Presentation Open Access
Extending OpenKIM with an Uncertainty Quantification Toolkit for Molecular Modeling
Kurniawan, Yonatan;
Petrie, Cody;
Transtrum, Mark;
Tadmor, Ellad;
Elliott, Ryan;
Karls, Daniel;
Wen, Mingjian
Atomistic simulations are an important tool in materials modeling. Interatomic potentials (IPs) are at the heart of such molecular models, and the accuracy of a model's predictions depends strongly on the choice of IP. Uncertainty quantification (UQ) is an emerging tool for assessing the reliability of atomistic simulations. The Open Knowledgebase of Interatomic Models (OpenKIM) is a cyberinfrastructure project whose goal is to collect and standardize the study of IPs to enable transparent, reproducible research. Part of the OpenKIM framework is the Python package, KIM-based Learning-Integrated Fitting Framework (KLIFF), that provides tools for fitting parameters in an IP to data. This paper introduces a UQ toolbox extension to KLIFF. We focus on two sources of uncertainty: variations in parameters and inadequacy of the functional form of the IP. Our implementation uses parallel-tempered Markov chain Monte Carlo (PTMCMC), adjusting the sampling temperature to estimate the uncertainty due to the functional form of the IP. We demonstrate on a Stillinger--Weber potential that makes predictions for the atomic energies and forces for silicon in a diamond configuration. Finally, we highlight some potential subtleties in applying and using these tools with recommendations for practitioners and IP developers.
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- Publication date:
- September 29, 2022
- DOI:
-
- Keyword(s):
- paper-presentation interatomic potential MCMC uncertainty quantification OpenKIM
- Grants:
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National Science Foundation:
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Collaborative Research: Reliable Materials Simulation based on the Knowledgebase of Interatomic Models (KIM) (1834332)
- Collaborative Research: Reliable Materials Simulation based on the Knowledgebase of Interatomic Models (KIM) (1834251)
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Collaborative Research: Reliable Materials Simulation based on the Knowledgebase of Interatomic Models (KIM) (1834332)
- Communities:
- License (for files):
- Creative Commons Attribution 4.0 International