mat-diffusion-analysis

What problem does it solve?

It calculates ionic diffusion coefficients and activation energies from atomistic molecular dynamics (MD) trajectories, turning raw trajectory data into temperature-dependent transport parameters.

Core Features & Use Cases

• Diffusivity & MSD extraction: Computes mean square displacement (MSD) and diffusivity for a chosen atomic species from ASE .traj trajectories using pymatgen’s DiffusionAnalyzer.
• Equilibration-aware analysis: Ignores an initial equilibration period (ignore_ps) so the fitted diffusive regime reflects long-time behavior.
• Arrhenius activation-energy fitting: Combines per-temperature diffusivity results and performs a weighted Arrhenius fit to obtain activation energy and extrapolated room-temperature conductivity.
• Deterministic, reproducible scripts: Provides ready-to-run Python scripts and standard output artifacts (plots and JSON results) for downstream reporting.

Quick Start

Run diffusion analysis on an MD trajectory by executing python .agents/skills/mat-diffusion-analysis/scripts/analyze_diffusion.py results/md_600K/trajectory.traj --species Li --temperature 600 --ignore_ps 5.0 --output_dir results/md_600K.