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].

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

This tool is developed by the Strachan Research Group:

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

1. Reeve, S. T. & Strachan, A. Functional uncertainty quantification for isobaric molecular dynamics simulations and defect formation energies. Modell. Simul. Mater. Sci. Eng. 27(4), 044002. (2019). (DOI: 10.1088/1361-651X/ab16fa)
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. Modell. 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).

Researchers should cite this work as follows:

• Sam Reeve, Alejandro Strachan (2019), "FunUQ for MD," https://nanohub.org/resources/funuq. (DOI: 10.21981/85G0-1G97).

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1. interatomic potentials
2. Jupyter notebooks
3. LAMMPS
4. materials science
5. molecular dynamics (MD)
6. uncertainty quantification (UQ)