diff --git a/deepmd_pt/utils/dataset.py b/deepmd_pt/utils/dataset.py
index 0dc9d22b..abc461ab 100644
--- a/deepmd_pt/utils/dataset.py
+++ b/deepmd_pt/utils/dataset.py
@@ -552,7 +552,11 @@ def single_preprocess(self, batch, sid):
             return batch
         else:
             batch['clean_type'] = clean_type
-            batch['clean_coord'] = clean_coord
+            if self.pbc:
+                _clean_coord = normalize_coord(clean_coord, region, nloc)
+            else:
+                _clean_coord = clean_coord.clone()
+            batch['clean_coord'] = _clean_coord
             # add noise
             for i in range(self.max_fail_num):
                 mask_num = 0
@@ -587,13 +591,13 @@ def single_preprocess(self, batch, sid):
                         )
                     else:
                         NotImplementedError(f"Unknown noise type {self.noise_type}!")
-                    noised_coord = clean_coord.clone().detach()
+                    noised_coord = _clean_coord.clone().detach()
                     noised_coord[coord_mask] += noise_on_coord
                     batch['coord_mask'] = torch.tensor(coord_mask,
                                                        dtype=torch.bool,
                                                        device=env.PREPROCESS_DEVICE)
                 else:
-                    noised_coord = clean_coord
+                    noised_coord = _clean_coord
                     batch['coord_mask'] = torch.tensor(np.zeros_like(coord_mask, dtype=np.bool),
                                                        dtype=torch.bool,
                                                        device=env.PREPROCESS_DEVICE)
@@ -611,7 +615,7 @@ def single_preprocess(self, batch, sid):
                                                       dtype=torch.bool,
                                                       device=env.PREPROCESS_DEVICE)
                 if self.pbc:
-                    _coord = normalize_coord(noised_coord, region, nloc)
+                    _coord = region.move_noised_coord_all_in_box(noised_coord, _clean_coord)
                 else:
                     _coord = noised_coord.clone()
                 batch['coord'] = _coord
@@ -626,7 +630,6 @@ def single_preprocess(self, batch, sid):
                         RuntimeError(f"Add noise times beyond max tries {self.max_fail_num}!")
                     continue
                 batch['atype'] = masked_type
-                batch['coord'] = noised_coord
                 batch['nlist'] = nlist
                 batch['nlist_loc'] = nlist_loc
                 batch['nlist_type'] = nlist_type
diff --git a/deepmd_pt/utils/preprocess.py b/deepmd_pt/utils/preprocess.py
index 58db6041..e4521178 100644
--- a/deepmd_pt/utils/preprocess.py
+++ b/deepmd_pt/utils/preprocess.py
@@ -36,7 +36,16 @@ def get_face_distance(self):
         """Return face distinces to each surface of YZ, ZX, XY."""
         return torch.stack([self._h2yz, self._h2zx, self._h2xy])
 
-
+    def move_noised_coord_all_in_box(self, noised_coord, clean_coord):
+        """Ensure all noised atoms are inside region"""
+        tmp_coord_noised = noised_coord.clone()
+        tmp_coord_clean = clean_coord.clone()
+        inter_coord_noised = self.phys2inter(tmp_coord_noised)
+        inter_coord_clean = self.phys2inter(tmp_coord_clean)
+        inter_coord_noised_update = torch.where(abs(inter_coord_noised-0.50)<0.50, inter_coord_noised, 2*inter_coord_clean-inter_coord_noised)
+        coord_noised_update = self.inter2phys(inter_coord_noised_update)
+        return coord_noised_update
+    
 def normalize_coord(coord, region: Region3D, nloc: int):
     """Move outer atoms into region by mirror.