Chem Neb Barrier

NEB Barrier Calculation

This skill calculates the activation energy barrier for atomic migration or chemical reaction transition states using the Nudged Elastic Band (NEB) method with Machine Learning Interatomic Potentials (MLIPs).

Supports both:

• Materials: solid-state diffusion barriers (periodic systems)
• Chemistry: molecular transition states (non-periodic systems)

The script auto-detects periodic boundary conditions from the input structures.

Tools

1. calculate_barrier.py

Performs the NEB calculation between two endpoint structures.

Usage:

Use with MACE (periodic materials)

# Env: mace-agent
python .agents/skills/chem-neb-barrier/scripts/calculate_barrier.py \
    --start_structure <path_to_start.cif> \
    --end_structure <path_to_end.cif> \
    --model_type mace \
    --n_images 5 \
    --fmax 0.05 \
    --output_dir <output_directory>

Use with MACE (non-periodic molecules)

# Env: mace-agent
python .agents/skills/chem-neb-barrier/scripts/calculate_barrier.py \
    --start_structure reactant.xyz \
    --end_structure product.xyz \
    --model_type mace \
    --model_name MACE-OFF23-small \
    --n_images 7 \
    --fmax 0.05 \
    --output_dir <output_directory>

Use with FairChem

# Env: fairchem-agent
python .agents/skills/chem-neb-barrier/scripts/calculate_barrier.py \
    --start_structure <path_to_start.cif> \
    --end_structure <path_to_end.cif> \
    --model_type fairchem \
    --n_images 5 \
    --fmax 0.05 \
    --output_dir <output_directory>

Use with MatGL

# Env: matgl-agent
python .agents/skills/chem-neb-barrier/scripts/calculate_barrier.py \
    --start_structure <path_to_start.cif> \
    --end_structure <path_to_end.cif> \
    --model_type matgl \
    --n_images 5 \
    --fmax 0.05 \
    --output_dir <output_directory>

Arguments:

• --start_structure: Path to the initial stable structure (CIF/POSCAR/XYZ).
• --end_structure: Path to the final stable structure (CIF/POSCAR/XYZ).
• --model_type: Type of MLIP to use (mace, fairchem, matgl).
• --model_name: Specific model name/path (optional, uses default if not specified).
• --model_head: Model head for multi-head models (e.g., omat, omol for UMA; omat_pbe, matpes_r2scan for MACE-MH).
• --n_images: Number of intermediate images (default: 7).
• --fmax: Force convergence criterion in eV/Å (default: 0.02).
• --interpolation: Method for initial path generation. Options: linear, idpp (default). Recommended to use idpp for dense systems.
• --climb: Use Climbing Image NEB (CI-NEB) (default: True).
• --output_dir: Directory to save results and plots.

Outputs:

• neb_trajectory.traj: ASE trajectory of the optimized path.
• neb_barrier_plot.png: Plot of energy vs reaction coordinate.
• neb_results.json: JSON file containing barrier energy and forces.
• neb_path.cif (periodic) or neb_path.xyz (non-periodic): Path structures.

Model Recommendations

Periodic Materials (solid-state diffusion)

• Recommended:

  • OMAT:
    • MACE-OMAT-0-small
    • MACE-MH-1 (head: omat_pbe)
    • uma-s-1p1 (head: omat)
  • MatPES:
    • MACE-MATPES-r2SCAN-0
    • MACE-MH-1 (head: matpes_r2scan)
    • CHGNet-MatPES-r2SCAN-2025.2.10-2.7M-PES
    • TensorNet-MatPES-r2SCAN-v2025.1-PES
  • These models are trained on datasets including transition states or diverse structures (OMat24, MatPES), making them more reliable for NEB.

• Discouraged:

  • MPtrj trained models (e.g., M3GNet-MP-2021, CHGNet-MPtrj-2023.12.1-2.7M-PES)
  • These are primarily trained on ground-state or near-equilibrium structures and may underestimate barriers or fail to converge for high-energy transition states.

Non-periodic Molecules (transition states)

• Recommended:
  • MACE-OFF23-small / MACE-OFF23-medium — trained on organic molecules
  • uma-s-1p1 (head: omol) — general molecular model
  • MACE-MH-1 (head: omol) — multi-head molecular model

Prerequisites

• Ensure the appropriate environment is active for the chosen model type (see mcp_config.json).
• CRITICAL: The start and end structures MUST be pre-relaxed using the same MLIP model used for the NEB calculation.
  • For periodic: Use relax_cell=False (fixed volume) to ensure consistency between endpoints.
  • For non-periodic: Ensure pbc=False is set on the structures.
  • Use fmax=0.02 eV/Å for tight convergence.
  • You can use the relax_structure tool from the corresponding MCP server for this.

Examples

See examples/ directory for sample inputs and outputs.

Author: Bowen Deng Contact: GitHub @learningmatter-mit