ASE Backend For PBC Computation #310
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laserkelvin
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Oct 21, 2024
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Added minor comments, but the I might have a bigger lift/ask: could you write a unit test to ensure the products (i.e. offsets, src and dst nodes) are the same?
You could potentially do a really high level comparison: make torch_geometric.data.Data with the edges from both algorithms, pack the data into the graphs, and just do a pmg_graph == ase_graph assertion.
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Related to #267 - possibly leading up to replacing |
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I also added two tests to check for equivalence of src and dst node calculation here |
laserkelvin
approved these changes
Oct 22, 2024
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This PR adds a flag to the
PeriodicBoundaryConditiontransform to use eitherpymatgenoraseas a backend. The ASE backend is implemented and makes use of the NeighborList utility in ASE. This requires creating an atoms object, and specifying a cutoff distance per node. The two functionscalculate_ase_periodic_shiftsandcalculate_periodic_shiftsare quite similar, however hard to combine due to the dependency on the different backends, so they are kept separate for now.Some parameters that may have an impact on results:
NeighborList:self_interaction,bothwaysAtoms:pbcFor example, blindly applying PBC in x, y, and z for a structure which is not meant to be periodic in these directions may impact results.