Mat Raman Spectra

Raman Spectra Calculation

Goal

To calculate the Raman spectrum of a crystalline material by:

1. Identifying Raman-active phonon modes via group-theory symmetry analysis of Γ-point phonons (MLIP-only path)
2. Optionally computing full Raman scattering intensities using DFT-level Born effective charges and dielectric tensors (DFT path)

Physical background: Raman scattering intensity of mode $\nu$ is proportional to $|(\hat{e}i \cdot \alpha\nu \cdot \hat{e}s)|^2$, where $\alpha\nu = d\boldsymbol{\alpha}/dQ_\nu$ is the Raman tensor (derivative of polarizability with respect to mode coordinate $Q_\nu$). Computing $\alpha_\nu$ requires DFT-level dielectric calculations; phonon frequencies alone can be obtained with MLIPs.

[!IMPORTANT] Two-tier approach:

• MLIP tier (Step 1–3): Predicts Raman peak positions (frequencies). Intensities are set equal as a placeholder. Sufficient for peak assignment and comparison with experiment when known structure is available.
• DFT tier (Step 4): Computes actual Raman intensities via Born charges and dielectric tensor from VASP DFPT. Required for quantitative intensity matching.

Prerequisites

• Pymatgen, phonopy installed in base-agent (for symmetry analysis and plotting)
• MLIP environment (mace-agent, matgl-agent, or fairchem-agent) for phonon calculation

Instructions

1. Relax Structure

Before computing phonons, ensure the structure is fully relaxed. Use the MCP tool for your chosen MLIP:

# Env: mace-agent
mcp_mace_load_model(model_name="MACE-MH-1")
mcp_mace_relax_structure(
    structure_data="input_structure.cif",
    relax_cell=True,
    fmax=0.001,       # tight convergence for phonons
    output_dir="relaxation/"
)

[!IMPORTANT] Use a tight force convergence (fmax ≤ 0.001 eV/Å) for phonon calculations. Poorly relaxed structures produce imaginary frequencies that indicate a false structural instability.

2. Calculate Phonons (MLIP)

Use the mat-phonon skill to compute Γ-point phonons. The output phonon.yaml is the required input for this skill.

# Env: mace-agent
python .agents/skills/mat-phonon/scripts/calculate_phonon.py \
    --structure relaxation/relaxed_structure.cif \
    --model_type mace \
    --model_name MACE-MH-1 \
    --supercell_matrix '[[2,0,0],[0,2,0],[0,0,2]]' \
    --output_dir phonon_results/

Verify the output: check phonon_results/phonon.yaml exists and there are no large imaginary modes at Γ.

3. Analyse Raman-Active Modes and Simulate Spectrum (MLIP Tier)

# Env: base-agent
python .agents/skills/mat-raman-spectra/scripts/analyze_raman_modes.py \
    --phonon-yaml phonon_results/phonon.yaml \
    --structure relaxation/relaxed_structure.cif \
    --output-dir raman_results/ \
    --broadening 5.0 \
    --freq-max 1000

Parameters:

Output files:

• raman_modes.json — table of all Γ-point modes with symmetry label, frequency, and Raman-activity classification
• raman_spectrum.png/svg — simulated spectrum (MLIP tier uses equal intensities; DFT tier uses computed intensities)
• raman_modes_table.csv — CSV table for further analysis

[!NOTE] On Raman intensity accuracy: The MLIP tier assigns equal intensity to all Raman-active modes. Peak positions are reliable; relative intensities are not. For quantitative comparison with experiment, proceed to Step 4.

4. Compute Full Raman Intensities (DFT Tier — Optional)

This step uses VASP DFPT via atomate2 to obtain Born effective charges and the macroscopic dielectric tensor, then combines them with MLIP phonon eigenvectors to compute Raman tensors.

4a. Run VASP DFPT for Born charges + dielectric tensor:

# Env: atomate2-agent
mcp_atomate2_submit_vasp_job(
    structure_path="relaxation/relaxed_structure.cif",
    job_type="dfpt_dielectric",     # computes LEPSILON + Born charges
    vasp_settings_json='{"EDIFF": 1e-8, "ENCUT": 520}',
    output_dir="vasp_dfpt/"
)

Wait for the job to complete, then retrieve results:

# Env: atomate2-agent
mcp_atomate2_get_task_result(
    task_id="<task_id>",
    output_dir="vasp_dfpt/results/"
)

4b. Compute Raman intensities:

# Env: base-agent
python .agents/skills/mat-raman-spectra/scripts/analyze_raman_modes.py \
    --phonon-yaml phonon_results/phonon.yaml \
    --structure relaxation/relaxed_structure.cif \
    --born-charges vasp_dfpt/results/OUTCAR \
    --output-dir raman_dft_results/ \
    --broadening 5.0

When --born-charges is provided, the script computes Raman tensors from the Born charges and dielectric tensor and uses the resulting intensities instead of equal weights.

5. Compare with Experiment (Optional)

If experimental Raman data is available as an image, use general-plot-digitizer or chem-db-spectra to extract peak positions and overlay with computed results.

Examples

Example: Rutile TiO₂

Rutile TiO₂ (point group D₄h) has 4 Raman-active modes at ~143, ~235, ~447, 612 cm⁻¹ experimentally.

# 1. Relax with MACE
mcp_mace_load_model(model_name="MACE-MH-1")
mcp_mace_relax_structure(structure_data="TiO2_rutile.cif", relax_cell=True, fmax=0.001, output_dir="relax/")

# 2. Phonons
python .agents/skills/mat-phonon/scripts/calculate_phonon.py \
    --structure relax/relaxed_structure.cif --model_type mace --model_name MACE-MH-1 \
    --supercell_matrix '[[3,0,0],[0,3,0],[0,0,4]]' --output_dir phonon/

# 3. Raman analysis
python .agents/skills/mat-raman-spectra/scripts/analyze_raman_modes.py \
    --phonon-yaml phonon/phonon.yaml --structure relax/relaxed_structure.cif \
    --output-dir raman/ --freq-max 800 --broadening 8.0

Expected: the script should identify B1g, Eg, A1g, and B2g modes (all Raman active in D₄h) with frequencies near experimental values.

Constraints

• Tight relaxation first: Use fmax ≤ 0.001 eV/Å. Large residual forces produce spurious imaginary modes.
• Supercell size: A 2×2×2 supercell (or larger) is recommended. The script reads pre-computed force constants from phonon.yaml; the supercell size affects the quality of Γ-point eigenvectors.
• MLIP tier intensities: Equal intensities are used as a placeholder. Do not compare intensities from the MLIP tier quantitatively with experiment.
• Acoustic modes: The three acoustic modes at Γ (near 0 cm⁻¹) are always excluded from the Raman spectrum.
• Environments: Step 2 (phonon calculation) requires mace-agent (or matgl-agent/fairchem-agent); Step 3 (analysis and plotting) runs in base-agent.

References

• Togo & Tanaka, "First principles phonon calculations in materials science", Scr. Mater., 2015. DOI
• Lazzeri & Mauri, "First-principles calculation of vibrational Raman spectra in large systems", Phys. Rev. Lett., 2003. DOI
• Batatia et al., "MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields", NeurIPS, 2022.

Author: Yu Yao Contact: GitHub @AI4SciDisc