Merge pull request #2227 from chc273/fix_c_mod_in_neighobrs

Fix c mod in neighobrs
materialsproject · Aug 25, 2021 · 9c5dc22 · 9c5dc22
2 parents 40817cc + c42bee1
commit 9c5dc22
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Showing 3 changed files with 1,523 additions and 1,333 deletions.
diff --git a/pymatgen/core/tests/test_structure.py b/pymatgen/core/tests/test_structure.py
@@ -471,6 +471,38 @@ def test_get_all_neighbors_and_get_neighbors(self):
         all_nn = s.get_all_neighbors(0.05)
         self.assertEqual([len(nn) for nn in all_nn], [0] * len(s))
 
+        # the following test is from issue #2226
+        poscar = """POSCAR
+ 1.0000000000000000
+     6.9082208665474800    0.0000000000000005    0.0000000000000011
+    -0.0000000000000008   14.1745610988433715    0.0000000000000004
+     0.0000000000000005   -0.0000000000000019   20.0189293405157045
+C
+ 14
+Direct
+  1.2615805559557376  1.4846778919841908  0.3162565598606580
+ -0.7615805559557360 -0.9846778919841882 -0.1837434401393425
+  1.2615805559557380 -0.4846778919841886 -0.1837434401393425
+ -0.7615805559557358  0.9846778919841882  0.3162565598606581
+ -0.2615805559557363 -0.4846778919841892  0.6837434401393432
+  0.7615805559557360  0.9846778919841881  0.1837434401393430
+ -0.2653510291469959  0.5275483828607898  0.1211255106369795
+  0.7653510291469972 -0.0275483828607906  0.6211255106369804
+  1.2653510291469956  0.5275483828607898  0.3788744893630209
+ -0.7653510291469972 -0.0275483828607906 -0.1211255106369797
+  1.2653510291469956  0.4724516171392097 -0.1211255106369793
+ -0.7653510291469972  0.0275483828607905  0.3788744893630209
+ -0.2653510291469959  0.4724516171392097  0.6211255106369801
+ -0.2705230397846415  1.4621722452479102  0.0625618775773844
+"""
+        s = Structure.from_str(poscar, fmt="poscar")
+        site0 = s.sites[1]
+        site1 = s.sites[9]
+        neigh_sites = s.get_neighbors(site0, 2.0)
+        self.assertTrue(len(neigh_sites) == 1)
+        neigh_sites = s.get_neighbors(site1, 2.0)
+        self.assertTrue(len(neigh_sites) == 1)
+
     def test_get_neighbor_list(self):
         s = self.struct
         c_indices1, c_indices2, c_offsets, c_distances = s.get_neighbor_list(3)