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Ase interface - add stress & tested OTF parser #107

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merged 53 commits into from
Nov 24, 2019
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@YuuuXie YuuuXie commented Oct 31, 2019

  1. fixed some bugs
  2. tested otf_parser on the ASE output file, unit test file is test_ase_setup/test_parser_otf.py
  3. Add stress for MGP, using the same formulation as our lammps pair style. So the unit test is to match MGP stress prediction in python with the stress prediction from lammps mgp pair style. unit test file is test_ase_setup/test_stress.py
    Note: since the lammps stress formula requires forces from pairs and triplets, if we want to implement stress for GP, we need to go into the kernel function, which is more complicated. So I just implemented for MGP now

close #86

YuuuXie and others added 25 commits October 14, 2019 15:43
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codecov-io commented Nov 4, 2019

Codecov Report

❗ No coverage uploaded for pull request base (master@a7aee43). Click here to learn what that means.
The diff coverage is 69.13%.

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@@           Coverage Diff           @@
##             master   #107   +/-   ##
=======================================
  Coverage          ?    54%           
=======================================
  Files             ?     31           
  Lines             ?   5055           
  Branches          ?      0           
=======================================
  Hits              ?   2730           
  Misses            ?   2325           
  Partials          ?      0
Impacted Files Coverage Δ
flare/mgp/splines_methods.py 59.25% <ø> (ø)
flare/mgp/utils.py 21.9% <0%> (ø)
flare/ase/otf_md.py 98.14% <100%> (ø)
flare/ase/logger.py 94.96% <100%> (ø)
flare/ase/otf.py 60.45% <34.04%> (ø)
flare/ase/calculator.py 81.31% <84.37%> (ø)
flare/mgp/mgp.py 98.33% <96.36%> (ø)

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@@ -4,7 +4,7 @@
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We should add the docs/build directory to the .gitignore

@YuuuXie YuuuXie merged commit 502da2e into master Nov 24, 2019
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ASE virial stress & test otf_parser for its output
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