Packmol Runner
2025A reproducible workflow for generating initial molecular simulation structures using Packmol and ASE. The project is designed to reduce repetitive manual setup and make packing workflows easier to reuse across different systems.
What it does
- Builds initial coordinates for bulk and slab-based simulation systems.
- Uses YAML-driven configuration to control composition and workflow behavior.
- Combines Packmol and ASE to make structure generation more reproducible and easier to automate.
My role
Designed the repository structure, organized the configuration-based workflow, and developed a reusable pipeline for generating simulation-ready structures across multiple use cases.
Figure
How to run
git clone https://github.com/Gibeom-KIM-02/packmol_runner
cd packmol_runnerSee the repository README for environment setup, YAML configuration, and workflow-specific commands.