enhance and add several Amber-related functions

[njzjz]

* move all constants into one file

• enhance amber functions
• add several functions

[njzjz]

It seems that there are many versions of unit converting constant...

[njzjz]

@amcadmus

[codecov-io]

Codecov Report

Merging #135 (61222a5) into devel (3443aec) will decrease coverage by 1.89%.
The diff coverage is 45.71%.

@@            Coverage Diff             @@
##            devel     #135      +/-   ##
==========================================
- Coverage   84.36%   82.47%   -1.90%     
==========================================
  Files          28       30       +2     
  Lines        3326     3400      +74     
==========================================
- Hits         2806     2804       -2     
- Misses        520      596      +76     

Impacted Files	Coverage Δ
dpdata/siesta/aiMD_output.py	97.43% <ø> (-0.05%)	⬇️
dpdata/system.py	75.47% <21.87%> (-4.67%)	⬇️
dpdata/amber/mask.py	31.57% <31.57%> (ø)
dpdata/amber/md.py	82.05% <68.29%> (-16.10%)	⬇️
dpdata/constant.py	100.00% <100.00%> (ø)
dpdata/cp2k/output.py	98.02% <100.00%> (ø)
dpdata/gaussian/log.py	100.00% <100.00%> (ø)
dpdata/gromacs/gro.py	97.91% <100.00%> (ø)
dpdata/qe/scf.py	96.84% <100.00%> (-0.07%)	⬇️
dpdata/qe/traj.py	85.00% <100.00%> (-0.32%)	⬇️
... and 6 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 3443aec...61222a5. Read the comment docs.

[amcadmus]

I do not see UT for the amber module nor the new methods added to the LabeledSystem. Please add.

[njzjz]

I am planning to split this PR into two PRs.

[codecov-commenter]

Codecov Report

Merging #135 (495cc13) into devel (3443aec) will increase coverage by 0.19%.
The diff coverage is 72.34%.

@@            Coverage Diff             @@
##            devel     #135      +/-   ##
==========================================
+ Coverage   84.36%   84.56%   +0.19%     
==========================================
  Files          28       29       +1     
  Lines        3326     3485     +159     
==========================================
+ Hits         2806     2947     +141     
- Misses        520      538      +18     

Impacted Files	Coverage Δ
dpdata/system.py	80.31% <56.79%> (+0.17%)	⬆️
dpdata/amber/mask.py	84.21% <84.21%> (ø)
dpdata/amber/md.py	97.46% <97.56%> (-0.68%)	⬇️
dpdata/vasp/outcar.py	96.26% <0.00%> (-0.04%)	⬇️
dpdata/cp2k/output.py	98.04% <0.00%> (+0.02%)	⬆️
dpdata/deepmd/comp.py	96.93% <0.00%> (+0.03%)	⬆️
dpdata/deepmd/raw.py	93.93% <0.00%> (+0.09%)	⬆️
dpdata/gromacs/gro.py	98.75% <0.00%> (+0.83%)	⬆️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 3443aec...495cc13. Read the comment docs.

[njzjz]

I do not see UT for the amber module nor the new methods added to the LabeledSystem. Please add.

ready to review

[amcadmus]

Could you please add UTs for pick_atom_idx, remove_atom_names and pick_by_amber_mask?

I understand that they are tested in TestAmberCorr, but the test is not so "unit". Once any bug happens in these methods, it would be not easy to locate them.

[njzjz]

I have split the unittests.