Parse CIF, XYZ, and Gaussian files into pymatgen structures.
npx skills add https://github.com/Hongyu-yu/matsci-ai-skills --skill pymatgen-io
Please help me install this Agent Skill. Skill: pymatgen-io Source: https://github.com/Hongyu-yu/matsci-ai-skills/tree/main/skills/pymatgen-io Command: npx skills add https://github.com/Hongyu-yu/matsci-ai-skills --skill pymatgen-io
Non-VASP IO tasks in materials science workflows are scattered across formats and codes; this skill centralizes CIF/XYZ/Gaussian/OpenBabel IO and adapters to CP2K, QE, Q-Chem, ABINIT, LAMMPS, FEFF, NWChem, Wannier90, phonopy, ShengBTE, etc., enabling easier data exchange.
Install pymatgen and begin parsing CIF/XYZ/Gaussian files with the appropriate pymatgen.io modules to obtain Structure or Molecule objects.
High-intent search queries and answers about installing and using this skill.
You convert CIF and XYZ files by using the pymatgen.io.cif and pymatgen.io.xyz modules to parse the formats directly into pymatgen Structure or Molecule objects for simulation pipelines.
Yes, you can parse Gaussian output files using the pymatgen.gaussian module, which translates the computational chemistry format into standard pymatgen Molecule objects and associated data structures.
Yes, pymatgen supports non-VASP file IO and format conversion for LAMMPS and Quantum Espresso through specific adapters, enabling data exchange between these codes and pymatgen structures.
The best way to interface Materials Project structures with Q-Chem or ABINIT is using pymatgen adapters, which convert online structure data into the required input formats for these simulation codes.
You need a Python environment with the pymatgen package installed to use the IO modules, and optionally ASE or OpenBabel if your workflow requires those specific adapter functionalities.
This toolkit focuses on non-VASP formats like CIF, XYZ, and Gaussian, along with adapters for CP2K, QE, and LAMMPS, because it centralizes scattered materials science data exchange tasks that are not covered by native VASP IO.
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