TestLandscapes.jl

Julia implementations of basic potential energy landscapes for testing sampling, optimization, etc.
Author gideonsimpson
Popularity
3 Stars
Updated Last
2 Years Ago
Started In
May 2019

TestLandscapes.jl

Julia implementations of basic potential energy landscapes for testing sampling, optimization, etc.

This package can be added with the command:

(@v1.XYZ) pkg> add TestLandscapes

Currently, these landscapes are in dimensions one and two, but they allow for exploration of multiple minima, along with energetic and entropic bottlenecks.

These codes do not include derivatives. These can be obtained using ForwardDiff, https://github.com/JuliaDiff/ForwardDiff.jl

StaticArrays is required by some of the potentials. This substantially improves performance.

Acknowledgements

This work was supported in part by the US National Science Foundation Grant DMS-1818716.

References

These landscapes are motivated by the following publications:

  • Illustration of transition path theory on a collection of simple examples, Metzner, Schütte, and Vanden-Eijnden, J. Chem. Phys., 125, 084110, 2006.
  • Free Energy Computations, Lelièvre, Rousset, and Stoltz, Imperial College Press, 2006.
  • Role of Ito’s lemma in sampling pinned diffusion paths in the continuous-time limit, Malsom and Pinski, Phys. Rev. E, 94, 042131, 2016.
  • Nonlinear reaction coordinate analysis in the reweighted path ensemble, Lechner, Rogal, Juraszek, Ensing, and Bolhuis, J. Chem. Phys., 133, 174110, 2010.

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