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
• 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")

Materials Project Integration

# Set up API key
export MP_API_KEY="your_api_key_here"

from mp_api.client import MPRester

with MPRester() as mpr:
    # Get structure by material ID
    struct = mpr.get_structure_by_material_id("mp-149")

    # Search for materials
    materials = mpr.materials.summary.search(
        formula="Fe2O3",
        energy_above_hull=(0, 0.05)
    )

Core Capabilities

1. Structure Creation and Manipulation

Create structures using various methods and perform transformations.

From files:

# Automatic format detection
struct = Structure.from_file("structure.cif")
struct = Structure.from_file("POSCAR")
mol = Molecule.from_file("molecule.xyz")

From scratch:

from pymatgen.core import Structure, Lattice

# Using lattice parameters
lattice = Lattice.from_parameters(a=3.84, b=3.84, c=3.84,
                                  alpha=120, beta=90, gamma=60)
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
struct = Structure(lattice, ["Si", "Si"], coords)

# From space group
struct = Structure.from_spacegroup(
    "Fm-3m",
    Lattice.cubic(3.5),
    ["Si"],
    [[0, 0, 0]]
)

Transformations:

from pymatgen.transformations.standard_transformations import (
    SupercellTransformation,
    SubstitutionTransformation,
    PrimitiveCellTransformation
)

# Create supercell
trans = SupercellTransformation([[2,0,0],[0,2,0],[0,0,2]])
supercell = trans.apply_transformation(struct)

# Substitute elements
trans = SubstitutionTransformation({"Fe": "Mn"})
new_struct = trans.apply_transformation(struct)

# Get primitive cell
trans = PrimitiveCellTransformation()
primitive = trans.apply_transformation(struct)

Reference: See references/core_classes.md for comprehensive documentation of Structure, Lattice, Molecule, and related classes.

2. File Format Conversion

Convert between 100+ file formats with automatic format detection.

Using convenience methods:

# Read any format
struct = Structure.from_file("input_file")

# Write to any format
struct.to(filename="output.cif")
struct.to(filename="POSCAR")
struct.to(filename="output.xyz")

Using the conversion script:

# Single file conversion
python scripts/structure_converter.py POSCAR structure.cif

# Batch conversion
python scripts/structure_converter.py *.cif --output-dir ./poscar_files --format poscar

Reference: See references/io_formats.md for detailed documentation of all supported formats and code integrations.

3. Structure Analysis and Symmetry

Analyze structures for symmetry, coordination, and other properties.

Symmetry analysis:

from pymatgen.symmetry.analyzer import SpacegroupAnalyzer

sga = SpacegroupAnalyzer(struct)

# Get space group information
print(f"Space group: {sga.get_space_group_symbol()}")
print(f"Number: {sga.get_space_group_number()}")
print(f"Crystal system: {sga.get_crystal_system()}")

# Get conventional/primitive cells
conventional = sga.get_conventional_standard_structure()
primitive = sga.get_primitive_standard_structure()

Coordination environment:

from pymatgen.analysis.local_env import CrystalNN

cnn = CrystalNN()
neighbors = cnn.get_nn_info(struct, n=0)