#define DIM 1/2

int index(int *i, int *size) {
#if DIM == 1
    return i[0];
#elif DIM == 2
    return i[0]*size[0]+i[1];
#endif
}

/* bla */

Cells *cells;
int i[DIM];
int size[DIM]; /* Array Größen */

for(i[0]=0; i<size[0]; i++) {
#if DIM==2
    for(i[1]=0; i<size[1]; i++) {
#endif
        do_stuff(cells[index(i, size)]);
#if DIM==2
    }
#endif
}

int args.nsites_arg = 100000;
...
float * hoppingRates;
hoppingRates = malloc(sizeof(float) * args.nsites_arg * args.nsites_arg);
createHoppingRates(hoppingRates, ...);

void  
createHoppingRates(float * rates...)
{
    size_t i, j, number, *neighbors, sum;

    for(i = 0; i < args.nsites_arg; ++i)
    {
        // get all neighbors for sites[i]
        neighbors = getNeighbors(sites[i], cells, a, rc);
        number = sizeof(neighbors)/sizeof(int);

        // calculate hopping rate to neighbor
        // store it in rates matrix
        for(j = 0; j < number; ++j)
        {
            sum = i * args.nsites_arg + neighbors[j];
            rates[sum] = calcHoppingRate(sites[i], sites[neighbors[j]]);
        }
    }

}

sum = (100000-1)*100000 + neighobr[j]