support assigning 'type_map' for mixed_type (#540)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

dpdata/deepmd/mixed.py

@@ -46,6 +46,17 @@ def _load_set(folder, nopbc: bool):
 def to_system_data(folder, type_map=None, labels=True):
     # data is empty
     data = load_type(folder)
+    old_type_map = data["atom_names"].copy()
+    if type_map is not None:
+        assert isinstance(type_map, list)
+        missing_type = [i for i in old_type_map if i not in type_map]
+        assert (
+            not missing_type
+        ), f"These types are missing in selected type_map: {missing_type} !"
+        index_map = np.array([type_map.index(i) for i in old_type_map])
+        data["atom_names"] = type_map.copy()
+    else:
+        index_map = None
     data["orig"] = np.zeros([3])
     if os.path.isfile(os.path.join(folder, "nopbc")):
         data["nopbc"] = True
@@ -63,7 +74,12 @@ def to_system_data(folder, type_map=None, labels=True):
         nframes = np.reshape(cells, [-1, 3, 3]).shape[0]
         all_cells.append(np.reshape(cells, [nframes, 3, 3]))
         all_coords.append(np.reshape(coords, [nframes, -1, 3]))
-        all_real_atom_types.append(np.reshape(real_atom_types, [nframes, -1]))
+        if index_map is None:
+            all_real_atom_types.append(np.reshape(real_atom_types, [nframes, -1]))
+        else:
+            all_real_atom_types.append(
+                np.reshape(index_map[real_atom_types], [nframes, -1])
+            )
         if eners is not None:
             eners = np.reshape(eners, [nframes])
         if labels: