alterlab-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 the Materials Project database. Supports 100+ file formats from various computational codes.

When to Use This Skill

Use 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 (band gaps, DOS, band structures)
• Generating surfaces/slabs or studying interfaces
• Accessing the Materials Project database programmatically
• Setting up high-throughput computational workflows
• Working with VASP, Gaussian, Quantum ESPRESSO, or other codes

Quick Start

uv pip install pymatgen           # core
uv pip install pymatgen mp-api    # + Materials Project API access
uv pip install pymatgen[analysis] # extended analysis tools
uv pip install pymatgen[vis]      # visualization tools

from pymatgen.core import Structure, Lattice

struct = Structure.from_file("POSCAR")        # auto format detection
struct.to(filename="structure.cif")           # write any format
print(struct.composition.reduced_formula)
print(struct.get_space_group_info())
print(f"{struct.density:.2f} g/cm³")

export MP_API_KEY="your_api_key_here"   # for Materials Project access

Core Capabilities (routing)

Each capability has a copy-paste code block in references/core_examples.md and deeper module docs in the references listed below.

1. Structure creation & manipulation — from files, from scratch (lattice params or space group), transformations (supercell, substitution, primitive). → core_classes.md
2. File-format conversion — from_file()/to() plus scripts/structure_converter.py for single/batch. → io_formats.md
3. Structure analysis & symmetry — SpacegroupAnalyzer, CrystalNN, plus scripts/structure_analyzer.py. → analysis_modules.md
4. Phase diagrams & thermodynamics — PhaseDiagram, energy-above-hull, decomposition, plus scripts/phase_diagram_generator.py. → analysis_modules.md, transformations_workflows.md
5. Electronic structure — band structures and DOS from Vasprun, band gaps, metallicity. → analysis_modules.md, io_formats.md
6. Surfaces & interfaces — SlabGenerator, WulffShape, AdsorbateSiteFinder. → analysis_modules.md, transformations_workflows.md
7. Materials Project access — MPRester search and retrieval with property filters. → materials_project_api.md
8. Computational workflow setup — VASP input sets (MPRelaxSet, MPStaticSet, MPNonSCFSet), Gaussian, Quantum ESPRESSO. → io_formats.md, transformations_workflows.md
9. Advanced analysis — XRD patterns, elastic tensors, magnetic ordering. → analysis_modules.md