fix: select the minimum interstitial distance

Fixes #1902

Coding-Agent: Codex

Codex-Version: codex-cli 0.149.0

Model: gpt-5.6-sol

Reasoning-Effort: xhigh

Author: njzjz-bot

dpgen/auto_test/Interstitial.py

@@ -13,6 +13,15 @@
 from dpgen.auto_test.reproduce import make_repro, post_repro
 
 
+def _smallest_nonzero_distance(distance_matrix):
+    """Return the minimum positive distance from a structure distance matrix."""
+    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))
+
+
 class Interstitial(Property):
     def __init__(self, parameter, inter_param=None):
         parameter["reproduce"] = parameter.get("reproduce", False)
@@ -191,7 +200,9 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                         temp = jj.get_supercell_structure(
                             sc_mat=np.diag(self.supercell, k=0)
                         )
-                        smallest_distance = list(set(temp.distance_matrix.ravel()))[1]
+                        smallest_distance = _smallest_nonzero_distance(
+                            temp.distance_matrix
+                        )
                         if (
                             "conf_filters" in self.parameter
                             and "min_dist" in self.parameter["conf_filters"]

tests/auto_test/test_interstitial_distance.py

@@ -0,0 +1,21 @@
+import unittest
+
+import numpy as np
+
+from dpgen.auto_test.Interstitial import _smallest_nonzero_distance
+
+
+class TestInterstitialDistance(unittest.TestCase):
+    def test_smallest_nonzero_distance(self):
+        distance_matrix = np.array(
+            [
+                [0.0, 2.5, 1.25],
+                [2.5, 0.0, 3.0],
+                [1.25, 3.0, 0.0],
+            ]
+        )
+        self.assertEqual(_smallest_nonzero_distance(distance_matrix), 1.25)
+
+
+if __name__ == "__main__":
+    unittest.main()