Hongyu-yu/pymatgen-io
skills/pymatgen-io/SKILL.md
Use for non-VASP input/output tasks in pymatgen.io: CIF/XYZ/Gaussian/OpenBabel and DFT/MD code IO such as CP2K, Q-Chem, ABINIT, LAMMPS, FEFF, NWChem, Quantum ESPRESSO, Wannier90, phonopy/shengbte, etc.
$ install --global
skillsauthnpx skillsauth add Hongyu-yu/matsci-ai-skills pymatgen-ioInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- pymatgen-io
- description:
- Use for non-VASP input/output tasks in pymatgen.io: CIF/XYZ/Gaussian/OpenBabel and DFT/MD code IO such as CP2K, Q-Chem, ABINIT, LAMMPS, FEFF, NWChem, Quantum ESPRESSO, Wannier90, phonopy/shengbte, etc.
- short-description:
- pymatgen IO (non-VASP)
Pymatgen IO (Non-VASP)
Overview
Pymatgen IO (non-VASP) handles file formats and interfaces for many DFT/MD codes other than VASP.
Required Python Environment
Ensure pymatgen is installed in your Python environment:
pip install pymatgen
# or
conda install -c conda-forge pymatgen
Example usage pattern:
from pymatgen.io.cif import CifParser
# your code here
When to Use This Skill
- Parse or write CIF, XYZ, Gaussian, or related formats
- Interface with CP2K, QE, Q-Chem, ABINIT, LAMMPS, FEFF, NWChem, etc.
Core Capabilities
1. Common Formats
- CIF, XYZ, Gaussian, and adapters (ASE/OpenBabel if installed)
2. Code Interfaces
- Q-Chem, CP2K, Quantum ESPRESSO, ABINIT, LAMMPS, FEFF
3. Conversion
- Convert external formats to
Structure/Molecule
Quick Workflow
- Identify the input/output format or code interface.
- Parse into
StructureorMoleculeobjects. - Write converted outputs or parse results.
Resources
scripts/
Executable examples in the scripts/ directory:
2013-01-01-Getting_crystal_structures_from_online_sources.py- Fetching structures from online sources and parsing formats.
references/
Detailed reference material (load as needed):
references/io-non-vasp.md- IO patterns and examplesreferences/docs/- Local API docs forpymatgen.io
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