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ajkerr0 / kappa

A python package to calculate thermal conductivity across molecular interfaces.
MIT License
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Consider inputting bondLists instead of neighborLists for molecule creation #24

Closed ajkerr0 closed 8 years ago

ajkerr0 commented 8 years ago

Instead of using nList that is indexed like posList to determine bonds, why not make the user input bondLists explicitly?

Pros: -That way there can be no mistake in determining the bondList. -It is more explicit; no need to interpret what nearest neighbor means in the context of kappa -Keeps all the molecule attributes that need to join in the same ndarray format.

Cons: -The code is already there to use nLists; we would have to go back through the pre-generated molecules to build their bondLists straight up -Python lists are easy in this regard that you can just 'append' new neighbors when molecules are chained together

Maybe give the user an option to input either?

ajkerr0 commented 8 years ago

Maybe add a function that checks if nLists are self-consistent ie. If atom i lists atom j as a neighbor then the reverse ought to be true.

ajkerr0 commented 8 years ago

Closing this issue for now at least because this isn't an actual problem and it only makes the code more complicated for the sake of giving users one small option. If many parameters could be optioned like this then we should consider this.