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

Abstract

We present JeLLyFysh-Version1.0, an open-source Python application for eventchain 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.

Event-Chain Monte Carlo: Foundations, Applications, and Prospects

“…Thinning thus greatly simplifies ECMC when the mere evaluations of U M and of its derivatives are time-consuming. The JeLLyFysh application of subsection 6.2 implements thinning for potentials in a variety of settings (see [38]).…”

“…The open-source "JeLLyFysh" application [38] is the first general-purpose open-source implementation of ECMC. The configuration files of its Version 1.0 realize proof-of-concept of ECMC for interacting particle systems including the treatment of the Coulomb interaction.…”

“…If confirmed, the out-state is committed to the state of the system. Output may also be generated (see [38,Figure 5]).…”

Event-Chain Monte-Carlo Simulations of Dense Soft Matter Systems

“…The simulations for these soft matter applications have been performed within the highly modular polyeventchain framework, which is particularly suited for soft matter applications and will be presented in detail elsewhere. Jellyfish provides a similar EC framework with a focus on all atom simulations [22,23].…”

Non-equilibrium response and slow equilibration in hard disk systems

“…The invention of Event-Chain Monte Carlo (ECMC) [7] was the most crucial contribution to tackle the 2D melting problem [8,9]. Then its variants have been actively developed such as for all-atom model with generalized potential [10], hybrid scheme with EDMD [11] and Newtonian Event-Chain MC [12]. In general, particle positions' equilibration is much difficult, especially in highly dense systems rather than velocities due to the excluded volume effect being dominant.…”