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Add vibrations py

This update to vibrations.py allows vibrations to be calculated directly from an atoms object containing embedded atoms objects. This would be the case if a vasprun.xml file was read after a vibrational calculation in vasp. This will work for all vibrational calculations that worked originally from pickles. There is an addition of an imagetype option which can be either 'pickle' or 'atoms. 'pickle' is the default.

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