Switch to AMReX geometry parameters and use negative extents

[mirenradia]

This is heavily related to #1 but I thought I'd move discussions on it into a separate issue.

The relevant AMReX geometry parameters are:

• geometry.prob_lo
• geometry.prob_hi
• amr.n_cell

In addition to simplifying the horrible mess of Ni, N, N_full, etc. parameters, we also want to shift the position of the grid such that the centre is at the origin (i.e. $(0,\,0,\,0)$ ). Assuming there is no reflective symmetry, if want the domain to have side lengths $L_i$ for $i=1,2,3$, the low end will be $(-L_1/2,\,-L_2/2,\,-L_3/2)$ and the high end will be $(L_1/2,\,L_2/2,\,L_3/2)$.

I have made a start on this on the enhancement/negative_extents branch but it probably makes sense for these changes to be made either as part of work on #1 or after that is done.