# Mat Diffusion Analysis

> Calculate ionic diffusion coefficients and activation energy from MD trajectories using pymatgen.

- Skill: `learningmatter-mit/mat-diffusion-analysis` (Agent Skill, multi-file: 11 files)
- Install (CLI): `npx skillmds@latest add learningmatter-mit/mat-diffusion-analysis`
- Raw SKILL.md: https://api.skillmd.com/api/skills/learningmatter-mit/mat-diffusion-analysis/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: AI & ML
- Author: learningmatter-mit (https://skillmd.com/u/learningmatter-mit)
- Updated: 2026-09-22
- Page: https://skillmd.com/skills/learningmatter-mit/mat-diffusion-analysis

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# 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](../mace/SKILL.md) or [matgl](../matgl/SKILL.md)).
    - **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](../mat-md-monitors/SKILL.md)) to automatically stop simulations once the transport properties have converged.
        ```python
        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).
    ```bash
    # 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.

3.  **Activation Energy Fitting**: Once all individual results are generated, use the fitting script to combine data and perform a weighted Arrhenius fit.
    ```bash
    # Env: base-agent
    python .agents/skills/mat-diffusion-analysis/scripts/calculate_activation_energy.py results/
    ```
    - The script looks for `md_*K/diffusion_results.json` patterns.
    - It performs error propagation to calculate uncertainty in $E_a$ and extrapolated room-temperature conductivity.

## Examples

- **Superionic Conductor (LGPS)**: A complete workflow demonstration including supercell preparation, multi-temperature MD, and final Arrhenius plotting for $Li_{10}GeP_2S_{12}$ is available in the [LGPS Example](examples/LGPS/README.md).

## Constraints
- **Trajectory Format**: Trajectories MUST be in ASE `.traj` format.
- **Environments**: All analysis scripts require the **base-agent** conda environment.
- **Linearity**: The diffusivity calculation assumes a linear diffusive regime. Always inspect the generated MSD plots to ensure linearity after the `ignore_ps` period.
- **Atom Count**: To ensure statistical significance, the system should contain a sufficient number of mobile ions (> 20 recommended).
- **Paths**: Always use relative paths from the project root when executing scripts.

## See Also
- [mat-md-monitors](../mat-md-monitors/SKILL.md): Real-time monitoring tools for MD simulations.
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**Author:** Bowen Deng
**Contact:** [GitHub @learningmatter-mit](https://github.com/learningmatter-mit)