pymatgen-materials

Pymatgen Materials Science

Materials science analysis using pymatgen for crystal structures, phase diagrams, electronic structure, and computational materials workflows.

When to Use

• Crystal structure creation, manipulation, and visualization
• Phase diagram construction and thermodynamic stability analysis
• Electronic structure (band structure, DOS) parsing and plotting
• Symmetry analysis and space group determination
• Reading/writing VASP, CIF, POSCAR, and other structure formats

When NOT to Use

• Molecular chemistry or drug design (use rdkit-chemistry)
• Protein or biomolecular structure (use biopython-bio)
• General plotting without materials context (use matplotlib-viz)
• Machine learning on materials data (use dedicated ML frameworks)

Crystal Structure Creation

from pymatgen.core import Structure, Lattice, Molecule

# Create from spacegroup and Wyckoff positions
structure = Structure.from_spacegroup(
    "Fm-3m", Lattice.cubic(5.43), ["Si"], [[0, 0, 0]]
)

# Create from file
structure = Structure.from_file("POSCAR")
structure = Structure.from_file("structure.cif")

# Create manually with lattice parameters
lattice = Lattice.from_parameters(a=3.84, b=3.84, c=3.84, alpha=90, beta=90, gamma=90)
structure = Structure(lattice, ["Cu", "Cu", "Cu", "Cu"],
                      [[0, 0, 0], [0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]])

# Hexagonal lattice
lattice = Lattice.hexagonal(a=2.46, c=6.71)

Structure Properties and Manipulation

# Basic properties
print(structure.lattice)                      # lattice vectors
print(structure.lattice.abc)                  # a, b, c lengths
print(structure.lattice.angles)               # alpha, beta, gamma
print(structure.volume)                       # unit cell volume
print(structure.density)                      # density in g/cm^3
print(structure.composition)                  # chemical formula
print(len(structure))                         # number of sites

# Space group and symmetry
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
sga = SpacegroupAnalyzer(structure)
print(sga.get_space_group_symbol())           # e.g., "Fm-3m"
print(sga.get_space_group_number())           # e.g., 225
print(sga.get_point_group_symbol())           # e.g., "m-3m"
conventional = sga.get_conventional_standard_structure()
primitive = sga.get_primitive_standard_structure()

# Supercell and perturbation
supercell = structure.copy()
supercell.make_supercell([2, 2, 2])
structure.perturb(0.01)                       # random perturbation

# Write to file
structure.to(filename="POSCAR")
structure.to(filename="output.cif")
structure.to(fmt="poscar")                    # return as string