ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems

C Niethammer and S Becker and M Bernreuther and M Buchholz and W Eckhardt and A Heinecke and S Werth and HJ Bungartz and CW Glass and H Hasse and J Vrabec and M Horsch, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10, 4455-4464 (2014).

DOI: 10.1021/ct500169q

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multicenter rigid potential models based on Lennard-Jones sites, point charges, and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, such as fluids at interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer.

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