Cleaning up the restarts

[aaronjridley]

There was a lot of stuff to clean up:

• Many of the grid combinations didn't work, but I think that all combinations of grids should work now (dipole, sphere, cubesphere in neutral and ion).
• Restarts were not working properly, but now do.
• Indices perturbing after a restart works with writing perturbed values, and reading in a different perturbed value (this is needed for the data assimilation).
• Maybe fixed setting the lower boundary with dipole? I need to check this.

Anyways, these are good changes that are really needed to work with restarts and all of the grids.