Hoellmer Qin Faulkner Maggs Krauth 2019
From Werner KRAUTH
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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. | 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. | ||
- | '''Computer Physics Communications [https://doi.org/10.1016/j.cpc.2020.107168 Computer Physics Communications 253 107168 | + | '''[https://doi.org/10.1016/j.cpc.2020.107168 Computer Physics Communications 253 107168 (2020)]''' (open-source paper). |
- | 2020 (2020)]''' (open-source paper). | + | |
[http://arxiv.org/pdf/1907.12502 Electronic version (from arXiv)] | [http://arxiv.org/pdf/1907.12502 Electronic version (from arXiv)] | ||
[https://github.com/jellyfysh/JeLLyFysh https://github.com/jellyfysh GitHub repertory], from which the project may be [https://en.wikipedia.org/wiki/Fork_(software_development) forked]. | [https://github.com/jellyfysh/JeLLyFysh https://github.com/jellyfysh GitHub repertory], from which the project may be [https://en.wikipedia.org/wiki/Fork_(software_development) forked]. |
Revision as of 23:10, 1 June 2020
P. Hoellmer, L. Qin, M. F. Faulkner, A. C. Maggs, W. Krauth JeLLyFysh-Version1.0 -- a Python application for all-atom event-chain Monte Carlo (2020)
Paper
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.
Computer Physics Communications 253 107168 (2020) (open-source paper).
Electronic version (from arXiv)
https://github.com/jellyfysh GitHub repertory, from which the project may be forked.