pymatgen-io

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." metadata: 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

1. Identify the input/output format or code interface.
2. Parse into Structure or Molecule objects.
3. 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 examples
• references/docs/ - Local API docs for pymatgen.io