and cols to zero and the 
     * diagonal entry to 1*/
    count = 0;
    for (y = 0; y < rows; y++) {
        for (x = 0; x < cols; x++) {
            stat = N_get_array_2d_c_value(status, x, y);
            if (stat > N_CELL_ACTIVE && stat < N_MAX_CELL_STATE) {
                if (les->type == N_SPARSE_LES) {
                    /*set the rows to zero */
                    for (i = 0; i < les->Asp[count]->cols; i++)
                        les->Asp[count]->values[i] = 0.0;
                    /*set the cols to zero */
                    for (i = 0; i < les->rows; i++) {
                        for (j = 0; j < les->Asp[i]->cols; j++) {
                            if (les->Asp[i]->index[j] == count)
                                les->Asp[i]->values[j] = 0.0;
                        }
                    }

                    /*entry on the diagonal */
                    les->Asp[count]->values[0] = 1.0;

                }
                else {
                    /*set the rows to zero */
                    for (i = 0; i < les->cols; i++)
                        les->A[count][i] = 0.0;
                    /*set the cols to zero */
                    for (i = 0; i < les->rows; i++)
                        les->A[i][count] = 0.0;

                    /*entry on the diagonal */
                    les->A[count][count] = 1.0;
                }
            }
            if (stat >= N_CELL_ACTIVE)
                count++;
        }
    }

    return 0;

}

/* **************************************************************** */
/* **** make an entry in the les (2d) ***************************** */
/* **************************************************************** */
int make_les_entry_2d(int i, int j, int offset_i, int offset_j, int count,
                      int pos, N_les * les, G_math_spvector * spvect,
                      N_array_2d * cell_count, N_array_2d * status,
                      N_array_2d * start_val, double entry, int cell_type)
{
    int K;

    int di = offset_i;

    int dj = offset_j;

    K = N_get_array_2d_c_value(cell_count, i + di, j + dj) -
        N_get_array_2d_c_value(cell_count, i, j);

    /* active cells build the linear equation system */
    if (cell_type == N_CELL_ACTIVE) {
        /* dirichlet or transmission cells must be handled like this */
        if (N_get_array_2d_c_value(status, i + di, j + dj) > N_CELL_ACTIVE &&
            N_get_array_2d_c_value(status, i + di, j + dj) < N_MAX_CELL_STATE)
            les->b[count] -=
                N_get_array_2d_d_value(start_val, i + di, j + dj) * entry;
        else if (N_get_array_2d_c_value(status, i + di, j + dj) ==
                 N_CELL_ACTIVE) {
            if ((count + K) >= 0 && (count + K) < les->cols) {
                G_debug(5,
                        " make_les_entry_2d: (N_CELL_ACTIVE) create matrix entry at row[%i] col[%i] value %g\n",
                        count, count + K, entry);
                pos++;
                if (les->type == N_SPARSE_LES) {
                    spvect->index[pos] = count + K;
                    spvect->values[pos] = entry;
                }
                else {
                    les->A[count][count + K] = entry;
                }
            }
        }
    }                           /* if dirichlet cells should be used then check for all valid cell neighbours */
    else if (cell_type == N_CELL_DIRICHLET) {
        /* all valid cells */
        if (N_get_array_2d_c_value(status, i + di, j + dj) > N_CELL_INACTIVE
            && N_get_array_2d_c_value(status, i + di,
                                      j + dj) < N_MAX_CELL_STATE) {
            if ((count + K) >= 0 && (count + K) < les->cols) {
                G_debug(5,
                        " make_les_entry_2d: (N_CELL_DIRICHLET) create matrix entry at row[%i] col[%i] value %g\n",
                        count, count + K, entry);
                pos++;
                if (les->type == N_SPARSE_LES) {
                    spvect->index[pos] = count + K;
                    spvect->values[pos] = entry;
                }
                else {
                    les->A[count][count + K] = entry;
                }
            }
        }
    }

    return pos;
}


/* *************************************************************** * 
 * ******************** N_assemble_les_3d ************************ * 
 * *************************************************************** */
N_les *N_assemble_les_3d(int les_type, N_geom_data * geom,
                         N_array_3d * status, N_array_3d * start_val,
                         void *data, N_les_callback_3d * call)
{
    return N_assemble_les_3d_param(les_type, geom, status, start_val, data,
                                   call, N_CELL_ACTIVE);
}

N_les *N_assemble_les_3d_active(int les_type, N_geom_data * geom,
                                N_array_3d * status, N_array_3d * start_val,
                                void *data, N_les_callback_3d * call)
{
    return N_assemble_les_3d_param(les_type, geom, status, start_val, data,
                                   call, N_CELL_ACTIVE);
}

N_les *N_assemble_les_3d_dirichlet(int les_type, N_geom_data * geom,
                                   N_array_3d * status,
                                   N_array_3d * start_val, void *data,
                                   N_les_callback_3d * call)
{
    return N_assemble_les_3d_param(les_type, geom, status, start_val, data,
                                   call, N_CELL_DIRICHLET);
}

N_les *N_assemble_les_3d_param(int les_type, N_geom_data * geom,
                               N_array_3d * status, N_array_3d * start_val,
                               void *data, N_les_callback_3d * call,
                               int cell_type)
{
    int i, j, k, count = 0, pos = 0;

    int cell_type_count = 0;

    N_array_3d *cell_count;

    N_les *les = NULL;

    int **index_ij;

    G_debug(2,
            "N_assemble_les_3d: starting to assemble the linear equation system");

    cell_count =
        N_alloc_array_3d(geom->cols, geom->rows, geom->depths, 1, DCELL_TYPE);

    /* First count the number of valid cells and save  
     * each number in a new 3d array. Those numbers are used 
     * to create the linear equation system.*/

    if (cell_type == N_CELL_DIRICHLET) {
        /* include dirichlet cells in the les */
        for (k = 0; k < geom->depths; k++) {
            for (j = 0; j < geom->rows; j++) {
                for (i = 0; i < geom->cols; i++) {
                    /*use all non-inactive cells for les creation */
                    if (N_CELL_INACTIVE <
                        (int)N_get_array_3d_d_value(status, i, j, k) &&
                        (int)N_get_array_3d_d_value(status, i, j,
                                                    k) < N_MAX_CELL_STATE)
                        cell_type_count++;
                }
            }
        }
    }
    else {
        /*use only active cell in the les */
        for (k = 0; k < geom->depths; k++) {
            for (j = 0; j < geom->rows; j++) {
                for (i = 0; i < geom->cols; i++) {
                    /*count only active cells */
                    if (N_CELL_ACTIVE
                        == (int)N_get_array_3d_d_value(status, i, j, k))
                        cell_type_count++;

                }
            }
        }
    }

    G_debug(2,
            "N_assemble_les_3d: number of  used cells %i\n", cell_type_count);

    if (cell_type_count == 0.0)
        G_fatal_error
            ("Not enough active cells [%i] to create the linear equation system. Check the cell status. Only active cells (value = 1) are used to create the equation system.",
             cell_type_count);

    /* allocate the memory for the linear equation system (les). 
     * Only valid cells are used to create the les. */
    les = N_alloc_les_Ax_b(cell_type_count, les_type);

    index_ij = (int **)G_calloc(cell_type_count, sizeof(int *));
    for (i = 0; i < cell_type_count; i++)
        index_ij[i] = (int *)G_calloc(3, sizeof(int));

    count = 0;
    /*count the number of cells which should be used to create the linear equation system */
    /*save the k, i and j indices and create a ordered numbering */
    for (k = 0; k < geom->depths; k++) {
        for (j = 0; j < geom->rows; j++) {
            for (i = 0; i < geom->cols; i++) {
                if (cell_type == N_CELL_DIRICHLET) {
                    if (N_CELL_INACTIVE <
                        (int)N_get_array_3d_d_value(status, i, j, k) &&
                        (int)N_get_array_3d_d_value(status, i, j,
                                                    k) < N_MAX_CELL_STATE) {
                        N_put_array_3d_d_value(cell_count, i, j, k, count);
                        index_ij[count][0] = i;
                        index_ij[count][1] = j;
                        index_ij[count][2] = k;
                        count++;
                        G_debug(5,
                                "N_assemble_les_3d: non-inactive cells count %i at pos x[%i] y[%i] z[%i]\n",
                                count, i, j, k);
                    }
                }
                else if (N_CELL_ACTIVE ==
                         (int)N_get_array_3d_d_value(status, i, j, k)) {
                    N_put_array_3d_d_value(cell_count, i, j, k, count);
                    index_ij[count][0] = i;
                    index_ij[count][1] = j;
                    index_ij[count][2] = k;
                    count++;
                    G_debug(5,
                            "N_assemble_les_3d: active cells count %i at pos x[%i] y[%i] z[%i]\n",
                            count, i, j, k);
                }
            }
        }
    }

    G_debug(2, "N_assemble_les_3d: starting the parallel assemble loop");

#pragma omp parallel for private(i, j, k, pos, count) schedule(static)
    for (count = 0; count < cell_type_count; count++) {
        i = index_ij[count][0];
        j = index_ij[count][1];
        k = index_ij[count][2];

        /*create the entries for the */
        N_data_star *items = call->callback(data, geom, i, j, k);

        G_math_spvector *spvect = NULL;

        /*allocate a sprase vector */
        if (les_type == N_SPARSE_LES)
            spvect = G_math_alloc_spvector(items->count);
        /* initial conditions */

        les->x[count] = N_get_array_3d_d_value(start_val, i, j, k);

        /* the entry in the vector b */
        les->b[count] = items->V;

        /* pos describes the position in the sparse vector.
         * the first entry is always the diagonal entry of the matrix*/
        pos = 0;

        if (les_type == N_SPARSE_LES) {
            spvect->index[pos] = count;
            spvect->values[pos] = items->C;
        }
        else {
            les->A[count][count] = items->C;
        }
        /* western neighbour, entry is col - 1 */
        if (i > 0) {
            pos =
                make_les_entry_3d(i, j, k, -1, 0, 0, count, pos, les, spvect,
                                  cell_count, status, start_val, items->W,
                                  cell_type);
        }
        /* eastern neighbour, entry col + 1 */
        if (i < geom->cols - 1) {
            pos = make_les_entry_3d(i, j, k, 1, 0, 0, count, pos, les, spvect,
                                    cell_count, status, start_val, items->E,
                                    cell_type);
        }
        /* northern neighbour, entry row -1 */
        if (j > 0) {
            pos =
                make_les_entry_3d(i, j, k, 0, -1, 0, count, pos, les, spvect,
                                  cell_count, status, start_val, items->N,
                                  cell_type);
        }
        /* southern neighbour, entry row +1 */
        if (j < geom->rows - 1) {
            pos = make_les_entry_3d(i, j, k, 0, 1, 0, count, pos, les, spvect,
                                    cell_count, status, start_val, items->S,
                                    cell_type);
        }
        /*only for a 7 star entry needed */
        if (items->type == N_7_POINT_STAR || items->type == N_27_POINT_STAR) {
            /* the upper cell (top), entry depth + 1 */
            if (k < geom->depths - 1) {
                pos =
                    make_les_entry_3d(i, j, k, 0, 0, 1, count, pos, les,
                                      spvect, cell_count, status, start_val,
                                      items->T, cell_type);
            }
            /* the lower cell (bottom), entry depth - 1 */
            if (k > 0) {
                pos =
                    make_les_entry_3d(i, j, k, 0, 0, -1, count, pos, les,
                                      spvect, cell_count, status, start_val,
                                      items->B, cell_type);
            }
        }

        /*How many entries in the les */
        if (les->type == N_SPARSE_LES) {
            spvect->cols = pos + 1;
            G_math_add_spvector(les->Asp, spvect, count);
        }

        if (items)
            G_free(items);
    }

    N_free_array_3d(cell_count);

    for (i = 0; i < cell_type_count; i++)
        G_free(index_ij[i]);

    G_free(index_ij);

    return les;
}

int N_les_integrate_dirichlet_3d(N_les * les, N_geom_data * geom,
                                 N_array_3d * status, N_array_3d * start_val)
{
    int rows, cols, depths;

    int count = 0;

    int i, j, x, y, z, stat;

    double *dvect1;

    double *dvect2;

    G_debug(2,
            "N_les_integrate_dirichlet_3d: integrating the dirichlet boundary condition");

    rows = geom->rows;
    cols = geom->cols;
    depths = geom->depths;

    /*we nned to additional vectors */
    dvect1 = (double *)G_calloc(les->cols, sizeof(double));
    dvect2 = (double *)G_calloc(les->cols, sizeof(double));

    /*fill the first one with the x vector data of Dirichlet cells */
    count = 0;
    for (z = 0; z < depths; z++) {
        for (y = 0; y < rows; y++) {
            for (x = 0; x < cols; x++) {
                stat = (int)N_get_array_3d_d_value(status, x, y, z);
                if (stat > N_CELL_ACTIVE && stat < N_MAX_CELL_STATE) {
                    dvect1[count] =
                        N_get_array_3d_d_value(start_val, x, y, z);
                    count++;
                }
                else if (stat == N_CELL_ACTIVE) {
                    dvect1[count] = 0.0;
                    count++;
                }
            }
        }
    }

#pragma omp parallel default(shared)
    {
        /*performe the matrix vector product and */
        if (les->type == N_SPARSE_LES)
            G_math_Ax_sparse(les->Asp, dvect1, dvect2, les->rows);
        else
            G_math_d_Ax(les->A, dvect1, dvect2, les->rows, les->cols);
#pragma omp for schedule (static) private(i)
        for (i = 0; i < les->cols; i++)
            les->b[i] = les->b[i] - dvect2[i];
    }

    /*now set the Dirichlet cell rows and cols to zero and the 
     * diagonal entry to 1*/
    count = 0;
    for (z = 0; z < depths; z++) {
        for (y = 0; y < rows; y++) {
            for (x = 0; x < cols; x++) {
                stat = (int)N_get_array_3d_d_value(status, x, y, z);
                if (stat > N_CELL_ACTIVE && stat < N_MAX_CELL_STATE) {
                    if (les->type == N_SPARSE_LES) {
                        /*set the rows to zero */
                        for (i = 0; i < les->Asp[count]->cols; i++)
                            les->Asp[count]->values[i] = 0.0;
                        /*set the cols to zero */
                        for (i = 0; i < les->rows; i++) {
                            for (j = 0; j < les->Asp[i]->cols; j++) {
                                if (les->Asp[i]->index[j] == count)
                                    les->Asp[i]->values[j] = 0.0;
                            }
                        }

                        /*entry on the diagonal */
                        les->Asp[count]->values[0] = 1.0;

                    }
                    else {
                        /*set the rows to zero */
                        for (i = 0; i < les->cols; i++)
                            les->A[count][i] = 0.0;
                        /*set the cols to zero */
                        for (i = 0; i < les->rows; i++)
                            les->A[i][count] = 0.0;

                        /*entry on the diagonal */
                        les->A[count][count] = 1.0;
                    }
                }
                count++;
            }
        }
    }

    return 0;

}

/* **************************************************************** */
/* **** make an entry in the les (3d) ***************************** */
/* **************************************************************** */
int make_les_entry_3d(int i, int j, int k, int offset_i, int offset_j,
                      int offset_k, int count, int pos, N_les * les,
                      G_math_spvector * spvect, N_array_3d * cell_count,
                      N_array_3d * status, N_array_3d * start_val,
                      double entry, int cell_type)
{
    int K;

    int di = offset_i;

    int dj = offset_j;

    int dk = offset_k;

    K = (int)N_get_array_3d_d_value(cell_count, i + di, j + dj, k + dk) -
        (int)N_get_array_3d_d_value(cell_count, i, j, k);

    if (cell_type == N_CELL_ACTIVE) {
        if ((int)N_get_array_3d_d_value(status, i + di, j + dj, k + dk) >
            N_CELL_ACTIVE &&
            (int)N_get_array_3d_d_value(status, i + di, j + dj,
                                        k + dk) < N_MAX_CELL_STATE)
            les->b[count] -=
                N_get_array_3d_d_value(start_val, i + di, j + dj,
                                       k + dk) * entry;
        else if ((int)N_get_array_3d_d_value(status, i + di, j + dj, k + dk)
                 == N_CELL_ACTIVE) {
            if ((count + K) >= 0 && (count + K) < les->cols) {
                G_debug(5,
                        " make_les_entry_3d: (N_CELL_ACTIVE) create matrix entry at row[%i] col[%i] value %g\n",
                        count, count + K, entry);
                pos++;
                if (les->type == N_SPARSE_LES) {
                    spvect->index[pos] = count + K;
                    spvect->values[pos] = entry;
                }
                else {
                    les->A[count][count + K] = entry;
                }
            }
        }
    }
    else if (cell_type == N_CELL_DIRICHLET) {
        if ((int)N_get_array_3d_d_value(status, i + di, j + dj, k + dk)
            != N_CELL_INACTIVE) {
            if ((count + K) >= 0 && (count + K) < les->cols) {
                G_debug(5,
                        " make_les_entry_3d: (N_CELL_DIRICHLET) create matrix entry at row[%i] col[%i] value %g\n",
                        count, count + K, entry);
                pos++;
                if (les->type == N_SPARSE_LES) {
                    spvect->index[pos] = count + K;
                    spvect->values[pos] = entry;
                }
                else {
                    les->A[count][count + K] = entry;
                }
            }
        }
    }

    return pos;
}