Calculate a boolean array where ``A[i,j] is True`` indicates a
        bond between the i-th and j-th atom.

def _jit_give_bond_array(pos, bond_radii, self_bonding_allowed=False):
        """Calculate a boolean array where ``A[i,j] is True`` indicates a
        bond between the i-th and j-th atom.
        """
        n = pos.shape[0]
        bond_array = np.empty((n, n), dtype=nb.boolean)

        for i in range(n):
            for j in range(i, n):
                D = 0
                for h in range(3):
                    D += (pos[i, h] - pos[j, h])**2
                B = (bond_radii[i] + bond_radii[j])**2
                bond_array[i, j] = (B - D) >= 0
                bond_array[j, i] = bond_array[i, j]
        if not self_bonding_allowed:
            for i in range(n):
                bond_array[i, i] = False
        return bond_array