tako.transitionState Settings

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tako.transitionState

Runs a fixed combined CI-NEB, optional dimer, and optional vibration-count workflow. A resolved result requires stage-specific convergence checks and does not expose the band, barrier, full modes, or restart state.

Signature: await tako.transitionState(initialStructure, { calculator, properties, transitionStateFinalStructure, transitionStateImageCount, transitionStateNebMaxSteps, transitionStateDimerMaxSteps, transitionStateFmaxEvPerAngstrom, transitionStateMaxstepAngstrom, transitionStateSpringConstant, transitionStateVibrationCheck })

Theory

• A transition state is a first-order saddle on the potential energy surface: a maximum along the reaction coordinate and a minimum in every orthogonal direction, with exactly one imaginary vibrational frequency.
• The combined search linearly interpolates Cartesian endpoint positions, runs improved-tangent climbing-image NEB from step one with a static optimizer, then optionally refines the highest interior image with a hardcoded BFGS dimer initialized from the band tangent.
• The optional fixed 0.01-bohr two-point vibration check counts projected internal imaginary modes. It runs even when NEB or dimer reports nonconvergence, and the public result does not return mode vectors for connectivity verification.

Usage Notes

• Provide transitionStateFinalStructure with the same atoms in the same order as the initial structure, exactly as for tako.reactionPath.
• The initial endpoint supplies cell, PBC, constraints, charge, and spin for every image. The final endpoint contributes positions and element order; equivalent-atom mapping and matching cell/constraints are caller invariants.
• Set transitionStateDimerMaxSteps: 0 to skip dimer refinement and keep the NEB saddle estimate. The visible UI cannot select zero.
• Require result.neb.converged, non-null converged result.dimer, and result.vibrations.imaginaryModes === 1 separately. Completion alone is not a convergence or first-order-saddle predicate.
• The one returned frame/final atoms contain final saddle geometry, but their/top-level energy and fmax are NEB values. Run a separate single point for coherent refined-saddle scalars.

Settings

Example

const initial = await tako.input("input/reactant.extxyz");
const final = await tako.input("input/product.extxyz");
const calculator = tako.calculator.gfn2({ dispersion: "d4" });
const result = await tako.transitionState(initial, {
  calculator,
  transitionStateFinalStructure: final,
  transitionStateVibrationCheck: true,
});
await tako.output("output/transition-state.json", result);

Result

Transition-state summary with NEB and optional dimer stage scalars, final saddle structure, minimal vibration/quality summaries, and one hybrid compatibility frame. No NEB path, barrier, optimizer trace, full frequencies/modes, coherent refined-saddle energy, settings record, or restart state is returned.

Errors and Promise Behavior

• Rejects when the final structure is absent, atom counts differ, or element symbols differ at any index. It does not reject mismatched cell/PBC/constraints or swapped equivalent atoms.
• Calculator, NEB, dimer, or vibration execution failure rejects the whole promise. No structured earlier-stage result is exposed because the combined call uses no event sink.
• NEB or dimer numerical nonconvergence does not reject and does not stop later stages; inspect both stage flags explicitly.
• Cancellation terminates the worker and exposes no band, saddle checkpoint, optimizer state, dimer orientation, or vibration cache. A retry starts from endpoint interpolation.
• Frames or derived workspace artifacts must not be mistaken for returned fields: the public object contains one saddle frame only and no barrier/path/vibration artifacts.