args: add init_bulk_jdata_arginfo and init_surf_jdata_arginfo

[HuangJiameng]

Arginfo and two examples on init have been updated. But there are still a few problems.

1. How does parameter "out_dir", "type_map", "atom_masses" work in init process?
2. Which kind of example does al.json belong to? Should "stages" be added into it?
3. I am unfamiliar with parameter "mid_point", "lmp_cmd" in cu.surf.hcp.111.json, please add it into arginfo.
4. Is parameter "super_cell" necessary when from_poscar is True?
5. Explanations for "head_ratio" and "vacuum_numb"?

[njzjz]

I am not familiar with these modules as well. You may request other contributors' reviews.

[njzjz]

Also, they should be added to the documentation.

[hongriTianqi]

Arginfo and two examples on init have been updated. But there are still a few problems.

1. How does parameter "out_dir", "type_map", "atom_masses" work in init process?

As with "atom_masses", ABACUS needs to be fed with an atomic mass list when generating supercells, because the STRU file needs element's masses. This is done in the stru_ele function in gen.py.

[codecov-commenter]

Codecov Report

Base: 38.16% // Head: 38.35% // Increases project coverage by +0.19% 🎉

Coverage data is based on head (720eff7) compared to base (6347ba8).
Patch coverage: 93.65% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #936      +/-   ##
==========================================
+ Coverage   38.16%   38.35%   +0.19%     
==========================================
  Files          99       99              
  Lines       17885    17947      +62     
==========================================
+ Hits         6825     6884      +59     
- Misses      11060    11063       +3     

Impacted Files	Coverage Δ
dpgen/data/surf.py	66.46% <0.00%> (ø)
dpgen/data/arginfo.py	96.34% <100.00%> (+8.84%)	⬆️
dpgen/generator/run.py	61.95% <0.00%> (-0.06%)	⬇️

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[njzjz]

Can you add the parameter document?

[njzjz]

Can you add the parameter document?

Do you need help?

[HuangJiameng]

Can you add the parameter document?

Do you need help?

Sorry for missing the message. Isn't parameter document added in doc_<param-name> in arginfo?

[njzjz]

Refer doc/init/init-bulk-mdata.rst.

[njzjz]

Adding TOC?

[Vibsteamer]

best wishes to your endeavors

[HuangJiameng]

best wishes to your endeavors

Thank you for your comprehensive review and suggestions!