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 0.2 - published on 10 Apr 2019

doi:10.21981/85G0-1G97 cite this

Open source: license | download

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    Notebook screenshot of functional error Simulation manager notebook Functional derivative perturbation width comparison Functional derivative perturbation height comparison Functional derivative method comparison

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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. Functional uncertainty quantification for isobaric molecular dynamics simulations and defect formation energies. (Accepted, MSMSE 2019).
  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 (2019), "FunUQ for MD," http://nanohub.org/resources/funuq. (DOI: 10.21981/85G0-1G97).

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