Hongyu-yu/pymatgen-core
skills/pymatgen-core/SKILL.md
Use for pymatgen core objects and structure manipulation: Element/Specie/Composition, Lattice/Site/Structure/Molecule, oxidation states, structure edits, transformations, and serialization.
$ install --global
skillsauthnpx skillsauth add Hongyu-yu/matsci-ai-skills pymatgen-coreInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- pymatgen-core
- description:
- Use for pymatgen core objects and structure manipulation: Element/Specie/Composition, Lattice/Site/Structure/Molecule, oxidation states, structure edits, transformations, and serialization.
- short-description:
- pymatgen core structures
Pymatgen Core
Overview
Pymatgen core provides the fundamental objects for representing chemistry, lattices, sites, and structures. Use it to build, edit, and serialize structures and molecules before moving into specialized analysis or IO modules.
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.core import Structure, Lattice, Element
# your code here
When to Use This Skill
- Build or edit
Structure/Moleculeobjects - Work with compositions, oxidation states, or lattice transforms
- Serialize objects for storage or downstream workflows
Core Capabilities
1. Structures and Molecules
Structure/IStructurefor periodic systemsMolecule/IMoleculefor non-periodic systems- Site operations and lattice utilities
2. Chemistry Primitives
Element,Specie,Composition, and oxidation states- Formula reduction and fraction calculations
3. Transformations and Serialization
- Structure edits and transformations
- Monty
as_dict()/from_dict()serialization
Quick Workflow
- Identify the primary object type (
Structure,Molecule, orComposition). - Load/build and validate oxidation states or primitive cells.
- Apply transformations or edits.
- Serialize with
as_dict()or export via.to().
Resources
scripts/
Executable examples in the scripts/ directory:
2013-01-01-Basic_functionality.py- Basic structure, lattice, and composition operations.2013-01-01-Ordering_Disordered_Structures.py- Ordering disordered structures and site occupancy handling.
references/
Detailed reference material (load as needed):
references/modules.md- Core objects and usage patternsreferences/docs/usage.md- Local usage overviewreferences/docs/pymatgen.core.md- API details
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