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

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

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@esoteric-ephemera esoteric-ephemera commented Oct 4, 2024 •
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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 and others added 17 commits September 3, 2024 16:16
@esoteric-ephemera esoteric-ephemera changed the title [WIP] Add NEB jobs / workflows [WIP] Add NEB, ApproxNEB jobs / workflows Oct 14, 2024
@esoteric-ephemera
temp name change ep_output --> ep_structures
7bee40b
@esoteric-ephemera
string dict keys rather than ints ; move pydantic typing out of type_…
e7b9390 
…checking block
@esoteric-ephemera
try to get optional job logic working / better naming
2ca71d5
@esoteric-ephemera
partial lint
9b496d5
@esoteric-ephemera
fix typing import
a99d482
@esoteric-ephemera
fix typing import
9aad2ec
@esoteric-ephemera
change image relax maker to use custodian double relax
ff864cc
@esoteric-ephemera
partial lint
105f7aa
@esoteric-ephemera
ensure no vasp_gam cmd sent to custodian doublerelaxation job
7a9fb93
@esoteric-ephemera
patch neb from endpoints job
2adb9cf
@esoteric-ephemera
fix document collation
433918f
@esoteric-ephemera
tweak approx neb, ensure neb interpolation is enum
3056ef9
@esoteric-ephemera
strip hostname in vasp neb postproces
491795e
@esoteric-ephemera
tweak output parsing
c55b2cd
@esoteric-ephemera
add VASP NEB tests
f69edbb
@esoteric-ephemera
partial lint
c2978c1
@esoteric-ephemera
add working approx neb test
f370324
@esoteric-ephemera
partial lint
29f5df7
@esoteric-ephemera
move some vasp schemas to emmet; modify approx neb to allow for minim…
fe16c70 
…um hop distance checks
@esoteric-ephemera
ruff
3bd358f
@esoteric-ephemera
flesh out ase neb jobs, add option to ApproxNeb to start from migrati…
04c6dad 
…on graph
@esoteric-ephemera
ApproxNEB --> ApproxNeb for consistent naming
c743c60
@esoteric-ephemera
ruff ruff ruff
68a87b0
@esoteric-ephemera
merge main / resolve conflicts
adec024
@esoteric-ephemera
default min_hop_distance for approxneb to be twice ionic radius
6980a49
@esoteric-ephemera
Merge remote-tracking branch 'upstream/main' into neb
d40b733
@esoteric-ephemera
unset host structure magmoms in approx neb endpoint calcs
cb23484
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@esoteric-ephemera @hmlli