Tutorials

Step-by-step guides for running NEB calculations.

Start with HCN Isomerization to validate your installation, then work through increasing complexity.

Examples by Complexity

Beginner (1-5 atoms)

  • HCN → HNC Isomerization

    • 3 atoms, linear H-transfer

    • Validates installation

    • Expected barrier: ~1.8 eV

    • Run: pixi run -e eon hcn

Intermediate (6-10 atoms)

  • S_N2 Reaction

    • 6 atoms, backside attack

    • Demonstrates IRA value

    • Expected barrier: ~1.1 eV

    • Run: pixi run -e eon sn2

  • Vinyl Alcohol Tautomerization

    • 8 atoms, H-transfer

    • Keto-enol tautomerization

    • Expected barrier: ~2.2 eV

    • Run: pixi run -e eon vinyl-alcohol

Advanced (10+ atoms)

  • Diels-Alder Reaction

    • 16 atoms, ring closure

    • Multi-molecular reaction

    • Expected barrier: ~1.2 eV

    • Run: pixi run -e eon diels-alder

Your Own System

  • Add Your Own System - Complete step-by-step guide

    • Structure preparation

    • Configuration

    • Validation

    • Troubleshooting

Common Issues

Problem

Solution

eonclient not found

Install with pixi install -e eon

Plotting fails

Check RGPYCRUMBS_AUTO_DEPS=1

High barrier (>5 eV)

Check atom permutation

NEB doesn’t converge

Increase images, reduce max_move

Next Steps