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[WIP] Add NEB, ApproxNEB jobs / workflows #1007

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@esoteric-ephemera esoteric-ephemera commented Oct 4, 2024

Adding NEB workflows and schemas for VASP / ASE / MLFF. This hopefully brings atomate2 to full parity with the feature set of atomate

@hmlli is leading the port of ApproxNEB flows for VASP

Very open to suggestions, particularly for document schema structure

Key updates:

  • Generic NEB schemas (one for single-barrier/hop NEB, one for combined pathways)
  • Different VASP run logic / makers / validators for NEB jobs
  • Parsing of VASP output handled by new NebTaskDoc class in emmet

To-do:

  • Better parsing of NEB outputs (collated into container doc with analysis of barrier)
  • ASE NEB optimizer
  • Subclass ASE NEB for MLFF
  • Tests

@esoteric-ephemera esoteric-ephemera changed the title [WIP] Add NEB jobs / workflows [WIP] Add NEB, ApproxNEB jobs / workflows Oct 14, 2024
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codecov bot commented Dec 12, 2024

Codecov Report

Attention: Patch coverage is 6.21019% with 589 lines in your changes missing coverage. Please review.

Project coverage is 4.21%. Comparing base (4244da9) to head (3f1653e).
Report is 9 commits behind head on main.

Files with missing lines Patch % Lines
src/atomate2/common/jobs/approx_neb.py 0.00% 113 Missing ⚠️
src/atomate2/vasp/jobs/approx_neb.py 0.00% 94 Missing ⚠️
src/atomate2/vasp/jobs/neb.py 0.00% 86 Missing ⚠️
src/atomate2/vasp/flows/approx_neb.py 0.00% 50 Missing ⚠️
src/atomate2/ase/utils.py 20.00% 40 Missing ⚠️
src/atomate2/ase/neb.py 0.00% 37 Missing ⚠️
src/atomate2/common/flows/approx_neb.py 0.00% 32 Missing ⚠️
src/atomate2/forcefields/neb.py 0.00% 30 Missing ⚠️
src/atomate2/vasp/sets/approx_neb.py 0.00% 23 Missing ⚠️
src/atomate2/common/jobs/neb.py 0.00% 22 Missing ⚠️
... and 6 more
Additional details and impacted files
@@            Coverage Diff             @@
##             main   #1007       +/-   ##
==========================================
- Coverage   72.82%   4.21%   -68.61%     
==========================================
  Files         187     197       +10     
  Lines       13637   14242      +605     
  Branches     1370    1455       +85     
==========================================
- Hits         9931     601     -9330     
- Misses       3161   13610    +10449     
+ Partials      545      31      -514     
Files with missing lines Coverage Δ
src/atomate2/ase/md.py 77.71% <100.00%> (+2.71%) ⬆️
src/atomate2/vasp/flows/electrode.py 0.00% <0.00%> (-90.00%) ⬇️
src/atomate2/vasp/jobs/base.py 0.00% <0.00%> (-77.78%) ⬇️
src/atomate2/common/schemas/neb.py 73.68% <73.68%> (ø)
src/atomate2/vasp/sets/core.py 0.00% <0.00%> (-82.07%) ⬇️
src/atomate2/utils/testing/vasp.py 0.00% <0.00%> (-79.85%) ⬇️
src/atomate2/vasp/run.py 0.00% <0.00%> (-39.35%) ⬇️
src/atomate2/common/jobs/neb.py 0.00% <0.00%> (ø)
src/atomate2/vasp/sets/approx_neb.py 0.00% <0.00%> (ø)
src/atomate2/forcefields/neb.py 0.00% <0.00%> (ø)
... and 7 more

... and 160 files with indirect coverage changes

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