  We present a plane wave/pseudopotential implementation of the method to
calculate electron transport properties of nanostructures. The conductance is
calculated via the Landauer formula within formalism of Green's functions.
Nonorthogonal Wannier-type atomic orbitals are obtained by the sequential
unitary rotations of virtual and occupied Kohn-Sham orbitals, which is followed
by two-step variational localization. We use these non-orthogonal Wannier type
atomic orbitals to partition the Kohn-Sham Hamiltonian into
electrode-contact-electrode submatrices. The electrode parts of the system are
modeled by two metal clusters with additional Lorentzian broadening of discrete
energy levels. We examined our implementation by modeling the transport
properties of Na atomic wires. Our results indicate that with the appropriate
level broadening the small cluster model for contacts reproduces odd-even
oscillations of the conductance as a function of the nanowire length.
