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BUG: force contiguous calling find_points_in_spheres #3108

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merged 2 commits into from
Jun 26, 2023
Merged

BUG: force contiguous calling find_points_in_spheres #3108

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0a378b4
BUG: force contiguous calling find_points_in_spheres
lbluque Jun 26, 2023
2887f3d
TST: test get_neighbor_list for strained structures
lbluque Jun 26, 2023
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8 changes: 4 additions & 4 deletions pymatgen/core/structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1522,10 +1522,10 @@ def get_neighbor_list(
else:
if sites is None:
sites = self.sites
site_coords = np.array([site.coords for site in sites], dtype=float)
cart_coords = np.array(self.cart_coords, dtype=float)
lattice_matrix = np.array(self.lattice.matrix, dtype=float)
pbc = np.array(self.pbc, dtype=int)
site_coords = np.ascontiguousarray([site.coords for site in sites], dtype=float)
cart_coords = np.ascontiguousarray(self.cart_coords, dtype=float)
lattice_matrix = np.ascontiguousarray(self.lattice.matrix, dtype=float)
pbc = np.ascontiguousarray(self.pbc, dtype=int)
center_indices, points_indices, images, distances = find_points_in_spheres(
cart_coords,
site_coords,
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6 changes: 6 additions & 0 deletions pymatgen/core/tests/test_structure.py
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Expand Up @@ -538,6 +538,12 @@ def test_get_neighbor_list(self):
p_indices1, p_indices2, p_offsets, p_distances = s._get_neighbor_list_py(3)
self.assert_all_close(sorted(c_distances), sorted(p_distances))

s = Structure(s.lattice, s.species, s.frac_coords)
s.apply_strain(0.01)
c_indices1, c_indices2, c_offsets, c_distances = s.get_neighbor_list(3)
p_indices1, p_indices2, p_offsets, p_distances = s._get_neighbor_list_py(3)
self.assert_all_close(sorted(c_distances), sorted(p_distances))

# @skipIf(not os.getenv("CI"), "Only run this in CI tests")
# def test_get_all_neighbors_crosscheck_old(self):
# warnings.simplefilter("ignore")
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