Refactor HDF5 functionality

[jcoulter12]

HDF5 read write should be refactored for two key reasons:

1. HighFive has made changed a number of things in the syntax for their parallel read/write functionality.
2. We are now reading in HDF5 files for phonon-phonon interactions, el-ph interactions and in the near future other quantities as well.

The HDF5 read/write functions are currently scattered, and should be merged somehow into one or two utility files for the sake of code legibility and also future maintenance of the code.