Refine and Verify a Transition State

The Transition state (dimer + vibration check) workflow accepts atom-matched initial and final structures, constructs a linearly interpolated climbing-image band, refines its highest interior image with a dimer search, and performs a fixed numerical vibration check. The visible dialog shares controls with standalone NEB and dimer operations, but the current combined runtime consumes only a subset. This page identifies that boundary exactly.

The saddle-point equations, dimer rotation and translation, Hessian index, verification criteria, and implementation limitations are developed in Transition States and the Dimer Method. JavaScript belongs in Transition-State Search with Tako Script.

Prepare the endpoints

Optimize the initial and final states with the same calculator, charge, unpaired-electron count, cell convention, and constraints. The two structures must have the same number of atoms and the same element at every array index. Tako checks those two conditions, but it does not verify atom IDs, chemical correspondence between equivalent atoms, matching cells, matching periodicity, matching constraints, or a continuous periodic mapping.

The combined workflow clones the initial structure for every band image and interpolates Cartesian positions toward the final coordinates. The initial cell, periodicity, constraints, charge, and spin therefore govern the entire band; the final structure supplies only the target positions and element sequence. Map periodic images consistently and make the two endpoint cells identical before opening the dialog. A structure carrying any cell is currently promoted to three-dimensional periodicity by the calculation input builder, so partially periodic slab or chain semantics are not preserved.

Open Reaction Path Setup

Select the initial structure, then choose Calc → Reaction Path / TS. The dialog title is Reaction Path Setup. In Workflow, select Transition state (dimer + vibration check).

The description below the selector states that the workflow performs CI-NEB, dimer refinement, and a vibration check. The vibration stage is enabled by selecting this workflow rung; there is no separate vibration checkbox or finite-difference control in the dialog.

The adjacent CI-NEB → Dimer refine (true saddle) rung calls the same combined transition-state operation with the vibration check disabled. It is not a direct standalone dimer run. The standalone dimer operation exists internally but has no public tako.dimer call.

Select the images

In Images, set First image and Final image to the prepared endpoint projects. Total images includes both endpoints and is normalized to the range 3–21. The combined operation fixes the endpoints and refines the interior images.

Inspect both structures after selection. The interface does not display an atom-mapping table and cannot detect an exchange between equivalent atoms. A smooth energy profile cannot repair incorrect atom correspondence.

Configure the combined NEB stage

The NEB section is shared with the standalone reaction-path workflow. For the combined transition-state operation, only four numerical values from this section reach the runtime:

The following visible choices are ignored by the combined operation:

Climbing is active from the first combined NEB step. There is no ordinary-NEB preclimb phase. This differs from the staged CI-NEB behavior documented for the standalone reaction-path command.

The combined runtime continues to the dimer stage even if the NEB budget ends with converged: false. A completed job therefore does not imply that its band converged; inspect the returned neb.converged and residual explicitly.

Configure Dimer refinement

The Dimer refinement region appears for the dimer and transition-state workflow rungs.

In the current combined workflow, only Max dimer steps reaches transitionStateDimerMaxSteps. The interface default is 120 steps because this region uses the standalone-dimer defaults; the direct Tako Script transition-state default is 50. The input has a minimum of 1, so the interface cannot request the Script-only zero-step branch that skips dimer refinement.

Every other visible value in this region is currently ignored by the combined operation:

This mismatch is a current product limitation. Record the effective constants above with the result; only Max dimer steps controls the combined calculation.

The dimer begins at the highest-energy interior image selected after the NEB stage. If the dimer budget is positive, the refined geometry replaces that image as the saddle structure. Dimer nonconvergence does not reject the calculation and does not prevent the vibration stage.

Start the workflow

Choose Start. The Console announces one combined “NEB + dimer + vibration check” workflow even for the dimer-only rung where the vibration check is disabled. It does not stream per-step NEB, dimer, or vibration progress. A calculation error in any stage rejects the operation; no structured result from earlier stages is retained.

Cancellation terminates the worker. There is no band checkpoint, dimer orientation, optimizer state, or vibration cache that can resume the job. A retry reconstructs the band from the endpoints.

Interpret the vibration check

For the transition-state rung, Tako runs a two-point central finite-difference vibration calculation with a displacement of 0.01 bohr (approximately 0.00529177 Å). These parameters are fixed and not visible in Reaction Path Setup.

The calculation excludes fully fixed atoms. Partially constrained atoms remain in the active atom list and are displaced along all three Cartesian axes while constrained force components are zeroed; their numerical Hessian can therefore be distorted. Remove partial constraints or validate their effect before using the imaginary-mode count as a saddle classification.

The public result reports only whether any imaginary mode exists, the number of imaginary modes, and the lowest signed frequency. It does not return the full frequency list, normal-mode vectors, Hessian, finite-difference settings, or a trajectory for following the mode. hasImaginaryMode: true means one or more, not exactly one. A first-order saddle requires imaginaryModes === 1, and chemical connectivity still requires an independent mode-following or displacement check outside this combined result.

The vibration calculation runs even when NEB or dimer reports nonconvergence. Its successful completion does not retroactively validate either preceding stage.

Open the outputs

The combined calculation creates the ordinary input snapshot plus these output artifacts:

The result does not contain the NEB path images, individual path energies, barrier, reaction energy, per-step traces, full vibration spectrum, normal mode, or restart data.

The sole frames[0] object has a serious stage-coherence boundary: its geometry is the final saddle geometry, but its step, energy, and force maximum are copied from the NEB stage. Top-level atoms likewise describe the final saddle, whereas top-level final_energy_ev and final_fmax_ev_per_angstrom are NEB values. Do not pair those scalars with the refined geometry as a dimer single-point result. Run a separate single point on the saddle geometry when a coherent energy/force record is required.

saddle_image is the zero-based index of the highest NEB image selected before dimer refinement. It remains a band index, not a statement that the final dimer geometry occupies an exposed band trajectory.

Apply the acceptance gates

Read each stage separately:

The field saddle_quality.nebResidual is currently left in the engine’s internal Hartree/bohr convention even though its name has no unit. Use neb.final_fmax_ev_per_angstrom for the public NEB residual in eV/Å. saddle_quality.dimerFmax is converted to eV/Å. Do not compare the two unlabeled quality fields numerically.

Diagnose failures

Preserve the two endpoint structures, atom mapping, initial cell/PBC/constraints, calculator checkpoint, workflow rung, effective combined values, raw result, separate saddle single point, and independent connectivity evidence. The exhaustive field-level contract is generated in tako.transitionState Settings.