q734738781/cp2k-pathway-calculations
skills/materials/cp2k-pathway-calculations/SKILL.md
Use this skill for source-grounded CP2K NEB and dimer path-refinement preparation through the single cp2k_prepare tool.
$ install --global
skillsauthnpx skillsauth add q734738781/CatMaster cp2k-pathway-calculationsInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
Security Scan Results
3 of 9 scanners reported clean
Some scanners were skipped, did not run, or reported a non-clean status. Review each row below.
3
Scanners Passed
9
Scanners in report
Clean
TrivyContainer and dependency vulnerability scanner
95%
Clean
SemgrepStatic code analysis for vulnerabilities
95%
Clean
mcp-scan (Snyk)Model Context Protocol security validation
95%
Skipped
Snyk (dep)Open source security scanning
50%
Skipped
Socket.devSupply chain security analysis
50%
Skipped
VirusTotalMulti-engine malware detection
50%
Skipped
CrowdStrikeAdvanced threat intelligence
50%
Skipped
OSV-ScannerOpen Source Vulnerability database check
50%
Skipped
OWASP Dep-Check
50%
Last scanned: Jun 7, 2026, 5:14 AM81.0s2 files scanned
SKILL.md
- 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
- Verify image count, atom count, and atom ordering before preparation.
- Use
cp2k_prepare(recipe="neb")for an existing image directory, orrecipe="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_prepareremote_submissionremote_submission_batchget_avail_remote_taskexecute
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 todynamics_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
- 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_preparefor CP2K conventional and pathway preparation.
Output Contract
Return:
- image or TS-guess source path
- prepared CP2K path stage path
manifest.jsonpath- 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/
Related Skills
q734738781/cp2k-aimd-preparation
data-ai
VerifiedTrustedCommunity
Use this skill for source-grounded CP2K AIMD preparation, restart staging, generic execution handoff through cp2k_execute, and run-health inspection.
9SKILL.mdUpdated Jun 7, 2026
q734738781/cp2k-vibrational-analysis
testing
VerifiedTrustedCommunity
Use this skill for CP2K vibrational-analysis preparation and task-specific thermochemistry parsing after an accepted stationary point.
7SKILL.mdUpdated Jun 7, 2026
q734738781/cp2k-electronic-properties
testing
VerifiedTrustedCommunity
Use this skill for CP2K DOS/PDOS, band-style, and population-analysis follow-up planning where parsing is task-specific and should usually be scripted.
7SKILL.mdUpdated Jun 7, 2026
q734738781/cp2k-dft-preparation
tools
VerifiedTrustedCommunity
Use this skill for source-grounded CP2K conventional DFT preparation in materials workflows: single-point, fixed-cell geometry optimization, cell optimization, frequency, and DOS-style stages.
7SKILL.mdUpdated Jun 7, 2026