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Resolve "Unify the usage of the terms atoms, structure, configuration, occupation, decoration"

Magnus Rahm requested to merge 339-unify-the-usage-of-the-terms-atoms-structure-configuration-occupation-decoration into master

This glorious and inspiring MR makes the following changes in terminology:

  • atoms -> structure
  • decoration -> occupation

Also included in the MR is

  • A bunch of docstring edits made by @erhart

Backward compatibility

This MR breaks backward compatibility when it comes to reading cluster spaces, cluster expansions, data containers etc, because of the name change atoms -> structure which is used as "arcname" in the tar archives. If this is unacceptable we could keep "atoms" as the arcname (when I think about it I think I would prefer to do so).

icet Structure

The change from atoms to structure is a little awkward in a few places due to the existence of an icet class called Structure. Since that class is nothing a typical user should ever have to touch, I don't think we should let it affect the terminology too much. I have tried to minimize its exposure by inlining most conversions from ASE Atoms to icet Structure. Where both are used simultaneously, the icet Structure is usually called icet_structure. In tests of the Structure class, I have gone super explicit and used ase_atoms and icet_structure.

Closes #339 (closed)

Edited by Magnus Rahm

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