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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JeLLyFysh-Version1.0 - 用于全原子事件链蒙特卡罗的 Python 应用程序

我们提出了 JeLLyFysh-Version1.0，这是一个用于事件链蒙特卡罗 (ECMC) 的开源 Python 应用程序，这是一种事件驱动的不可逆马尔可夫链蒙特卡罗算法，用于统计力学、生物物理学和电化学中的经典 N 体模拟。该应用程序的架构密切反映了 ECMC 的数学公式。涵盖了局部电位、长程库仑相互作用和多体弯曲电位，以及边界电位和细胞系统，包括细胞否决算法。配置文件说明了许多相互作用的原子、偶极子和水分子的具体实现。