Improved version of the PHOBOS Glauber Monte Carlo

Glauber models are used to calculate geometric quantities in the initial state of heavy ion collisions, such as impact parameter, number of participating nucleons and initial eccentricity. Experimental heavy-ion collaboration, in particular at RHIC and LHC, use Glauber Model calculations for various geometric observables. In this document, we describe the assumptions inherent to the approach, and provide an updated implementation (v2) of the Monte Carlo based Glauber Model calculation, which originally was used by the PHOBOS collaboration. The main improvement w.r.t. the earlier version (arXiv:0805.4411) are the inclusion of Tritium, Helium-3, and Uranium, as well as the treatment of deformed nuclei and Glauber-Gribov fluctuations of the proton in p+A collisions. A users' guide (updated to reflect changes in v2) is provided for running various calculations.