pymatgen-io
Skill19 starsChanged 10 months agoMITView on GitHub
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.
- Installs packages
We split this skill into the rules it gives an agent
2 rules. About 0 are common, 2 are distinctive, and 0 are very specific to this project.
≈0
Common · estimate
Many files like this have a rule of this kind.
≈2
Distinctive · estimate
This author's own choices. Worth a look.
0
Very specific
Tied to their project's names, files or tools. Probably skip.
- Common
- Distinctive
- Very specific
- Distinctive: line 16
Ensure pymatgen is installed in your Python environment:
- Distinctive: line 49
Write converted outputs or parse results.
≈ “Common” is an estimate: at least 1 in 5 of the 308,232 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.
Files
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 pymatgenExample usage pattern:
from pymatgen.io.cif import CifParser
# your code hereWhen 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
In this repository48 other files it gives its agents.
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- pymatgen-phononSkill
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- python-aseSkill
- python-jaxSkill
- python-multiobjective-optimizationSkill
- python-optimizationSkill
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- python-regression-statisticsSkill
- pytorch-lightningSkill
- scikit-learnSkill
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