pymatgen

Pymatgen - Python Materials Genomics

Overview

Pymatgen is a comprehensive Python library for materials analysis that powers the Materials Project. Create, analyze, and manipulate crystal structures and molecules, compute phase diagrams and thermodynamic properties, analyze electronic structure (band structures, DOS), generate surfaces and interfaces, and access Materials Project's database of computed materials. Supports 100+ file formats from various computational codes.

When to Use This Skill

This skill should be used when:

• Working with crystal structures or molecular systems in materials science
• Converting between structure file formats (CIF, POSCAR, XYZ, etc.)
• Analyzing symmetry, space groups, or coordination environments
• Extracting Wyckoff letters, multiplicities, and representative fractional coordinates from CIF files (see references/wyckoff-positions-from-cif.md — use get_symmetry_dataset().wyckoffs, not get_symmetrized_structure().wyckoff_symbols)
• Computing phase diagrams or assessing thermodynamic stability
• Analyzing electronic structure data (band gaps, DOS, band structures)
• Generating surfaces, slabs, or studying interfaces
• Accessing the Materials Project database programmatically
• Setting up high-throughput computational workflows
• Analyzing diffusion, magnetism, or mechanical properties
• Working with VASP, Gaussian, Quantum ESPRESSO, or other computational codes

Quick Start Guide

Installation

# Core pymatgen
uv pip install pymatgen

# With Materials Project API access
uv pip install pymatgen mp-api

# Optional dependencies for extended functionality
uv pip install pymatgen[analysis]  # Additional analysis tools
uv pip install pymatgen[vis]       # Visualization tools

Basic Structure Operations

from pymatgen.core import Structure, Lattice

# Read structure from file (automatic format detection)
struct = Structure.from_file("POSCAR")

# Create structure from scratch
lattice = Lattice.cubic(3.84)
struct = Structure(lattice, ["Si", "Si"], [[0,0,0], [0.25,0.25,0.25]])

# Write to different format
struct.to(filename="structure.cif")

# Basic properties
print(f"Formula: {struct.composition.reduced_formula}")
print(f"Space group: {struct.get_space_group_info()}")
print(f"Density: {struct.density:.2f} g/cm³")