Fix: fix AtomicData.py mask handling and ensure proper numpy arrays

dptb/data/AtomicData.py

@@ -1009,16 +1009,22 @@ def neighbor_list_and_relative_vec(
     shifts = shifts[mask]
 
     # 2. for i == j
-    
+
     mask = torch.ones(len(first_idex), dtype=torch.bool)
     mask[first_idex == second_idex] = False
     # get index bool type ~mask  for i == j.
-    o_first_idex = first_idex[~mask]
-    o_second_idex = second_idex[~mask]
-    o_shift = shifts[~mask]
+    # Convert mask to numpy for consistent indexing behavior
+    mask_np = mask.cpu().numpy()
+    o_first_idex = first_idex[~mask_np]
+    o_second_idex = second_idex[~mask_np]
+    o_shift = shifts[~mask_np]
     o_mask = mask[~mask]  # this is all False, with length being the number all  the bonds with i == j.
 
-
+    # Ensure arrays are proper numpy arrays (not scalars) for isolated systems
+    o_first_idex = np.atleast_1d(o_first_idex)
+    o_second_idex = np.atleast_1d(o_second_idex)
+    o_shift = np.atleast_2d(o_shift)
+
     # using the dict key to remove the duplicate bonds, because it is O(1) to check if a key is in the dict.
     rev_dict = {}
     for i in range(len(o_first_idex)):
@@ -1042,10 +1048,12 @@ def neighbor_list_and_relative_vec(
     del o_shift
     mask[~mask] = o_mask
     del o_mask
-
-    first_idex = torch.LongTensor(first_idex[mask], device=out_device)
-    second_idex = torch.LongTensor(second_idex[mask], device=out_device)
-    shifts = torch.as_tensor(shifts[mask], dtype=out_dtype, device=out_device)
+
+    # Convert mask to numpy for indexing numpy arrays (avoids torch/numpy compatibility issues)
+    mask_np = mask.cpu().numpy()
+    first_idex = torch.as_tensor(first_idex[mask_np], dtype=torch.long, device=out_device)
+    second_idex = torch.as_tensor(second_idex[mask_np], dtype=torch.long, device=out_device)
+    shifts = torch.as_tensor(shifts[mask_np], dtype=out_dtype, device=out_device)
 
     if not reduce:
         assert self_interaction == False, "for self_interaction = True,  i i 0 0 0 will be duplicated."