  An efficient implementation of the nonequilibrium Green function (NEGF)
method combined with the density functional theory (DFT) using localized
pseudo-atomic orbitals (PAOs) is presented for electronic transport
calculations of a system connected with two leads under a finite bias voltage.
In the implementation, accurate and efficient methods are developed especially
for evaluation of the density matrix and treatment of boundaries between the
scattering region and the leads. Equilibrium and nonequilibrium contributions
in the density matrix are evaluated with very high precision by a contour
integration with a continued fraction representation of the Fermi-Dirac
function and by a simple quadratureon the real axis with a small imaginary
part, respectively. The Hartree potential is computed efficiently by a
combination of the two dimensional fast Fourier transform (FFT) and a finite
difference method, and the charge density near the boundaries is constructed
with a careful treatment to avoid the spurious scattering at the boundaries.
The efficiency of the implementation is demonstrated by rapid convergence
properties of the density matrix. In addition, as an illustration, our method
is applied for zigzag graphene nanoribbons, a Fe/MgO/Fe tunneling junction, and
a LaMnO$_3/$SrMnO$_3$ superlattice, demonstrating its applicability to a wide
variety of systems.
