Skills pymatgen

🔬

pymatgen

Name: pymatgen
Author: K-Dense-AI

Safe ⚡ Contains scripts⚙️ External commands📁 Filesystem access🌐 Network access🔑 Env variables

Analyze crystal structures with pymatgen

Also available from: davila7

Work with crystal structures and materials data. Convert file formats, compute phase diagrams, analyze symmetry, and access the Materials Project database for computational materials science research.

Supports: Claude Codex Code(CC)

🥉 75 Bronze

Download the skill ZIP

Upload in Claude

Go to Settings → Capabilities → Skills → Upload skill

Toggle on and start using

Test it

Using "pymatgen". Read structure from POSCAR and show its properties

Expected outcome:

Formula: Fe2O3 (hematite)
Lattice: a=5.04 Å, b=5.04 Å, c=13.77 Å
Space group: R-3c (#167)
Crystal system: trigonal
Density: 5.27 g/cm³
Number of sites: 10

Using "pymatgen". Convert CIF to POSCAR format

Expected outcome:

Successfully converted structure.cif to converted.POSCAR
Structure contains 10 atoms (Fe4 O6)
Format: POSCAR (VASP format)

Using "pymatgen". Query Materials Project for perovskites

Expected outcome:

Found 23 stable perovskite structures
Example: SrTiO3 (mp-5229) - band gap 3.2 eV
Example: BaTiO3 (mp-2987) - band gap 2.8 eV
Energy above hull: all < 0.01 eV/atom

Security Audit

Safe

v4 • 1/17/2026

All 537 static findings are false positives. The static analyzer incorrectly flagged markdown documentation syntax (code blocks, inline code formatting) as shell commands and cryptographic terms in documentation text as weak algorithms. The actual Python code uses secure patterns for API key management (environment variables) and performs legitimate materials science file I/O operations. No malicious code, data exfiltration, or security risks found.

Files scanned

4,081

Lines analyzed

findings

Total audits

Risk Factors

⚡ Contains scripts (6)

references/analysis_modules.md:139-144 references/io_formats.md:185-188 references/io_formats.md:400-403 references/transformations_workflows.md:212-215 references/transformations_workflows.md:434-437 SKILL.md:122-126

⚙️ External commands (447)

📁 Filesystem access (10)

references/core_classes.md:269 references/io_formats.md:115 references/io_formats.md:122 references/materials_project_api.md:29 references/materials_project_api.md:29 references/materials_project_api.md:29 references/materials_project_api.md:29 references/materials_project_api.md:414 scripts/structure_analyzer.py:251 scripts/structure_analyzer.py:258

🌐 Network access (14)

references/materials_project_api.md:19 references/materials_project_api.md:504 references/materials_project_api.md:505 references/materials_project_api.md:506 references/materials_project_api.md:507 scripts/phase_diagram_generator.py:42 skill-report.json:6 skill-report.json:207 SKILL.md:370 SKILL.md:675 SKILL.md:676 SKILL.md:677 SKILL.md:678 SKILL.md:679

🔑 Env variables (23)

Audited by: claude View Audit History →

Quality Score

Architecture

100

Maintainability

Content

Community

100

Security

Spec Compliance

What You Can Build

Research stable compounds

Build phase diagrams and identify stable materials using data from the Materials Project database.

Convert structure formats

Convert crystal structure files between CIF, POSCAR, XYZ and other formats for different simulation codes.

Analyze crystal symmetry

Determine space groups, symmetry operations, and coordination environments from structure files.

Try These Prompts

Read structure file

Read the structure from file 'POSCAR' and show its composition, lattice parameters, and space group.

Convert format

Convert 'structure.cif' to POSCAR format and save as 'converted.POSCAR'.

Phase diagram

Build a phase diagram for the Li-Fe-O system and identify stable compounds.

Materials Project

Search the Materials Project for stable perovskite structures with band gap between 1.5 and 3.0 eV.

Best Practices

Always use environment variables (MP_API_KEY) for API credentials, never hardcode keys
Validate structures after reading to check for overlapping atoms or unrealistic bond lengths
Use SpacegroupAnalyzer to reduce structures to primitive cells before analysis

Avoid

Do not hardcode API keys in scripts - use environment variables instead
Do not skip symmetry analysis when comparing structures - different space groups may look similar
Do not assume automatic format detection always works - specify format when unsure

Frequently Asked Questions

What file formats does pymatgen support?

Pymatgen supports 100+ formats including CIF, POSCAR, XYZ, PDB, JSON, YAML, and inputs/outputs for VASP, Gaussian, Quantum ESPRESSO, LAMMPS, and more.

How do I get a Materials Project API key?

Create an account at https://next-gen.materialsproject.org/ and generate an API key from your dashboard. Set it as the MP_API_KEY environment variable.

Can pymatgen analyze molecular dynamics trajectories?

Yes, use Xdatcar to read VASP MD trajectories and DiffusionAnalyzer to compute diffusivity and conductivity from AIMD data.

How do I generate a supercell?

Use SupercellTransformation with a scaling matrix, for example: [[2,0,0],[0,2,0],[0,0,2]] for a 2x2x2 supercell.

Does pymatgen work with other simulation codes?

Yes, pymatgen integrates with VASP, Gaussian, Quantum ESPRESSO, LAMMPS, CP2K, ABINIT, and can convert to/from ASE format.

How do I analyze coordination environments?

Use CrystalNN from pymatgen.analysis.local_env for general cases, or VoronoiNN for Voronoi-based neighbor finding.