FunUQ for MD

By Sam Reeve1, Alejandro Strachan2

1. Lawrence Livermore National Laboratory 2. Purdue University

Functional uncertainty quantification for molecular dynamics

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Version 0.1 - published on 22 Oct 2018

doi:10.4231/D3WH2DH4R cite this

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Abstract

This tool is a collection of Jupyter notebooks which go through all steps of functional uncertainty quantification (FunUQ) for interatomic potentials in molecular dynamics, matching cases from multiple papers. The main steps are:

  • Define folders, simulation system, and models
  • (Run simulations)
  • Calculate functional derivatives
  • Calculate correction for quantities of interest due to changing from one function to another

If you use this tool for your research, please cite this tool and consider also citing the FunUQ literature [1-3].

 

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LAMMPS molecular dynamics simulation code [4], an open source project distributed by Sandia National Laboratory: http://lammps.sandia.gov/doc/Manual.html

Bio

This tool is developed by the Strachan Research Group:

https://nanohub.org/groups/strachangroup/

References

  1. Reeve, S. T. Strachan, A. Quantifying uncertainties originating from interatomic potentials in molecular dynamics. (Submitted to MSMSE 2018).
  2. Reeve, S. T. Strachan, A. Error correction in multi-fidelity molecular dynamics simulations using functional uncertainty quantification. J. Comput. Phys. 334, 207-220 (2017). (DOI: 10.1016/j.jcp.2016.12.039)
  3. Strachan, A., Mahadevan, S., Hombal, V. & Sun, L. Functional derivatives for uncertainty quantification and error estimation and reduction via optimal high-fidelity simulations. Modelling Simul. Mater. Sci. Eng. 21, 065009 (2013). (DOI: 10.1088/0965-0393/21/6/065009)
  4. Plimpton, S. Fast Parallel Algorithms for Short-Range Molecular Dynamics. J. Comput. Phys. 117, 1–19 (1995).

Cite this work

Researchers should cite this work as follows:

  • Sam Reeve; Alejandro Strachan (2018), "FunUQ for MD," http://nanohub.org/resources/funuq. (DOI: 10.4231/D3WH2DH4R).

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