MatterGen Structure Generation Skill

This skill provides tools for generating novel inorganic material structures using MatterGen, a state-of-the-art diffusion-based generative model for crystalline materials.

1. Prerequisites

[!IMPORTANT] ARM/aarch64 Support: MatterGen CAN work on ARM-based systems like NVIDIA DGX Spark. However, PyG dependencies (torch-scatter, torch-cluster) must be compiled from source with CUDA_HOME properly configured. See installation guide below.

• The mattergen-agent conda environment must be installed and configured.
• MatterGen requires Python 3.10 and CUDA 13.0 compatible GPU for efficient generation.
• For ARM/aarch64 systems: See Installing torch-scatter on ARM for detailed installation instructions.

2. Available Models

MatterGen provides several pretrained models:

• mattergen_base: Base unconditional generative model
• mp_20_base: Materials Project base model
• dft_mag_density: Model for magnetic density conditioning
• chemical_system: Model for chemical system conditioning

3. MCP Tool Usage

The MCP tool automatically loads models when needed - no explicit load step required.

Unconditional Generation

Generate novel structures without conditioning:

from mcp_base import mcp_mattergen_generate_structures

result = mcp_mattergen_generate_structures(
    model_name="mattergen_base",
    num_structures=10,
    batch_size=10,
    output_dir="research/my_project/generated"
)

Chemical System Conditioning

Generate structures from a specific chemical system (controls which elements appear):

result = mcp_mattergen_generate_structures(
    chemical_system="Li-Fe-P-O",  # Automatically uses chemical_system model
    guidance_scale=1.0,  # Recommended for chemical system conditioning
    num_structures=20,
    batch_size=10,
    output_dir="research/cathode_materials/generated"
)

[!NOTE] Chemical system conditioning controls which elements appear, but NOT the exact stoichiometry. For example, chemical_system="Li-Zr-Cl" can generate Li3Cl5, LiZrCl4, Li2ZrCl5, etc., but you cannot specify exactly "Li2ZrCl6".

4. Fine-Tuning (Skill Scripts)

Fine-tune MatterGen on custom datasets using the skill scripts:

Step 1: Prepare Training Data

cd /home/bdeng/projects/AtomisticSkills/.agents/skills/ml-generative-mattergen
conda activate mattergen-agent

# Convert structures and properties to CSV format
python scripts/prepare_training_data.py \
  --structures-json training_structures.json \
  --property-name "formation_energy" \
  --output training_data.csv

Training data JSON format:

[
  {
    "structure": {<pymatgen Structure dict>},
    "properties": {"formation_energy": -2.5}
  },
  ...
]

Step 2: Run Fine-Tuning

python scripts/run_finetuning.py \
  --training-data training_data.csv \
  --property-name "formation_energy" \
  --base-model "mattergen_base" \
  --epochs 100 \
  --output-dir finetuned_formation_energy

Fine-tuning parameters:

• --training-data: Path to CSV from Step 1
• --property-name: Property to condition on (must match CSV column)
• --base-model: Starting model (mattergen_base, chemical_system, etc.)
• --epochs: Training epochs (100-200 recommended)
• --learning-rate: Learning rate (default: 5e-6)
• --batch-size: Batch size (default: 32)

[!TIP]

• Start with 2 epochs for quick testing
• Use 100-200 epochs for actual fine-tuning
• GPU required (fine-tuning on CPU is extremely slow)

5. Output Files

Generation Output

• structure_XXXX.cif: Generated structure files
• generation_metadata.json: Metadata about generation parameters

Fine-Tuning Output

• checkpoints/: Model checkpoint files (.ckpt)
• config.yaml: Hydra configuration used
• Training logs and metrics

6. Limitations

[!WARNING] Chemical System vs. Stoichiometry

• chemical_system parameter controls which elements are encouraged to be present.
• It does NOT guarantee that all specified elements will be in the output structure.
• It does NOT prevent other elements from occasionally appearing if guidance is too low.
• Example: chemical_system="Li-Zr-Cl" might generate LiCl, ZrCl4, or even structures missing Li, alongside the desired ternaries (e.g., Li2ZrCl6).
• Action Required: You MUST write a post-processing script to filter the output .cif files and keep only the ones that match your exact target elemental composition.

[!WARNING] CSP Mode Not Available

• Target composition control (target_compositions parameter) requires CSP-trained models
• CSP models are NOT publicly available - must be custom-trained
• Public models (mattergen_base, chemical_system, etc.) are generation models only

7. Best Practices

[!IMPORTANT]

• GPU Required: MatterGen requires a CUDA-compatible GPU. CPU is extremely slow.
• Batch Size: Use larger batches (10-50) for efficient GPU utilization
• Guidance Scale: Higher values (1.0-5.0) enforce stronger conditioning
• Composition Filtering: Always filter the generated output CIFs using pymatgen to verify that the structures contain exactly the target elements.
• Validation: Always validate generated structures via relaxation and stability analysis

[!TIP]

• Start with unconditional generation to understand model behavior
• Use chemical_system conditioning to explore specific element combinations
• Fine-tune on domain-specific data for specialized applications (e.g., cathode materials)

8. Workflow Integration

MatterGen works well in combination with:

• Structure relaxation: Use MCP MLIP tools to optimize generated structures
• Stability analysis: Calculate E_hull to identify stable phases
• Property prediction: Use MLIPs or DFT to calculate properties
• High-throughput screening: Generate → Relax → Screen workflow

9. Examples

See examples/ for:

• Unconditional generation workflow
• Chemical system conditioning
• Fine-tuning on custom datasets with complete example data

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Author: Bowen Deng Contact: GitHub @learningmatter-mit