[kfir4444]

What

A double-ended TS search on an ASE calculator: an NEB TS-guess adapter (ase_neb) that runs on the potential of the TS-guess level, e.g. an MLIP. Plus a fix to the near-attack folding of H-shift guesses, which the adapter also uses.

Stack: third of four PRs on #1072: worker (#1073) ← Hessians (#1075) ← NEB (this one) ← TS scans (#1077).

Changes

1. H-shift folding moved only a donor's direct neighbors. get_near_attack_xyz() rotated the donor's neighbors but left, e.g., a methyl's H atoms behind, which broke the folded guesses of the n-butylperoxy 1,5-H shift. The whole donor side now turns, and a ring bond is not turned about.
2. An ASE NEB adapter (ase_neb). ARC had no double-ended TS search on an ASE calculator. The adapter relaxes NEB, DyNEB or AutoNEB bands (ase.mep) on the TS-guess level's potential and returns the highest interior image as a TS guess, which ARC optimizes and checks like any other.
   • Endpoints come from the optimized reactant and product geometries in a common atom order, Kabsch-aligned. Bimolecular fragments are placed 3 Å apart, and intramolecular H transfers are folded into a near-attack conformation first.
   • Several atom maps give several bands.
   • It runs for reactions with one single-molecule side (ase_neb_settings).

Checks

• Production: in the benchmark's unimolecular set, rerun with it (and with the TS-scan fixes of Keep ASE TS rotor scans on the saddle, batch their force calls, and check that they keep the reactive bonds #1077), it gave verified TSs for 7 of the 8 reactions the first UMA-S run had not verified and 4 of the 6 UMA-M ones. These include the n-butylperoxy 1,5-H shift, whose folded Z-matrix guesses had been broken (1).
• Tests, locally: as for Run ASE jobs through a persistent worker that keeps models loaded #1073, plus ts/ase_neb_test.py and linear_utils/isomerization_test.py.

Tests

• test_get_near_attack_xyz_keeps_substituents_on_the_donor (1)
• test_run_neb (EMT; NEB, DyNEB, AutoNEB, two bands, mismatched endpoints); ase_neb_test.py: endpoints of dissociations, isomerizations and an HO₂ elimination, Kabsch alignment, near-attack folding, the level, the input file; test_has_one_molecule_side; test_process_completed_tsg_queue_jobs_from_an_ase_output (2)