Fix coordination number bug (#3954)

Author: jmmshn

src/pymatgen/analysis/graphs.py

@@ -808,8 +808,7 @@ def get_coordination_of_site(self, n: int) -> int:
         Returns:
             int: number of neighbors of site n.
         """
-        n_self_loops = sum(1 for n, v in self.graph.edges(n) if n == v)
-        return self.graph.degree(n) - n_self_loops
+        return self.graph.degree(n)
 
     def draw_graph_to_file(
         self,
@@ -2478,8 +2477,7 @@ def get_coordination_of_site(self, n) -> int:
         Returns:
             int: the number of neighbors of site n.
         """
-        n_self_loops = sum(1 for n, v in self.graph.edges(n) if n == v)
-        return self.graph.degree(n) - n_self_loops
+        return self.graph.degree(n)
 
     def draw_graph_to_file(
         self,

tests/analysis/test_graphs.py

@@ -409,7 +409,7 @@ def test_from_local_env_and_equality_and_diff(self):
         diff = struct_graph.diff(sg2)
         assert diff["dist"] == 0
 
-        assert self.square_sg.get_coordination_of_site(0) == 2
+        assert self.square_sg.get_coordination_of_site(0) == 4
 
     def test_from_edges(self):
         edges = {