Fix: set the maximal cutoff radius of orbital as the lower bound of search_radius in neighboring search tasks carried in out_mat_l

[kirk0830]

Linked Issue

Fix #6641

What's changed?

• use the maximal cutoff radius of orbitals as the default search radius in neighboring atoms searching, because the parameter search_radius is always left unset (-1), this caused the too rough evaluation on neighboring list
• include the origin atom itself in calculation of <a|L|b> matrix (this is a bug!)
• add more annotations
• polish the output to avoid potential misunderstanding and confusion

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

• no

[mohanchen]

LGTM