NEB Orchestrator

Author:

Rohit Goswami

Version:

0.1.0

License:

MIT

CI Status License: MIT

Modular Snakemake workflow for automated Nudged Elastic Band (NEB) calculations using eOn with machine learning potentials (PET-MAD/uPET).

Quick Start

git clone https://github.com/HaoZeke/eon_orchestrator.git
cd eon_orchestrator
pixi install -e eon

# Validate workflow (no eOn needed)
pixi run validate

# Run example (requires eOn)
pixi run -e eon hcn

Features

  • Each workflow stage is a separate, reusable Snakemake rule module

  • pixi manages all dependencies for reproducibility

  • PET-MAD/uPET machine learning potentials from HuggingFace

  • 1D energy profiles and 2D RMSD landscape visualization

  • Tested on five example systems (3 to 22 atoms)

System Applicability

Optimized for gas-phase molecular systems (5-50 atoms): single or multiple bond breaking/forming, isomerization, proton transfer, and conformational changes.

Surface reactions, condensed phase, or enzymatic systems require modifications to cell parameters and boundary conditions.

Getting Started

Reference

Developer Guide

Community