The ls1 mardyn release paper

Please cite this paper in all publications that use ls1 mardyn.

C. Niethammer, S. Becker, M. Bernreuther, M. Buchholz, W. Eckhardt, A. Heinecke, S. Werth, H.-J. Bungartz, C. W. Glass, H. Hasse, J. Vrabec, and M. Horsch (2014): ls1 mardyn: The massively parallel molecular dynamics code for large systems., Journal of Chemical Theory and Computation 10 (10): 4455-4464.

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.

Supercomputing for molecular dynamics simulations

A. Heinecke, W. Eckhardt, M. Horsch, and H.-J. Bungartz (2015): Supercomputing for Molecular Dynamics Simulations. Springer, Heidelberg (ISBN 978-3-319-17147-0).

This work presents modern implementations of molecular dynamics algorithms, e.g. as employed by ls1 mardyn, a simulation program for engineering applications. The text focuses on HPC-related aspects, taking Intel Xeon and Intel Xeon Phi clusters as representatives of current platforms. The work describes distributed and shared-memory parallelization on these platforms, including load balancing, with a particular focus on the efficient implementation of the compute kernels. The text also discusses the software architecture of the ls1 mardyn code.

Hybrid molecular-continuum methods

P. Neumann, W. Eckhardt, and H.-J. Bungartz (2014): Hybrid molecular-continuum methods: From prototypes to coupling software, Computers and Mathematics with Applications 67 (2): 272-281.

In this contribution, we review software requirements in hybrid molecular-continuum simulations. For this purpose, we analyze a prototype implementation which combines two frameworks - the molecular dynamics framework MarDyn and the framework Peano for spatially adaptive mesh-based simulations - and point out particular challenges of a general coupling software. Based on this analysis, we discuss the software design of our recently published coupling tool. We explain details on its overall structure and show how the challenges that arise in respective couplings are resolved by the software.

(By MarDyn, the authors refer to the ls1 mardyn program.)