Replace hardcoded `double`s with `amrex::Real`s

[mirenradia]

Ask discussed with @julianakwan, we should go through and change doubles to amrex::Reals consistently (e.g. for y and z coords), so that we can easily test the switch to single precision if needed. This can be done is a separate PR to the removal of the data_t types.

Originally posted by @KAClough in #103