Enabled reading [virtual_sites*] from .rtp file.

The gen_lonepairs() function will support any type of virtual
site, but since only F_VSITE3 is needed at the moment, that is
all that has been added.

The new function is used to pre-determine which atoms are to be
virtualized, i.e. if LP are already present in the input coordinate
file, then they will be treated as virtual sites very simply, rather
than relying on existing vsite construction functions.

Change-Id: I3bc09b756b11f9552764cdd4c5dcea7369890f15