Merge pull request #95 from sparks-baird/fill-diagonal-zero

fill distance_matrix diagonals with zeros in arrays_to_structures
sparks-baird · Jun 14, 2022 · d9ee96a · d9ee96a
2 parents a773a48 + 2208564
commit d9ee96a
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/src/xtal2png/core.py b/src/xtal2png/core.py
@@ -612,6 +612,8 @@ def arrays_to_structures(self, data: np.ndarray):
             space_group_scaled, data_range=self.space_group_range
         )
         distance_matrix = rgb_unscaler(distance_scaled, data_range=self.distance_range)
+        for dm in distance_matrix:
+            np.fill_diagonal(dm, 0.0)
         # technically unused, but to avoid issue with pre-commit for now:
         volume, space_group, distance_matrix