q734738781/trajectory-analysis
skills/dynamics/trajectory-analysis/SKILL.md
Use this skill for generic CP2K/LAMMPS trajectory and run-health checks and for deciding when task-specific trajectory parsing is required.
$ install --global
skillsauthnpx skillsauth add q734738781/CatMaster trajectory-analysisInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- trajectory-analysis
- description:
- Use this skill for generic CP2K/LAMMPS trajectory and run-health checks and for deciding when task-specific trajectory parsing is required.
- allowed-tools:
- md_trajectory_summary analyze_trajectory lammps_log_summary cp2k_output_summary execute
trajectory-analysis
Overview
Use this skill for generic MD health summaries. It is not a replacement for task-specific mechanistic analysis.
Quick Start
- Locate the result directory or trajectory file.
- Use
md_trajectory_summaryfor frame counts, final frame export, restart-file presence, generic thermo/log evidence, CP2K.enerfiles, and LAMMPS RDF/MSD tables. - Use
analyze_trajectoryfor ASE-readable trajectories when MSD/RDF artifacts are requested. - Write a focused parser under
scripts/for system-specific residence, reaction, adsorption, or free-energy questions.
Allowed tools
md_trajectory_summaryanalyze_trajectorylammps_log_summarycp2k_output_summaryexecute
Workflow
1. Start with health, not interpretation
- Check frame count, atom count, final frame export, time span if recoverable, log completion, energy/thermo files, and restart files.
- Inspect temperature, energy, and pressure drift before interpreting a trajectory.
2. Keep observables explicit
- RDF and MSD require explicit species or group choices; if they were produced by in-run LAMMPS computes, summarize file presence and numeric rows before interpretation.
- Mechanistic labels such as diffusion path, desorption event, residence time, or reaction coordinate usually require a task-specific script.
Method-critical defaults
- Generic summaries may prove that a run produced data; they do not prove equilibration or scientific convergence.
- Do not infer barriers or free energies from raw MD without the appropriate method and parser.
Output Contract
Return:
- trajectory file path
- summary JSON path
- log or CP2K output summary path if available
- any task-specific parser path
- explicit limitations
References
- Local source note:
references/md_trajectory_outputs_reference.md - LAMMPS output how-to: https://docs.lammps.org/Howto_output.html
- LAMMPS compute rdf: https://docs.lammps.org/compute_rdf.html
- LAMMPS compute msd: https://docs.lammps.org/compute_msd.html
- CP2K MOTION/MD: https://manual.cp2k.org/cp2k-2025_1-branch/CP2K_INPUT/MOTION/MD.html
- lammpsio docs: https://lammpsio.readthedocs.io/
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