diff --git a/dpgen2/op/collect_data.py b/dpgen2/op/collect_data.py
index b1e057e5..68f397ff 100644
--- a/dpgen2/op/collect_data.py
+++ b/dpgen2/op/collect_data.py
@@ -95,9 +95,9 @@ def execute(
 
         ms = dpdata.MultiSystems(type_map=type_map)
         for ii in labeled_data:
-            if len(list(ii.rglob("fparam.npy"))) > 0:
+            if ii and len(list(ii.rglob("fparam.npy"))) > 0:
                 setup_ele_temp(False)
-            if len(list(ii.rglob("aparam.npy"))) > 0:
+            if ii and len(list(ii.rglob("aparam.npy"))) > 0:
                 setup_ele_temp(True)
             ss = dpdata.LabeledSystem(ii, fmt="deepmd/npy")
             ms.append(ss)
diff --git a/dpgen2/op/run_lmp.py b/dpgen2/op/run_lmp.py
index 3ff366c9..cca2acfd 100644
--- a/dpgen2/op/run_lmp.py
+++ b/dpgen2/op/run_lmp.py
@@ -195,7 +195,8 @@ def execute(
                     with open("job.json", "w") as f:
                         json.dump(data, f, indent=4)
 
-        merge_pimd_files()
+            merge_pimd_files()
+
         ret_dict = {
             "log": work_dir / lmp_log_name,
             "traj": work_dir / lmp_traj_name,
diff --git a/dpgen2/op/select_confs.py b/dpgen2/op/select_confs.py
index cddcca55..e8ba891d 100644
--- a/dpgen2/op/select_confs.py
+++ b/dpgen2/op/select_confs.py
@@ -126,7 +126,7 @@ def validate_trajs(
             if tt is not None and mm is not None:
                 rett.append(tt)
                 retm.append(mm)
-                if optional_outputs:
+                if optional_outputs and any(optional_outputs):
                     oo = optional_outputs[i]
                     if oo is not None:
                         reto.append(oo)