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alterlab-pymatgen

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Updated 10-15 19:56

About this skill

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

Does NOT Trigger

Scenario Use Instead
Small organic molecules — SMILES, fingerprints, descriptors, substructure search alterlab-rdkit
Running DFT / conformer searches / pKa in a managed cloud quantum-chemistry service alterlab-rowan
Classical molecular dynamics of proteins or ligands (OpenMM, trajectories) alterlab-molecular-dynamics
Variational quantum circuits for molecular ground states (VQE) alterlab-pennylane

Quick Start

uv pip install pymatgen                # core (Python >= 3.11)
uv pip install pymatgen mp-api         # + Materials Project API access
uv pip install "pymatgen[optional]"    # extra analysis deps (phonopy, seekpath, ase, ...)
uv pip install "pymatgen[vis]"         # VTK structure visualization

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

Multi-step worked examples (high-throughput generation, band-structure pipeline, surface energy): references/common_workflows_code.md.

Bundled Resources

Scripts (scripts/)

  • structure_converter.py: convert between structure file formats (batch + auto detection). Usage: python scripts/structure_converter.py POSCAR structure.cif
  • structure_analyzer.py: symmetry, coordination, lattice parameters, distance matrix. Usage: python scripts/structure_analyzer.py structure.cif --symmetry --neighbors
  • phase_diagram_generator.py: phase diagrams from Materials Project, stability analysis. Usage: python scripts/phase_diagram_generator.py Li-Fe-O --analyze "LiFeO2"

All scripts include detailed help, e.g. python scripts/structure_converter.py --help

References (references/)

  • core_examples.md: copy-paste code for all nine core capabilities
  • common_workflows_code.md: multi-step worked workflow code
  • core_classes.md: Element, Structure, Lattice, Molecule, Composition classes
  • io_formats.md: file-format support and code integration (VASP, Gaussian, etc.)
  • analysis_modules.md: phase diagrams, surfaces, electronic structure, symmetry
  • materials_project_api.md: complete Materials Project API guide
  • transformations_workflows.md: transformations framework and 10 common workflows

Best Practices

Structures: use auto format detection; prefer IStructure when immutable; reduce to primitive cell with SpacegroupAnalyzer; validate for overlapping atoms / bad bond lengths. File I/O: prefer from_file()/to(); specify format when detection fails; use as_dict()/from_dict() for version-safe storage. MP API: always use the context manager; batch queries; cache results; filter by property. Workflows: prefer input sets over manual INCAR; verify convergence; track transformations for provenance. Performance: use primitive cells; bound neighbor-search cutoffs; parallelize where possible.

Units and Conventions

Lengths in Å, energies in eV, angles in degrees, magnetic moments in μB, time in fs. Convert with pymatgen.core.units.

Integration

Integrates with ASE, Phonopy, BoltzTraP, Atomate/Fireworks, AiiDA, Zeo++, and OpenBabel.

Troubleshooting

  • Import errors: uv pip install "pymatgen[optional,vis]" (there is no [analysis] extra)
  • API key not found: export MP_API_KEY="your_key_here"
  • Structure read failures: try explicit format, e.g. Structure.from_file("file.txt", fmt="cif")
  • Symmetry analysis fails: increase tolerance, e.g. SpacegroupAnalyzer(struct, symprec=0.1)

Additional Resources

Docs: https://pymatgen.org/ · Materials Project: https://materialsproject.org/ · GitHub: https://github.com/materialsproject/pymatgen · Forum: https://matsci.org/ · Example notebooks: https://github.com/materialsvirtuallab/matgenb

Version Notes

Designed for pymatgen 2024.x and later (current 2026.9.x as of 2026-09; calendar versioning). Since 2026 the pymatgen distribution is a thin package on top of pymatgen-core; imports (pymatgen.core, pymatgen.io.vasp, …) are unchanged. For the Materials Project API use the mp-api package (current 0.46.x; from mp_api.client import MPRester) rather than the legacy pymatgen.ext.matproj client. Requirements: Python ≥ 3.11, pymatgen ≥ 2024.x, mp-api for Materials Project access.

Part of the AlterLab Academic Skills suite.