Bugfix: OTF parser, ASE md step, OTF checkpoint

[YuuuXie]

OTF

• close issue: OTF parser fails at "Cutoffs: {'twobody': 3.0, 'threebody': 5.0}" #205 OTF parser fails at cutoffs
• close issue: otf parser tests (test_parse_otf.py) is based on a fixed output file #10 test_parser_otf.py is based on a fixed file
  • added a function in test_otf_parser at the end of test_otf and test_ase_otf, making sure that OtfAnalysis and make_gp will not report error
  • test_parser_otf.py is not yet changed, since it's based on an old file, which is a validation of backward compatibility
• OTF checkpoint: close issue: OTF restart module/method #49 , How to resume DFT calculation #212

ASE

• One bug with ASE MD. The ASE's md engine has a function called step(), which does something like:

def step(self):
    f = atoms.get_forces()
    new_positions = function_update_positions(forces)
    atoms.set_positions(new_positions)
    new_f = atoms.get_forces()
    return new_f

and we are using this step function in otf. The consequence is when the atoms' calculator is DFT, both f and new_f will be calculated by the DFT calculator, but we don't want the new_f to be. I changed the md_step function in ase/otf.py to adapt to this.

Note: when using NPT the adaptation is not applied if the pfactor is not set to None, this will be left as a TODO.

• In Structure, the functions from_ase_atoms & to_ase_atoms now also transfer forces, energy, stress. close Structure.from_ase_atoms does not copy forces #158
• ASE OTF compatibility with ASE Trajectory. close [ASE interface] Logger's compatibility with ASE Trajectory #137
  • Add note here, saying that this is not recommended, not tested thoroughly

Docs

• Update the corresponding docstrings and tutorials

[codecov-commenter]

Codecov Report

Merging #214 into development will decrease coverage by 0.13%.
The diff coverage is 94.01%.

@@               Coverage Diff               @@
##           development     #214      +/-   ##
===============================================
- Coverage        54.84%   54.70%   -0.14%     
===============================================
  Files               47       47              
  Lines            10613    10609       -4     
===============================================
- Hits              5821     5804      -17     
- Misses            4792     4805      +13     

Impacted Files	Coverage Δ
flare/gp.py	89.90% <ø> (-0.21%)	⬇️
flare/mgp/mgp.py	91.27% <ø> (-1.76%)	⬇️
flare/ase/atoms.py	93.22% <50.00%> (-4.90%)	⬇️
flare/mgp/mapxb.py	84.23% <75.00%> (-0.44%)	⬇️
flare/struc.py	90.66% <78.57%> (-1.15%)	⬇️
flare/output.py	93.45% <93.33%> (-1.49%)	⬇️
flare/otf.py	91.30% <94.52%> (+0.73%)	⬆️
flare/ase/otf.py	88.27% <94.59%> (+4.27%)	⬆️
flare/ase/calculator.py	65.71% <95.00%> (+10.81%)	⬆️
flare/otf_parser.py	95.30% <97.11%> (+4.53%)	⬆️
... and 8 more

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[stevetorr]

Just a comment but the body of this PR is really beautifully formatted, nice job! I want to steal some of these ideas (I like the check boxes).