Some update alignment of code.

### Describe Current Status and Possible Solution

The code of DeePTB is developed fastly. So some of its modules, after modification, have been updated to be more convenient for usage. However, there exist other modules that needed to be modified to align with the change, while some of them haven't. This issue tracks the modification alignment needed.

### Additional Context

_No response_

No files, modules, tests, or entry points are identified in the issue. Start by reviewing recent module changes and their callers to identify inconsistent interfaces; done means the affected modules are aligned, with regression coverage confirmed.

Written by the indexing model from the issue text.