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arXiv · 1907.12502

JeLLyFysh-Version1.0 -- a Python application for all-atom event-chain Monte Carlo

Philipp Hoellmer·Liang Qin·Michael F. Faulkner·A. C. Maggs·Werner Krauth
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Abstract

We present JeLLyFysh-Version1.0, an open-source Python application for event-chain Monte Carlo (ECMC), an event-driven irreversible Markov-chain Monte Carlo algorithm for classical N-body simulations in statistical mechanics, biophysics and electrochemistry. The application's architecture closely mirrors the mathematical formulation of ECMC. Local potentials, long-ranged Coulomb interactions and multi-body bending potentials are covered, as well as bounding potentials and cell systems including the cell-veto algorithm. Configuration files illustrate a number of specific implementations for interacting atoms, dipoles, and water molecules.

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Philipp Hoellmer, Liang Qin, Michael F. Faulkner, A. C. Maggs, Werner Krauth. 2019-07-29. JeLLyFysh-Version1.0 -- a Python application for all-atom event-chain Monte Carlo. https://doi.org/10.1016/j.cpc.2020.107168

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