Fix pbc conv args Final Draft #306
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allaffa
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Nov 9, 2024
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Fix pbc conv args final draft
Main points:
(1) I create edge_shifts in preprocessing with ASE, then apply those shifts in conv_args.
------The edge shifts adjust the relative vector for a connection. After additional research, I believe this to be the best way for fewer lines of code and being streamlined. It is also the approach of top competitors and does not disrupt gradient flow------
(2) Correctly applying PBC in models that update the position is currently not supported (SchNet / EGNN).
------At the core level, we have the problem that the positional update could make a node cross the supercell, even if we were to recalculate the shifts after each layer. I still allow the models to run, but simply continue to use the naive relative vectors------
(3) data.pbc is now a requirement for periodic boundary conditions
------I make an effort to include it in any examples that use PBC------
@allaffa Assuming this passes the tests I'll schedule a meeting to go over the PR.