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Added dnn to next_neighbors

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This commit is contained in:
Sebastian Kloth 2023-12-26 11:07:30 +01:00
parent 97e29e6de3
commit 2615798088
1 changed files with 7 additions and 4 deletions
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src/mdevaluate/atoms.py
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@ -251,17 +251,20 @@ def next_neighbors(
atoms = atoms % np.diag(box) atoms = atoms % np.diag(box)
tree = KDTree(atoms, boxsize=np.diag(box)) tree = KDTree(atoms, boxsize=np.diag(box))
distances, indices = tree.query( distances, indices = tree.query(
query_atoms, number_of_neighbors, distance_upper_bound=distance_upper_bound query_atoms,
number_of_neighbors + dnn,
distance_upper_bound=distance_upper_bound,
) )
else: else:
atoms_pbc, atoms_pbc_index = pbc_points( atoms_pbc, atoms_pbc_index = pbc_points(
query_atoms, box, thickness=distance_upper_bound+0.1, index=True, **kwargs query_atoms, box, thickness=distance_upper_bound + 0.1, index=True, **kwargs
) )
tree = KDTree(atoms_pbc) tree = KDTree(atoms_pbc)
distances, indices = tree.query( distances, indices = tree.query(
query_atoms, number_of_neighbors, distance_upper_bound=distance_upper_bound query_atoms,
number_of_neighbors + dnn,
distance_upper_bound=distance_upper_bound,
) )
indices = atoms_pbc_index[indices] indices = atoms_pbc_index[indices]
return distances[:, dnn:], indices[:, dnn:] return distances[:, dnn:], indices[:, dnn:]