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

Philipp Hoellmer (1) , Liang Qin , Michael F. Faulkner , A. Maggs , Werner Krauth , Philipp Höllmer , Michael Faulkner

1 Rheinische Friedrich-Wilhelms-Universität Bonn

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.

Domains: Physics [physics]

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⟩