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Sarkas - A Fast Pure Python Molecular Dynamics Code


Molecular dynamics (MD) simulations are a powerful technique to understand many-body systems at the atomistic level, helping us understand the influence of micro-scale structural and temporal properties on the observed macroscopic properties of interest. Though there exists MD codes for such simulations, to our knowledge there isn't a pure-Python production-scale MD code. This motivated us to develop Sarkas - a production-scale pure-Python open-source MD code for particles interacting through Coulomb and screened Coulomb potentials. Though pure-Python, Sarkas is high-performant with execution speeds comparable to compiled languages (eg. C). This is due to the extensive use of Numpy arrays and a just-in-time compilation using Numba. Sarkas simulates 3D systems with potential energy and forces computed using a highly efficient Particle-Particle Particle-Mesh (PPPM) algorithm. The systems of our interest are strongly coupled plasmas such as dusty plasmas, ultracold neutral plasmas and warm dense matter. The user-friendliness of Python combined with high performance enables Sarkas to serve as a useful design tool for experimentalists to efficiently sample a wide parameter space of interest.


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