Fix bugs related to lammps PIMD (#266)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **Bug Fixes**
- Improved control flow for LAMMPS task execution by adjusting file
merging process.
- Enhanced validation of optional outputs to ensure they contain valid
values.
	- Added checks to prevent errors when validating file paths.

- **Style**
- Improved code readability with formatting adjustments and additional
newlines.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: zjgemi <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Han Wang <[email protected]>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

Author: 4 people

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)

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,

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)