Some update alignment of code.

[floatingCatty]

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

[floatingCatty]

1. The LMDB dataset support. After refactoring the AtomicData option in info.json, the reading of the LMDB dataset will also be affected, but the change has not been made.

2. Test function. The test function is not been aligned with the code development for a long time. But users, from my experience, usually raise a similar request about how to evaluate the error of a model. Using API is too complex for start-up users, so an alignment test should be done soon.

3. The run option still uses the cutoff preset in AtomicData, which should align with the train to use the rcut load from the model.