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

cp2k-pathway-calculations

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

1. Verify image count, atom count, and atom ordering before preparation.
2. Use cp2k_prepare(recipe="neb") for an existing image directory, or recipe="dimer" for an existing transition-state guess.
3. Verify job.inp, manifest.json, and copied replica files.
4. Submit with remote_submission(task_name="cp2k_execute").
5. 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/