Feat: support virtual atom

[wanghan-iapcm]

• support virtual atoms. the atoms with type -1 will be treated as virtual.
• the atomic contribution of virtual atoms is zero
• provide ret_dict["mask"] to indicate which atomic contribution is real (==1) or virtual (==0)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 77.49%. Comparing base (80b6900) to head (cd2be16).
Report is 1 commits behind head on devel.

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #3469      +/-   ##
==========================================
+ Coverage   77.47%   77.49%   +0.01%     
==========================================
  Files         431      432       +1     
  Lines       37138    37161      +23     
  Branches     1620     1620              
==========================================
+ Hits        28773    28797      +24     
+ Misses       7497     7496       -1     
  Partials      868      868              

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