Extend the correlators for rotational systems

[toastedcrumpets]

The rotational energy must also be included for systems with rotational degrees of freedom.
See the notes of this reference entry for more details:
http://localhost/index.php/outputplugins#thermalconductivity

• Add in calculation/tracking of the internal energy of a particle to the Misc plugin, and extend the thermal conductivity correlator.
• Update the output reference documentation to reflect this improvement.
• Sort out the storage of rotational data (place it inside of the Species tag and add a way to calculate the degrees of freedom).
• Use the Species to calculate kinetic energies of Particles (including rotational).
• Update the Misc plugin to track these rotational energies.
• Update the output reference documentation to reflect this improvement (temperature and thermal conductivity).

[toastedcrumpets]

Updating the issue to reflect that the internal energy is now tracked correctly.