Extending OpenKIM with an Uncertainty Quantification Toolkit for Molecular Modeling

  • Yonatan Kurniawan (Creator)
  • Cody Petrie (Creator)
  • Mark Transtrum (Creator)
  • Ellad B Tadmor (Creator)
  • Ryan S Elliott (Creator)
  • Daniel Karls (Creator)
  • Mingjian Wen (Creator)



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.
Date made available2022

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