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ajkerr0 / kappa

A python package to calculate thermal conductivity across molecular interfaces.
MIT License
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Missing handling of occupied interfacial atoms #46

Closed ajkerr0 closed 8 years ago

ajkerr0 commented 8 years ago

There is no treatment for the atoms of Interfaces that have been previously chained at that spot. There is no consideration in the plotting of the faces (they look the same as the others), and there is not stopping users from chaining additional molecules at those points.

Maybe add an attribute like occupied that's a list of the occupied indices to the Intefaces. Draw them differently with plot.faces (with a different color like purple)? Also run a check in the chain code that would disallow the user of chaining that, by raising an error?

ajkerr0 commented 8 years ago

Maybe remove those atoms from the interface(s) period? Should this require a recalculation of the interface position? This would also handle the deletion of single atom Interfaces that was previously implemented (which should require deletion of Interfaces explicitly if Interface.atoms is an empty list).