diff --git a/.gitignore b/.gitignore index 6824191..0596685 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ __pycache__ src/tinyff/_version.py dist build +tmp diff --git a/src/tinyff/neighborlist.py b/src/tinyff/neighborlist.py index b6626bb..b077f12 100644 --- a/src/tinyff/neighborlist.py +++ b/src/tinyff/neighborlist.py @@ -26,6 +26,7 @@ __all__ = ("NLIST_DTYPE", "NBuildSimple", "NBuildCellLists") + NLIST_DTYPE = [ # First atoms. ("iatom0", int), @@ -189,7 +190,9 @@ def _apply_mic(deltas: NDArray[float], cell_lengths: NDArray[float]): deltas /= cell_lengths deltas -= np.round(deltas) deltas *= cell_lengths - return np.linalg.norm(deltas, axis=1) + dist = np.einsum("ij,ij->i", deltas, deltas) + np.sqrt(dist, out=dist) + return dist @attrs.define