mat-diffusion-analysis

Diffusion Analysis

Goal

To accurately calculate the ionic diffusivity ($D$) and activation energy ($E_a$) of specific atomic species in a material using Molecular Dynamics (MD) trajectories and the Arrhenius relation: $D(T) = D_0 \exp\left(-\frac{E_a}{k_B T}\right)$.

Instructions

1. MD Preparation: Run NVT or NPT MD simulations at multiple temperatures (typically 4-6 points between 600K and 1200K).

   • Use the run_md tool from a relevant potential skill (e.g., mace or matgl).
   • Batch Processing: You can pass a directory or a list of CIF paths to structure_data to run multiple MD simulations concurrently via the MCP tool.
   • Supercell Expansion: Ensure supercells are sufficiently large (> 10 Å in all dimensions). The run_md tool natively supports this via the supercell_min_length argument (defaults to 10.0 Å) which performs orthogonal expansion automatically.
   • Optimization: Use the diffusion monitor (see mat-md-monitors) to automatically stop simulations once the transport properties have converged.

     mace.run_md(
         structure_data=["candidates/A.cif", "candidates/B.cif"],
         temperature=600,
         supercell_min_length=10.0,
         monitor=True,
         monitor_type="diffusion",
         monitor_params={"specie": "Li", "threshold": 0.05, "check_interval_ps": 5.0}
     )
     

     Note: If the diffusion monitor triggers an early stop, it will automatically save the diffusion_{specie}.json and msd_{specie}.png directly into the trajectory output directory. You can skip Step 2 and proceed directly to Step 3 for any trajectories that converged early.

2. Individual Diffusivity Analysis: For each temperature directory that did not hit the early stopping criteria, run the analysis script to extract the diffusivity and Mean Square Displacement (MSD).

   # Env: base-agent
   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
   

   • --ignore_ps: Time to skip for equilibration. Default is 5.0 ps.
   • The script automatically detects the frame interval from the .log file if present.