Feat pt: Support multi structures input for single frame

[Chengqian-Zhang]

Support multi structures input for one frame:

background: When we predict the properties of small molecules, sometimes multiple 3D conformations are generated from the SMILES format structure, but their targets are the same. In each epoch we would like to pick only one of the 3D configurations as input.

Impletation: When the file "multistru" is present in the data folder (like nopbc), "coord.npy" can be written in the format (nframe * struc_num * natom * 3), where struc_num is the number of 3D conformations for each structure.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 72.91667% with 13 lines in your changes are missing coverage. Please review.

Project coverage is 77.47%. Comparing base (2851fb9) to head (fcce4df). Report is 1 commits behind head on devel.

Files	Patch %	Lines
deepmd/utils/data.py	76.19%	10 Missing :warning:
deepmd/pt/utils/neighbor_stat.py	50.00%	3 Missing :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #3566      +/-   ##
==========================================
- Coverage   77.49%   77.47%   -0.02%     
==========================================
  Files         432      432              
  Lines       37164    37185      +21     
  Branches     1620     1620              
==========================================
+ Hits        28801    28810       +9     
- Misses       7495     7507      +12     
  Partials      868      868              

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[Chengqian-Zhang]

@wanghan-iapcm Different 3D conformations of a molecule have exactly the same label, and each epoch takes one of all 3D conformations of this molecule. Because molecule may only has SMILES, the exact 3D sturcture is unknown.

[wanghan-iapcm]

@wanghan-iapcm Different 3D conformations of a molecule have exactly the same label, and each epoch takes one of all 3D conformations of this molecule. Because molecule may only has SMILES, the exact 3D sturcture is unknown.

I do not find any reason why different 3D configurations cannot be place in one batch.