fix: detect exact interstitial overlaps

Coding-Agent: Codex
Codex-Version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning-Effort: xhigh

Author: njzjz-bot

dpgen/auto_test/Interstitial.py

@@ -14,12 +14,17 @@
 
 
 def _smallest_nonzero_distance(distance_matrix):
-    """Return the minimum positive distance from a structure distance matrix."""
+    """Return the minimum distance between two distinct atoms.
+
+    Selecting by matrix index, instead of by value, keeps a real zero distance
+    caused by coincident atoms while excluding the zero-valued diagonal.
+    """
     distances = np.asarray(distance_matrix)
-    positive_distances = distances[distances > 0]
-    if positive_distances.size == 0:
-        raise ValueError("distance matrix does not contain a positive distance")
-    return float(np.min(positive_distances))
+    atom_pairs = np.triu_indices_from(distances, k=1)
+    pair_distances = distances[atom_pairs]
+    if pair_distances.size == 0:
+        raise ValueError("distance matrix does not contain a pair of atoms")
+    return float(np.min(pair_distances))
 
 
 class Interstitial(Property):

tests/auto_test/test_interstitial_distance.py

@@ -16,6 +16,17 @@ def test_smallest_nonzero_distance(self):
         )
         self.assertEqual(_smallest_nonzero_distance(distance_matrix), 1.25)
 
+    def test_exact_overlap_is_retained(self):
+        """An off-diagonal zero represents an invalid atomic overlap."""
+        distance_matrix = np.array(
+            [
+                [0.0, 0.0, 1.25],
+                [0.0, 0.0, 2.5],
+                [1.25, 2.5, 0.0],
+            ]
+        )
+        self.assertEqual(_smallest_nonzero_distance(distance_matrix), 0.0)
+
 
 if __name__ == "__main__":
     unittest.main()