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Refactor HDF5 functionality  #175

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@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.

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