nebscape 0.3.0

Automated workflow for surface reactions.

NEBscape

NEBscape automates the sampling of minimum energy paths (MEPs) for surface reactions, combining global geometry optimization, atom-mapping, and NEB calculations into a single workflow — requiring minimal human input.

Installation from source

git clone https://gitlab.mpcdf.mpg.de/hjung/nebscape.git
pip install .

Required Inputs

This workflow prepares initial and final geometry with global optimization (e.g. minima hopping) and provides automatic atom-mapping and generates possible permutation of symmetric atoms. Only following three inputs are required.

1. List of reaction SMILES string in reaction_smiles.txt (e.g. O=[C][CH2][O]>>[C-]#[O+].[CH2]=O)
2. slab information in slab.xyz (Slab should use tag to indicate which atoms are fixed (tag=0) and which atoms are relaxed(tag=1))
3. Calculator (e.g. MLIP like MACE)

Setting

This workflow uses wfl and expyre for remote submission, so configure the following related settings

• config.json file has to be set for remote submission to HPC (Can be found in /example)
• According to config.json, the remote_info entries should be adapted to your environment.

Documentation

• Home - overview
• Installation - installation
• Setting up Local Environment - setting for wfl and expyre
• Input Preparation - input file preparation
  • Setting File - configuration settings
• Geometry Generation - generating initial geometries
  • Minima Hopping - running minima hopping
  • Autoadsorbate - adsorbate placement
• Interpolation Generation - generating initial minimum energy paths
  • Atom Mapping - mapping atoms between endpoints
  • Geometry Selection - selecting endpoint geometries
  • FS-to-IS Alignment - aligning final to initial state
  • Index Permutation - permuting atom indices
• Running NEB - running the NEB calculation

(We are currently working on improving the documentation / tutorial. Let us know if you need help or suggestions.)

References

If you use this code, please cite our paper:

Hyunwook Jung, Emanuel Colombi Manzi, Tiago J. Goncalves, et al. From Global Optimization to Transition State Search: An Automated Workflow for Surface Reaction Barriers. ChemRxiv. 17 April 2026.

https://doi.org/10.26434/chemrxiv.15002133/v1

@article{
doi:10.26434/chemrxiv.15002133/v1,
author = {Hyunwook Jung  and Emanuel Colombi Manzi  and Tiago J. Goncalves  and Vanessa J. Bukas  and Sandip De  and Johannes T. Margraf  and Karsten Reuter  and Hendrik H. Heenen },
title = {From Global Optimization to Transition State Search: An Automated Workflow for Surface Reaction Barriers},
journal = {ChemRxiv},
volume = {2026},
number = {0417},
pages = {},
year = {2026},
doi = {10.26434/chemrxiv.15002133/v1},
URL = {https://chemrxiv.org/doi/abs/10.26434/chemrxiv.15002133/v1},
eprint = {https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15002133/v1}}

Contact

If you have any questions, please contact us at [e-mail] Also for any bugs or issues, you can use gitlab issues.

License

The NEBscape code is published and distributed under the MIT License.