where ρ 0 A is the reference density of the neutral atom A and v eff is the effective Kohn-Sham potential. In particular, the elements of the Hamiltonian matrix depend only on atoms A and B, therefore only the two-center elements of the Hamiltonian and overlap matrices are explicitly calculated as a function of the distance and the orientation, using the Slater-Koster transformation rules. One of the crucial parts of the use of DFTB method is to calculate the basis functions ϕ, and the atomic densities ρ 0 . The pseudoatomic orbitals and density are obtained by solving the modified atomic Kohn-Sham (KS) equations in which a confining potential, V conf , is added: