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avoid repeat calculations of distance_matrix #199

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Jul 29, 2022
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avoid repeat calculations of distance_matrix #199

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7 changes: 4 additions & 3 deletions src/xtal2png/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -690,14 +690,15 @@ def structures_to_arrays(
num_sites.append(s.num_sites)
space_group.append(_get_space_group(s))

if n_sites != s.distance_matrix.shape[0]:
dm = s.distance_matrix # avoid repeat calculation
if n_sites != dm.shape[0]:
raise ValueError(
f"len(atomic_numbers) {n_sites} and distance_matrix.shape[0] {s.distance_matrix.shape[0]} do not match" # noqa
f"len(atomic_numbers) {n_sites} and distance_matrix.shape[0] {dm.shape[0]} do not match" # noqa
) # noqa

# assume that distance matrix is square
padwidth = (0, self.max_sites - n_sites)
distance_matrix_tmp.append(np.pad(s.distance_matrix, padwidth))
distance_matrix_tmp.append(np.pad(dm, padwidth))
# [0:max_sites, 0:max_sites]

frac_coords = np.stack(frac_coords_tmp)
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