Fix energy jumps occur in rt-TDDFT calculations

[ESROAMER]

Reminder

• Have you linked an issue with this pull request?
• Have you added adequate unit tests and/or case tests for your pull request?
• Have you noticed possible changes of behavior below or in the linked issue?
• Have you explained the changes of codes in core modules of ESolver, HSolver, ElecState, Hamilt, Operator or Psi? (ignore if not applicable)

Linked Issue

Fix #6778

What's changed?

To fix the discontinuity caused by ions crossing boundaries, an additional phase must be added to the relevant matrix each time a crossing occurs. Here are the results after applying the fix.

Any changes of core modules? (ignore if not applicable)

An additional member variable boundary_shift was added to the class Atom to track ion boundary crossings.

[mohanchen]

Nice job!

[AsTonyshment]

👍

[mohanchen]

LGTM