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Improve index conversions

Sebastian Ohlmann requested to merge improve_index_conversions into develop

Description

Add functions for converting local and global indices and use them instead of dealing with mesh%vp. This improves on isolating the knowledge about the mesh parallelization to the mesh class. It also simplifies some code with loops that now don't have to know if they are parallel in domain or not

News snippet

Improve index conversions in the code

Checklist

  • I have checked that my code follows the Octopus coding standards
  • I have added tests for all the new features added in this request.

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