trajectory-analysis

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

1. Locate the result directory or trajectory file.
2. Use md_trajectory_summary for frame counts, final frame export, restart-file presence, generic thermo/log evidence, CP2K .ener files, and LAMMPS RDF/MSD tables.
3. Use analyze_trajectory for ASE-readable trajectories when MSD/RDF artifacts are requested.
4. Write a focused parser under scripts/ for system-specific residence, reaction, adsorption, or free-energy questions.

Allowed tools

• md_trajectory_summary
• analyze_trajectory
• lammps_log_summary
• cp2k_output_summary
• execute

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/