No abstract

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 which 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. * To whom correspondence should be addressed † High Performance Computing Center Stuttgart (HLRS), Germany ‡ Laboratory of Engineering Thermodynamics (LTD), Univ. of Kaiserslautern, Germany ¶ Scientific Computing in Computer Science (SCCS), TU München, Germany § Thermodynamics and Energy Technology (ThEt), Univ. of Paderborn, Germany 1 Presently, multi-center 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, e.g.for fluids at interfaces, as well as non-equilibrium molecular dynamics simulation of heat and mass transfer.

A new version release (2.0) of the molecular simulation tool ms2 [S. Deublein et al., Comput. Phys. Commun. 182 (2011) 2350] is presented. Version 2.0 of ms2 features a hybrid parallelization based on MPI and OpenMP for molecular dynamics simulation to achieve higher scalability. Furthermore, the formalism by Lustig [R.Lustig, Mol. Phys. 110 (2012) 3041] is implemented, allowing for a systematic sampling of Massieu potential derivatives in a single simulation run. Moreover, the Green-Kubo formalism is extended for the sampling of the electric conductivity and the residence time. To remove the restriction of the preceding version to electro-neutral molecules, Ewald summation is implemented to consider ionic long range interactions. Finally, the sampling of the radial distribution function is added.

No abstract

A new version release (4.0) of the molecular simulation tool ms2 (Deublein et al., 2011; is presented. Version 4.0 of ms2 features two additional potential functions to address the repulsive and dispersive interactions in a more versatile way, i.e. the Mie potential and the Tang-Toennies potential. This version further introduces Kirkwood-Buff integrals based on radial distribution functions, which allow the sampling of the thermodynamic factor of mixtures with up to four components, orientational distribution functions to elucidate mutual configurations of neighboring molecules, thermal diffusion coefficients of binary mixtures for heat, mass as well as coupled heat and mass transport, Einstein relations to sample transport properties with an alternative to the Green-Kubo formalism, dielectric constant of non-polarizable fluid models, vapor-liquid equilibria relying on the second virial coefficient and cluster criteria to identify nucleation.