Reproducible orchestration of best practices for reaction path optimization with the nudged elastic band

DOI

<p>The nudged elastic band (NEB) method is the standard approach for finding minimum energy paths and transition states on potential energy surfaces. Practical NEB calculations require several pre-processing steps: endpoint minimization, structural alignment, and initial path generation. These steps are typically handled by ad-hoc scripts or manual intervention, introducing errors and hindering reproducibility. We present a fully automated, open-source Snakemake workflow for small gas phase molecules that couples modern machine learning potentials (PET-MAD) to the eOn saddle point search software. Each step of the calculation lifecycle is encoded as an explicit dependency graph, from model retrieval and endpoint preparation through path initialization and band optimization. The workflow resolves all software dependencies from conda-forge, ensuring identical execution across platforms. Validation on the HCN to HNC isomerization demonstrates that the automated pipeline recovers the known single-barrier energy profile and product energy without manual intervention.</p> <p> </p> <p>This record contains the data needed to "rehydrate" the Github repository to the point of submission including the models and results.</p>

Identifier
DOI https://doi.org/10.24435/materialscloud:15-7q
Related Identifier https://neb-orchestrator.rgoswami.me
Related Identifier https://github.com/HaoZeke/eon_orchestrator
Related Identifier https://archive.materialscloud.org/communities/mcarchive
Related Identifier https://doi.org/10.24435/materialscloud:sv-k4
Metadata Access https://archive.materialscloud.org/oai2d?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai:materialscloud.org:z41cv-q4h43
Provenance
Creator Goswami, Rohit
Publisher Materials Cloud
Contributor Goswami, Rohit
Publication Year 2026
Rights info:eu-repo/semantics/openAccess; Creative Commons Attribution 4.0 International; https://creativecommons.org/licenses/by/4.0/legalcode
OpenAccess true
Contact archive(at)materialscloud.org
Representation
Language English
Resource Type info:eu-repo/semantics/other
Format text/markdown; application/x-xz
Discipline Materials Science and Engineering