def test_get_next_nearest_neighbors(self):
"""Check getting next nearest neighbors."""
sa = SiteAnalyzer(self.tin_dioxide)
info = sa.get_next_nearest_neighbors(5)
self.assertEqual(len(info), 14)
self.assertEqual(info[0]["element"], "O2-")
self.assertEqual(info[0]["connectivity"], "edge")
self.assertEqual(info[0]["geometry"]["type"], "trigonal planar")
self.assertEqual(info[0]["inequiv_index"], 2)
info = sa.get_next_nearest_neighbors(0,
inc_inequivalent_site_index=False)
self.assertTrue('inequiv_index' not in info[0])
info = sa.get_next_nearest_neighbors(0)
self.assertEqual(info[0]["element"], 'Sn4+')
self.assertEqual(info[0]["connectivity"], "edge")
self.assertEqual(info[0]["geometry"]["type"], "octahedral")
self.assertEqual(len(info[0]['angles']), 2)
self.assertAlmostEqual(info[0]['angles'][0], 101.62287790513848)
# check different structure without oxi state
sa = SiteAnalyzer(self.ba_n)
info = sa.get_next_nearest_neighbors(0)
self.assertEqual(len(info), 36)
self.assertEqual(info[5]["element"], "N")
self.assertEqual(info[5]["connectivity"], "edge")
self.assertEqual(info[5]["geometry"]["type"], "6-coordinate")
self.assertEqual(len(info[5]['angles']), 2)
self.assertAlmostEqual(info[5]['angles'][0], 83.91397867959587)
def test_get_next_nearest_neighbors(self):
"""Check getting next nearest neighbors."""
sa = SiteAnalyzer(self.tin_dioxide)
info = sa.get_next_nearest_neighbors(5)
self.assertEqual(len(info), 14)
idx = [i for i, s in enumerate(info) if s["connectivity"] == "edge"][0]
self.assertEqual(info[idx]["element"], "O2-")
self.assertEqual(info[idx]["connectivity"], "edge")
self.assertEqual(info[idx]["geometry"]["type"], "trigonal planar")
self.assertEqual(info[idx]["inequiv_index"], 2)
info = sa.get_next_nearest_neighbors(0, inc_inequivalent_site_index=False)
self.assertTrue("inequiv_index" not in info[0])
info = sa.get_next_nearest_neighbors(0)
self.assertEqual(info[0]["element"], "Sn4+")
self.assertEqual(info[0]["connectivity"], "edge")
self.assertEqual(info[0]["geometry"]["type"], "octahedral")
self.assertEqual(len(info[0]["angles"]), 2)
self.assertAlmostEqual(info[0]["angles"][0], 101.62287790513848)
self.assertAlmostEqual(info[0]["distance"], 3.24322132)
# check different structure without oxi state
sa = SiteAnalyzer(self.ba_n)
info = sa.get_next_nearest_neighbors(0)
self.assertEqual(len(info), 36)
self.assertEqual(info[5]["element"], "N")
self.assertEqual(info[5]["connectivity"], "edge")
self.assertEqual(info[5]["geometry"]["type"], "6-coordinate")
self.assertEqual(len(info[5]["angles"]), 2)
self.assertAlmostEqual(info[5]["angles"][0], 83.91397867959587)
self.assertAlmostEqual(info[5]["distance"], 3.549136232944574)
def test_nnn_summaries_match(self):
"""Test nearest neighbour summary matching function."""
sa = SiteAnalyzer(self.ba_n, use_symmetry_equivalent_sites=True)
nnn_a = sa.get_next_nearest_neighbors(0)
nnn_b = sa.get_next_nearest_neighbors(3)
nnn_c = sa.get_next_nearest_neighbors(4)
self.assertTrue(nnn_summaries_match(nnn_a, nnn_b))
self.assertFalse(nnn_summaries_match(nnn_a, nnn_c))
# test not matching bond angles
self.assertTrue(
nnn_summaries_match(nnn_a,
nnn_b,
bond_angle_tol=1e-10,
match_bond_angles=False))