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Journal Articles Computer Physics Communications Year : 2020

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

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1
Liang Qin
  • Function : Author
Michael F. Faulkner
  • Function : Author
A. Maggs
Werner Krauth
Philipp Höllmer
Michael Faulkner

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.

Dates and versions

hal-03008359 , version 1 (16-11-2020)

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Cite

Philipp Hoellmer, Liang Qin, Michael F. Faulkner, A. Maggs, Werner Krauth, et al.. JeLLyFysh-Version1.0 — a Python application for all-atom event-chain Monte Carlo. Computer Physics Communications, 2020, 253, pp.107168. ⟨10.1016/j.cpc.2020.107168⟩. ⟨hal-03008359⟩

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