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deepmodeling / DMFF

DMFF (Differentiable Molecular Force Field) is a Jax-based python package that provides a full differentiable implementation of molecular force field models.
GNU Lesser General Public License v3.0
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Naming consistency in nbList #78

Closed jaketanderson closed 1 year ago

jaketanderson commented 1 year ago

When creating neighbor lists, there is inconsistency on which keyword is used for the cutoff distance.

https://github.com/deepmodeling/DMFF/blob/2690192df36d393346be219e74b02bc4aa385d01/dmff/common/nblist.py#L11-L20 https://github.com/deepmodeling/DMFF/blob/2690192df36d393346be219e74b02bc4aa385d01/dmff/common/nblist.py#L113-L119

In these pieces of code we see r_cutoff, r_cut, and rc. I recommend these be standardized so that issues don't pop up due to confusion. The classical demo notebook, for example, specified rc=4 as an argument to NeighborList but NeighborList takes no argument rc, only r_cutoff. I fixed that issue in PR #77.

Ericwang6 commented 1 year ago

Hi @jaketanderson , thanks for your suggestion and appreciate the fix in demo!