Quickstart Guide¶

Date:

2026-03-14

1 Prerequisites¶

pixi installed (https://pixi.sh)
Git

2 Installation¶

# Clone repository
git clone https://github.com/HaoZeke/eon_orchestrator.git
cd eon_orchestrator

# Install dependencies (includes eOn)
pixi install -e eon

3 Quick Validation¶

Test workflow without running NEB (no eOn client needed):

pixi run validate

Expected: Shows DAG with ~10 jobs

4 Run Your First NEB¶

# HCN isomerization (3 atoms, ~2 min)
pixi run -e eon hcn

# Check results
cat results/neb/hcn_isom/results.dat
ls -lh results/plots/hcn_isom/

5 Available Examples¶

Command	System	Atoms	Time
`pixi run -e eon hcn`	HCN → HNC	3	2 min
`pixi run -e eon sn2`	F⁻ + CH₃F	6	3 min
`pixi run -e eon vinyl-alcohol`	Enol → Keto	8	5 min
`pixi run -e eon diels-alder`	Diels-Alder	16	10 min

6 Your Own System¶

Copy example config:

cp examples/hcn_isom/config.yaml my_system.yaml

Edit paths to your structures:

systems:
  my_reaction:
    reactant: /path/to/reactant.con
    product: /path/to/product.con
    use_ira: true

Run:

#+begin_srcbash snakemake –configfile my_system.yaml-c4#+end_src

7 Next Steps¶

HCN Tutorial - Detailed walkthrough
Parameter Guide - Choosing NEB parameters
Developer Notes - Extending the workflow

8 Citation¶

R. Goswami, M. Gunde, and H. Jónsson, arXiv:2601.12630 (2026). doi: 10.48550/arXiv.2601.12630