Niethammer Christoph, Becker Stefan, Bernreuther Martin, Buchholz Martin, Eckhardt Wolfgang, Heinecke Alexander, Werth Stephan, Bungartz Hans-Joachim, Glass Colin W, Hasse Hans, Vrabec Jadran, Horsch Martin
High Performance Computing Center Stuttgart , Nobelstr. 19, 70569 Stuttgart, Germany.
University of Kaiserslautern , Laboratory of Engineering Thermodynamics, Erwin-Schrödinger-Str. 44, 67663 Kaiserslautern, Germany.
J Chem Theory Comput. 2014 Oct 14;10(10):4455-64. doi: 10.1021/ct500169q. Epub 2014 Oct 1.
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.
介绍了分子动力学模拟代码ls1 mardyn。它是一个具有高度可扩展性的代码，针对超级计算架构上的大规模并行执行进行了优化，目前保持着拥有超过四万亿个粒子的最大分子模拟的世界纪录。它能够将对势应用于以前超出分子动力学模拟范围的长度和时间尺度。通过高效的动态负载平衡方案，即使对于具有挑战性的异构配置，它也能提供高可扩展性。目前，支持基于 Lennard-Jones 位点、点电荷和高阶极性的多中心刚性势模型。由于其模块化设计，ls1 mardyn 可以扩展到新的物理模型、方法和算法，使未来的用户能够根据各自的需求进行定制。可能的应用包括具有复杂几何形状的场景，如界面处的流体，以及传热传质的非平衡分子动力学模拟。
