Details are presented of an efficient formalism for calculating transmission
and reflection matrices from first principles in layered materials. Within the
framework of spin density functional theory and using tight-binding muffin-tin
orbitals, scattering matrices are determined by matching the wave-functions at
the boundaries between leads which support well-defined scattering states and
the scattering region. The calculation scales linearly with the number of
principal layers N in the scattering region and as the cube of the number of
atoms H in the lateral supercell. For metallic systems for which the required
Brillouin zone sampling decreases as H increases, the final scaling goes as
H^2*N. In practice, the efficient basis set allows scattering regions for which
H^{2}*N ~ 10^6 to be handled. The method is illustrated for Co/Cu multilayers
and single interfaces using large lateral supercells (up to 20x20) to model
interface disorder. Because the scattering states are explicitly found,
``channel decomposition'' of the interface scattering for clean and disordered
interfaces can be performed.Comment: 22 pages, 13 figure