cp2k-pathway-calculations

name: cp2k-pathway-calculations description: Use this skill for source-grounded CP2K NEB and dimer path-refinement preparation through the single cp2k_prepare tool. allowed-tools: "cp2k_prepare remote_submission remote_submission_batch get_avail_remote_task execute"

Overview

Use this skill for CP2K pathway refinement after endpoints, images, or transition-state guesses already exist. The only bound preparation tool is cp2k_prepare.

Quick Start

Verify image count, atom count, and atom ordering before preparation.
Use cp2k_prepare(recipe="neb") for an existing image directory, or recipe="dimer" for an existing transition-state guess.
Verify job.inp, manifest.json, and copied replica files.
Submit with remote_submission(task_name="cp2k_execute").
Parse barrier or mode evidence with a focused script; do not infer barriers from preparation alone.

Allowed tools

cp2k_prepare
remote_submission
remote_submission_batch
get_avail_remote_task
execute

Workflow

1. Validate pathway structures

NEB images must have identical atom counts and symbol ordering.
cp2k_prepare(recipe="neb") does not generate endpoints or interpolate images.
cp2k_prepare(recipe="dimer") starts from a user-provided or previously generated transition-state guess.

2. Prepare controlled CP2K path stages

For NEB, keep band_type, k_spring, nproc_rep, endpoint optimization, and max iterations explicit when they affect results.
For dimer, keep optimizer, max force, max iterations, and any provided dimer vector traceable.
Keep all pathway work in materials_worker; AIMD and trajectory work belong to dynamics_worker.

3. Analyze narrowly

Use a focused script to parse image energies, barrier, endpoint relaxation, and convergence.
Report exact files parsed and whether endpoints were fixed or optimized.

Method-critical defaults

Parameter priority: honor explicit user requirements first; otherwise choose CP2K pathway overrides from the system class and pathway objective; if that judgment remains uncertain, run a narrow literature or official documentation check before finalizing the override.
Do not add CP2K settings overrides just to restate the tool baseline; only override when the user, system class, task objective, or a checked source justifies it.
Pathway preparation is not evidence of a barrier.
Atom ordering mismatches invalidate the path.
Project policy: do not create a separate pathway-preparation tool; use cp2k_prepare for CP2K conventional and pathway preparation.

Output Contract

Return:

image or TS-guess source path
prepared CP2K path stage path
manifest.json path
submitted receipt/context if executed
parser artifact path and limitations after analysis

References

Local source note: references/cp2k_pathway_reference.md
CP2K NEB exercise: https://www.cp2k.org/exercises%3Acommon%3Aneb
CP2K MOTION/BAND manual: https://manual.cp2k.org/cp2k-2025_1-branch/CP2K_INPUT/MOTION/BAND.html
CP2K transition-state section: https://manual.cp2k.org/cp2k-2025_1-branch/CP2K_INPUT/MOTION/GEO_OPT/TRANSITION_STATE.html
CP2K manual index: https://manual.cp2k.org/