Sarkas: A fast pure-python molecular dynamics suite for plasma physics

This is the authors' abstract. We don't add key points for this paper.

We present an open-source, performant, pure-python molecular dynamics (MD) suite for non-ideal plasmas. The code, Sarkas, aims to accelerate the research process by providing an MD code complete with pre- and post-processing tools. Sarkas offers the ease of use of Python while employing the Numba library to obtain execution speeds comparable to that of compiled languages. The available tools in Sarkas include graphical displays of the equilibration process through a Jupyter interface and the ability to compute quantities such as, radial distribution functions, autocorrelation functions, and Green-Kubo relations. Many force laws used to simulate plasmas are included in Sarkas, namely, pure Coulomb, Yukawa and Molière pair-potentials. Sarkas also contains quantum statistical potentials and fast Ewald methods are included where necessary. An object-oriented approach allows for easy modification of Sarkas, such as adding new time integrators, boundary conditions and force laws. Program Title: Sarkas CPC Library link to program files: https://doi.org/10.17632/zwpr5mpwms.1 Developer's repository link: https://github.com/murillo-group/sarkas Licensing provisions: MIT Programming language: Python Nature of problem: Molecular dynamics (MD) is an important tool for non-ideal plasma physics research. The wealth of MD codes available are not designed for plasma physics problems. The available codes are written in low-level languages and do not provide pre- and post-processing libraries. These are instead written by researchers in interpreted languages, forcing researchers to have a high level of computing background. Solution method: Development of an MD suite for plasma physics, complete with pre- and post-processing tools most commonly used in plasma physics. The suite is entirely written in Python for enhanced user-friendliness. The slow speed of Python is mitigated by using the Numba library which is a just-in-time compiler for Python.