Manual - Example - Implementation of Gennady's comments (new figure for sample, \alpha_0 \phi_0 replaced by \alpha_i,  \phi_i, remove identical remarks, url of NumPy moved to references)

Beam's alpha_i value can also be given as positive value now (internally it needs to be <=0 for incoming beams)

Changed convention for passing two doubles to define refractive indices: now n = 1 - delta + i beta (delta, beta are the two parameters)