Improve and generalize `NEGF` class

[sofiasanz]

• Currently the NEGF class does not allow to perform calculations with periodicity, i.e. it can only calculate the spin densities for infinite quasi 1D structures along a certain transport direction.

• On the other hand this class should be generalized to non-orthogonal basis also, since now it calculates the spin-densities by taking the diagonal elements of the density matrix calculated from the Green's function integration. For a non-orthogonal basis the overlap matrix should also play a role when building the spin-densities.