Mat Electronic Structure

Electronic Structure

Goal

To calculate the electronic band structure of a crystalline material, revealing the energy-momentum relationship for electrons and determining whether the material is metallic, semiconducting, or insulating. This includes computing the band gap ($E_g$), identifying direct vs. indirect transitions, and visualizing the dispersion along high-symmetry k-paths.

Instructions

1. Obtain or Prepare the Input Structure

Start with a relaxed crystalline structure in CIF or POSCAR format. You can:

• Search Materials Project using the mcp_base_search_materials_project_by_formula tool
• Use a structure from previous calculations
• Create a structure manually using pymatgen or ASE

2. Run Band Structure Calculation

Use the atomate2 MCP tool with calculation_type="band_structure":

mcp_atomate2_run_atomate2_vasp_calculation(
    structures_path="structure.cif",           # Input structure file
    output_dir="./band_structure_results",     # Output directory
    calculation_type="band_structure",         # Band structure calculation
    bandstructure_mode="line",                 # Options: "line", "uniform", "both"
    preset_type="omat",                        # VASP preset (omat, mp, matpes-pbe, matpes-r2scan)
    execution_mode="remote",                   # "local" or "remote"
    remote_settings={                          # Required for remote execution
        "project": "remote_perlmutter",
        "worker": "perlmutter_worker"
    }
)

Band structure modes:

• "line": Calculate along high-symmetry k-paths (for band structure plots)
• "uniform": Calculate on a uniform k-mesh (for density of states)
• "both": Perform both line and uniform calculations

The workflow automatically:

1. Runs a static SCF calculation to obtain the charge density
2. Runs a non-SCF calculation to compute band structure eigenvalues

Alternative: Retrieve Pre-Computed Data from Materials Project

Instead of running DFT calculations, you can retrieve existing electronic structure data from Materials Project:

# Env: base-agent
python .agents/skills/mat-electronic-structure/scripts/get_mp_electronic_structure.py \
    --material_id mp-149 \
    --output si_mp_bands.json \
    --plot

This retrieves:

• Pre-computed band structure along high-symmetry paths
• Density of states (DOS)
• Band gap (energy, direct/indirect)
• Fermi energy

When to use MP retrieval vs. calculations:

• Retrieve from MP: Quick screening, validation, known materials
• Run calculations: New materials, custom structures, specific DFT settings

3. Post-Process and Visualize Results

After the calculation completes, parse the results and generate a band structure plot:

# Env: base-agent
python .agents/skills/mat-electronic-structure/scripts/plot_band_structure.py \
    band_structure_results \
    --output band_structure.png

The script will:

• Parse the vasprun.xml.gz from the non-SCF job
• Extract band gap information (energy, directness, transition)
• Generate a publication-quality band structure plot

For DOS (uniform mode):

# Env: base-agent
python .agents/skills/mat-electronic-structure/scripts/plot_dos.py \
    dos_results \
    --output dos.png

The script will:

• Parse the vasprun.xml.gz from the uniform k-mesh job
• Extract band gap and Fermi level
• Generate a DOS plot

Alternative: Manual post-processing with pymatgen

from pymatgen.io.vasp import BSVasprun
from pymatgen.electronic_structure.plotter import BSPlotter

# Load band structure from atomate2 results
vasprun_path = "band_structure_results/results/structure_0/job_*/vasprun.xml.gz"
vasprun = BSVasprun(vasprun_path, parse_projected_eigen=False)
bs = vasprun.get_band_structure(line_mode=True)

# Get band gap
if not bs.is_metal():
    bg = bs.get_band_gap()
    print(f"Band gap: {bg['energy']:.3f} eV")
    print(f"Direct: {bg['direct']}")
    print(f"Transition: {bg['transition']}")

# Plot
plotter = BSPlotter(bs)
ax = plotter.get_plot(ylim=(-10, 10))
ax.get_figure().savefig("band_structure.png", dpi=300, bbox_inches='tight')

Examples

Silicon Band Structure Calculation

# 1. Search for Si structure
mcp_base_search_materials_project_by_formula(
    formula="Si",
    save_to_file="Si.cif"
)

# 2. Run band structure calculation
mcp_atomate2_run_atomate2_vasp_calculation(
    structures_path="Si.cif",
    output_dir="./Si_bands",
    calculation_type="band_structure",
    bandstructure_mode="line",
    preset_type="omat",
    execution_mode="local"
)

# 3. Plot results
# Env: base-agent
python .agents/skills/mat-electronic-structure/scripts/plot_band_structure.py Si_bands --output Si_bands.png

See examples/ for a complete Si band structure calculation showing an indirect band gap of 0.581 eV.

Silicon Density of States (DOS)

# 1. Use existing Si structure (or search Materials Project)

# 2. Run DOS calculation with uniform k-mesh
mcp_atomate2_run_atomate2_vasp_calculation(
    structures_path="Si.cif",
    output_dir="./Si_dos",
    calculation_type="band_structure",
    bandstructure_mode="uniform",  # Uniform k-mesh for DOS
    preset_type="omat",
    execution_mode="local"
)

# 3. Plot DOS
# Env: base-agent
python .agents/skills/mat-electronic-structure/scripts/plot_dos.py Si_dos --output Si_dos.png

See examples/ for the complete DOS calculation showing the distribution of electronic states.

Constraints

• Structure Requirements: Input must be a crystalline structure with well-defined symmetry. Band structure calculations are not meaningful for amorphous or highly disordered materials.
• VASP Setup: Requires properly configured VASP environment:
  • PMG_VASP_PSP_DIR must point to POTCAR directory (or set in ~/.pmgrc.yaml)
  • For remote execution: Atomate2/jobflow-remote must be configured
• Environments:
  • Band structure calculation: atomate2-agent (via MCP tool)
  • Post-processing scripts: base-agent (pymatgen, matplotlib)
• Functional Choice:
  • PBE (omat, mp presets) typically underestimates band gaps
  • For accurate gaps: Use hybrid functionals (HSE06) or GW methods (not yet supported)
  • MatPES presets (matpes-pbe, matpes-r2scan) use r2SCAN which improves gap predictions
• k-point Density: The automatic k-path generation uses pymatgen's HighSymmKpath. For very accurate results, you may need to manually specify denser k-paths.
• Spin-Polarization: Current implementation assumes non-spin-polarized calculations. For magnetic materials, additional configuration may be needed.

Foundation Potential Recommendations

For exploratory band structure analysis using MLIPs (not DFT):

• CHGNet: Can predict band gaps, but accuracy varies
• Note: MACE, M3GNet, and other MLIPs trained on PES data do not predict electronic properties

For production calculations, always use DFT (this skill) and choose the appropriate functional:

• Standard screening: PBE (omat/mp presets)
• Improved gaps: r2SCAN (matpes-r2scan preset)
• Accurate gaps: HSE06 or GW (requires custom INCAR settings)

Author: Bowen Deng Contact: GitHub @learningmatter-mit