diff --git a/dpdata/utils.py b/dpdata/utils.py
index e008120e..07e10caa 100644
--- a/dpdata/utils.py
+++ b/dpdata/utils.py
@@ -77,8 +77,17 @@ def sort_atom_names(data, type_map=None):
     """
     if type_map is not None:
         # assign atom_names index to the specify order
+        if not set(data["atom_names"]).issubset(set(type_map)):
+            # delete the types where atom_numbs == 0
+            real_index = np.array(data["atom_numbs"]) > 0
+            real_map = list(np.array(data["atom_names"])[real_index])
+            assert set(real_map).issubset(set(type_map))
+            data["atom_numbs"] = list(np.array(data["atom_numbs"])[real_index])
+            idx = np.zeros(len(data["atom_names"]), dtype=int)
+            idx[real_index] = np.arange(len(real_map))
+            data["atom_names"] = real_map
+            data["atom_types"] = idx[data["atom_types"]]
         # atom_names must be a subset of type_map
-        assert set(data["atom_names"]).issubset(set(type_map))
         # for the condition that type_map is a proper superset of atom_names
         # new_atoms = set(type_map) - set(data["atom_names"])
         new_atoms = [e for e in type_map if e not in data["atom_names"]]