Resolve "Make the hamiltonian instance part of system_t"

Description

This puts the hamiltonian object (hm) as an attribute of the system object (sys) and for all subroutine calls that have both sys and hm as arguments, the hm argument was deleted and the soubroutine accordingly modified to use sys%hm instead of hm

Checklist

• I have checked that my code follows the Octopus coding standards

Closes #170 (closed)