md.neighborlist_md.NeighborListMD

class md.neighborlist_md.NeighborListMD(cutoff: float, cutoff_shell: float, base_nbl: ~schnetpack.transform.neighborlist.NeighborListTransform, requires_triples: bool = False, collate_fn: callable = <function _atoms_collate_fn>)

Wrapper for neighbor list transforms to make them suitable for molecular dynamics simulations. Introduces handling of multiple replicas and a cutoff shell (buffer region) to avoid recomputations of the neighbor list in every step.

Parameters:

• cutoff (float) – Cutoff radius.

• cutoff_shell (float) – Buffer region. Atoms can move this much unitil neighbor list needs to be recomputed.

• base_nbl (schnetpack.transform.NeighborListTransform) – basic SchNetPack neighbor list transform.

• requires_triples (bool) – Compute atom triples, e.g. for angles (default=False).

• collate_fn (callable) – Collate function for batch generation. Used to combine neighbor lists of differnt replicas and molecules.