Move the density parameter out of System

[chrisjonesBSU]

After having a conversion with @marjanAlbouye, we think we should 1: only have density as a parameter in the Pack class (removing it from System) and 2: set a default value of 1 g/cm^3. We need to add a note/warning about PACKMOL often requiring larger boxes to pack systems of large molecules, and to use the run_update_volume method in Simulation as a way to achieve desired density rather than doing that in Pack.