The recent interest in high altitude discharges known as red sprites, blue jets, and elves has stimulated the modeling of transient atmospheric electricity. The modeling of these high altitude discharges require an initiating cloud-to-ground or intracloud lightning event in order to pre-condition the electric field between the cloud tops and the ionosphere. In this short paper we describe a finite difference time domain (FDTD) numerical solution of Maxwell's equations based on the Yee (Yee 1966) algorithm coupled with a uniaxial perfectly matched layer (PML, Berenger 1994) boundary treatment. The PML theory has advanced considerably since its original formulation in cartesian coordinates for lossless media, and is computationally efficient to implement. Another boundary treatment possibility for our sources that produce radiative and electrostatic fields, which we do not consider here, is a multipole expansion in the time domain for the electromagnetic fields.