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Cleanup PixelGmxInterface (part 1)

Tadej Novak requested to merge tadej/athena:itk/cleanup1 into master

First step of cleaning up PixelGmxInterface. It's a bit heavy on whitespace change so putting in a separate MR. It mainly adds AthMessaging and uses std namespace.

I moved some helper functions to the base GmxInterface, I hope that's fine.

/cc @dellacqu @nstyles

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