Also, some basic familiarity with plasma physics is recommended. E.g., plasma oscillations, cold plasma waves and the concept of dispersion relation will be invoked without too much explanation during the lectures. An excellent reference that goes into more than enough detail is Blandford and Thorne's unpublished book "APPLICATIONS OF CLASSICAL PHYSICS" , chapters 19 and 20. An introductory book by Francis Chen is also great.
As a warm-up exercise, try to write a simple code to integrate the location and velocity of a non-relativistic electron feeling the Lorentz force in constant electric and magnetic fields. The particle can move in two dimensions. The electric field is in the plane of motion, while the magnetic field is out of the plane. For simplicity, you can start with a Runge-Kutta method (we will learn that it's not that great for this problem), and consider two cases: E smaller than B by magnitude and E greater than B (cgs units).
For homework problems we will use the free code XOOPIC (X-windows Object Oriented Particle-In-Cell code). You can install either XOOPIC (see below), or the demo version of the comercial code based on XOOPIC: OOPIC-PRO (see below). OOPIC-PRO is easier to install, and as we don't need to modify the source files, it will suffice for problem sets.
Their commercial version is here from where you can download binaries (under Downloads menu). Evalutation versions are available for all major architectures.
An open source version is available under the name XOOPIC from http://langmuir.nuc.berkeley.edu/pub/codes/xoopic/ (choose the latest version). The website of the Berkeley group is http://langmuir.nuc.berkeley.edu/ . The installation can be a bit cumersome, as it needs a number of libraries that do not come with most standard distributions. Notably you will need XGRAFIX from http://langmuir.nuc.berkeley.edu/pub/codes/xgrafix/ .