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Bugfix: OTF parser, ASE md step, OTF checkpoint #214

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merged 69 commits into from
Aug 18, 2020
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YuuuXie
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@YuuuXie YuuuXie commented Aug 3, 2020

OTF

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.

Docs

  • Update the corresponding docstrings and tutorials

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codecov-commenter commented Aug 3, 2020

Codecov Report

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

Impacted file tree graph

@@               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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@YuuuXie YuuuXie changed the title [WIP] Bugfix: OTF parser, ASE md step, OTF checkpoint Bugfix: OTF parser, ASE md step, OTF checkpoint Aug 6, 2020
@YuuuXie YuuuXie marked this pull request as ready for review August 6, 2020 18:22
@stevetorr
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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).

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5 participants