q734738781/transition-state-neb

transition-state-neb

Overview

Use this skill to generate NEB image directories, prepare NEB-ready and dimer-ready VASP roots, derive reaction-direction guesses, and hand off a valid pathway batch for execution. Use it for setup-focused NEB work, dimer refinement, or custom mode-generation branches. Do not use it when a standard endpoint-pair-to-barrier workflow is enough; prefer reaction-neb-analysis for that narrower path.

Quick Start

1. First choose the narrow branch: standard NEB barrier workflow, setup-only NEB, dimer-from-NEB, or dimer-from-mode.
2. Validate the initial and final structures before generating images, including atom-order consistency and whether the path is really one local elementary step.
3. Estimate a reasonable intermediate-image count before dispatch instead of defaulting blindly, preferably with estimate_neb_image_count.
4. Use make_neb_geometry to create the flat numbered image-file tree.
5. Use vasp_neb_prepare to assemble the NEB root with canonical support files and NEB-critical INCAR settings.
6. If switching from NEB to an official VASP improved dimer refinement, derive a raw reaction-direction text block first, then feed it into vasp_dimer_prepare.
7. Run the resulting NEB or dimer folders through the standard VASP batch execution path.

Allowed tools

• estimate_neb_image_count
• make_neb_geometry
• vasp_neb_prepare
• vasp_dimer_prepare
• make_dimer_mode_from_neb
• make_dimer_mode_from_mace
• vasp_execute_batch
• mace_neb_batch
• analyze_vasp_neb_results

Workflow

0. Choose the narrowest branch before doing setup

• Use reaction-neb-analysis when the task is simply “endpoint pair -> NEB dispatch -> barrier summary”.
• Use this skill when you need one of the wider branches: primitive NEB setup without full barrier reporting, official VASP improved-dimer preparation, dimer-mode extraction from NEB, or dimer-mode extraction from MACE finite differences.
• Do not mix NEB and dimer outputs inside one ambiguous run root; keep the branch identity explicit.

1. Build the image set from a valid endpoint pair

• make_neb_geometry validates the endpoint pair before interpolation.
• Prefer estimate_neb_image_count before choosing n_images so the count is tied to the actual periodic endpoint displacement rather than visual guesswork.
• The initial and final endpoints must use the same atom ordering. Do not assume the interpolator will repair reordered atoms for you.
• Check whether the pathway is one local elementary step or an artificially long migration. A single NEB is usually the wrong contract for long-range diffusion or transport across several equivalent sites.
• If the start and end structures differ by a long migration, remodel the final state onto the nearest symmetry-equivalent destination and compute that primitive hop first instead of forcing one very long band.
• When no better prior estimate exists, use this practical first guess for the intermediate-image count: n_images ≈ ceil(sqrt(sum_i ||Δr_i||^2) / 0.8 Å), where Δr_i is the per-atom displacement after the intended endpoint matching/PBC convention is fixed.
• Under periodic boundary conditions, compute Δr_i with the same minimum-image convention (mic=true) you intend to use for interpolation. Do not estimate from wrapped fractional coordinates by eye.
• For routine local events, prefer about 4-8 intermediate images unless the displacement heuristic gives a stronger reason.
• If that estimate asks for more than about 8 intermediate images, stop and re-check whether the task is really one local event or an unrelated long migration that should be decomposed.
• If the periodic root-sum-squared displacement exceeds about 6 Å, treat that as a warning that the path is probably too long for one primitive NEB.
• It writes a flat numbered image-file tree (00.vasp, 01.vasp, ...) under output_dir. This is the preferred shared geometry format because it can be consumed directly by mace_neb_batch.
• For high-throughput work, make_neb_geometry also supports input_root/output_root batch mode: input_root/task0/IS.vasp + FS.vasp -> output_root/task0/00.vasp....
• If output_dir already exists, overwrite=true is required to replace it.

2. Prepare the NEB VASP root

• vasp_neb_prepare keeps geometry as a separate primitive: it can either consume an endpoint pair or reuse an existing image tree.
• In image-tree mode, prefer a flat numbered file tree (00.vasp, 01.vasp, ...). Legacy numbered directories (00/POSCAR, 01/POSCAR, ...) are still accepted.
• In image-tree mode, the same task directory must contain IS_OUTCAR and FS_OUTCAR. Do the preprocessing copy explicitly before calling the tool.
• For high-throughput work, vasp_neb_prepare also supports input_root/output_root batch mode where each child task directory is one complete NEB task containing its image tree plus IS_OUTCAR and FS_OUTCAR.
• It enforces the core NEB settings; iopt must be one of 7, 2, or 1.
• It writes the resulting support files plus neb_incar_patch.json, which is the authoritative diff from the canonical support-file baseline.
• In patch_policy="safe", NEB-critical keys remain protected; use force only for intentional overrides.

3. Hand off to execution as a VASP batch

• Treat the NEB image tree as a prepared VASP input set.
• Prefer a two-stage pathway run when the saddle is not already well localized: first run plain NEB with climbing image disabled to coarse-converge the band, then restart from those images with CI-NEB enabled for saddle refinement.
• Do not enable climbing image in the first rough-convergence stage unless the task has a strong reason to skip directly to refinement.
• When NEB/TS should use a separate submission preset, call vasp_execute_batch with task_name="vasp_execute_neb" so it routes through the dedicated DPDispatcher task/resources config instead of the generic VASP preset.
• Prefer task_name="vasp_execute_neb" by default for NEB/TS runs: the generic vasp_execute path can still run, but it will use the generic VASP resource preset rather than the NEB-specific submission configuration.
• Report image count, INCAR patch path, and execution status together; launch status alone is not enough.
• If the task is only setup or mode preparation, say that explicitly instead of implying the barrier-analysis branch was also completed.

4. Close the loop with barrier extraction

• Use analyze_vasp_neb_results after collection to produce the barrier summary, profile CSV, and profile plot.
• If image energies are incomplete, report partial collection rather than inferring a barrier.
• If the energy profile shows wave-like multiple up/down oscillations instead of one localized saddle region, treat that as evidence that the band may contain one or more previously unrecognized metastable intermediates.
• In that case, inspect the suspect images as candidate intermediate states and consider splitting the long path into shorter primitive hops through those states rather than forcing one overextended NEB.

5. Prepare official VASP improved-dimer jobs with a raw reaction-direction text block

• Use vasp_dimer_prepare for the official VASP improved dimer method (IBRION=44).
• Treat it as a relax-style VASP setup with one special extra requirement: the raw reaction-direction text block.
• vasp_dimer_prepare internally performs the required per-atom 1/sqrt(mass) transformation and then appends the resulting normalized vectors to the end of POSCAR after a separating blank line, which is what official IBRION=44 reads.
• Do not pre-mass-normalize the mode before passing it into vasp_dimer_prepare, or you will double-apply the mass weighting.
• Use this path for the official VASP dimer line. Do not assume MODECAR is part of this workflow.

6. Derive a dimer direction from NEB when a TS-adjacent path is already available

• make_dimer_mode_from_neb takes one NEB image tree and uses the displacement between the two images adjacent to the chosen TS image as the raw reaction-direction guess.
• Prefer this when a converged or nearly converged NEB already exists and the barrier region is well localized.
• If no ts_image_index is provided, the tool defaults to the central non-endpoint image.
• This tool writes both a raw text block and a mass-normalized text block, but the raw text block is the one you should feed into vasp_dimer_prepare.

7. Derive a dimer direction from ASE/MACE finite differences when NEB guidance is not enough

• make_dimer_mode_from_mace uses ASE finite-difference vibrations with a MACE calculator to estimate candidate modes on a TS guess.
• Restrict the finite-difference region to the chemically active atoms whenever possible; do not vibrate an entire large slab unless the task explicitly requires it.
• The tool reports all frequencies it found and exports one selected raw mode.
• If there are multiple imaginary modes, do not blindly trust the most negative one. Choose the mode that matches the chemically meaningful reaction coordinate.
• If no imaginary mode appears, the exported lowest-frequency mode is only a heuristic initial dimer direction.

8. Use VASP finite-difference frequencies only as a targeted local check, not a brute-force whole-slab default

• VASP finite-difference frequencies can also provide a dimer direction, but this is usually expensive.
• If you go this route, restrict the frequency job to the active reaction center and nearby atoms instead of the full slab whenever the scientific objective allows it.
• If you copy a mode from a VASP OUTCAR, extract the ordinary raw dx dy dz block into a text file and pass that text file into vasp_dimer_prepare. Do not feed the already mass-divided Eigenvectors after division by SQRT(mass) block into the tool.

9. For MACE NEB, use the dedicated managed tool instead of ad hoc scripts

• Prefer mace_neb_batch for managed MACE NEB work via DPDispatcher.
• The expected input contract is explicit task directories: either one task directory directly, or a batch root containing task0/, task1/, ... where each task directory contains flat numbered image files such as 00.vasp, 01.vasp, ...
• Do not create deeper nested task trees under a task directory.
• mace_neb_batch writes one task-level output directory per task, with final converged images as top-level 00.vasp, 01.vasp, ... plus a summary.json and shared artifacts like image_energies.csv, profile.png, and neb.traj.
• For MACE-driven path optimization, keep default_dtype=float64 by default. Only drop to float32 when the task is explicitly a cheaper exploratory run and the reduced numerical rigor is acceptable.

Method-critical defaults

• Keep endpoint preparation, image generation, and execution settings scientifically consistent across the whole pathway calculation.
• Do not treat launch success as pathway validity; evidence must include image count, INCAR patch, and outcome diagnostics.
• If the workflow does not require dimer refinement or custom mode logic, do not use this broader skill by default; the narrower reaction-neb-analysis route is easier to audit.
• Treat plain-NEB -> CI-NEB as the default convergence pattern for pathway searches: coarse-converge the band without climbing image first, then refine the saddle with climbing image enabled.
• When choosing NEB interpolation counts for routine runs, prefer small image counts such as 3, 4, 5, or 6 unless the pathway is clearly too sharp for that range.
• Use the displacement-norm heuristic above when the correct image count is not obvious, rather than guessing from cell size or visual intuition alone.
• If the heuristic suggests >8 intermediate images, treat that as a warning sign for a non-primitive long migration and reconsider the endpoint modeling before dispatch.
• If a computed band still develops a wave-like profile with several local minima/maxima, interpret that as a search hint for hidden intermediates and a cue to decompose the pathway.
• Treat default_dtype=float64 as the default for MACE geometry/path optimization. If a run intentionally uses float32 for throughput, report that choice explicitly with the execution evidence.
• For CI-NEB / climbing-image runs, prefer an odd number of intermediate images so there is a natural central image to climb.
• For plain NEB without climbing image, prefer an even number of intermediate images when the path is otherwise symmetric and no single central climbing image is needed.
• For official VASP dimer jobs, keep the electronic-structure footing aligned with the relax campaign and treat the appended dimer direction as the only special input.
• Mass weighting changes the direction, not just the scale. Never skip the per-atom 1/sqrt(mass) correction when converting a raw vibrational mode into a dimer direction.
• When several imaginary modes exist, the correct reaction-direction guess is the chemically meaningful one, not automatically the largest-magnitude imaginary mode.

Output Contract

Return:

• branch label (neb_setup, neb_run, dimer_from_neb, dimer_from_mace, or similar)
• NEB image root
• image count
• INCAR path and patch JSON path
• execution evidence path(s) if the run was dispatched
• For dimer work, also return the raw mode text path, the dimer-ready POSCAR path, and enough evidence to show which mode-selection logic was used.

References

• Pair this skill with vasp-batch-execution for dispatch and rerun handling instead of inventing a separate NEB execution path.
• Use reaction-neb-analysis when the images are finished and you need barrier extraction and profile artifacts.