Nano-scale chemically powered sphere-dimer motor

Nano-dimer is a molecular modelling software to study the dynamics of chemically powered self-propelled nanomotors (Kapral 2013; Colberg and Kapral 2017). The software combines molecular dynamics and multi-particle collision dynamics (Malevanets and Kapral 1999, 2000; Ihle and Kroll 2001) to simulate the molecular motion of a single to hundreds of sphere-dimer motors (Rückner and Kapral 2007) and their long-range hydrodynamic interaction in a solvent comprising several million particles.

Nano-dimer relies on novel computational techniques to scale from a multi-core processor to a parallel accelerator with thousands of scalar cores. The simulation algorithms are composed in the OpenCL C language using run-time code generation, which allows running simulations with optimal efficiency across a variety of devices, such as AMD GPUs, NVIDIA GPUs, and Intel CPUs.

A simulation is orchestrated using Lua scripts run with LuaJIT, an interpreter and tracing just-in-time compiler for the Lua language that provides native C data structures through its foreign function interface (FFI). Particle trajectories of nanomotors and solvent, and a versatile set of structural and dynamical observables are stored in an H5MD file, a file format for molecular data (de Buyl, Colberg, and Höfling 2014) based on the hierarchical data format (HDF5).

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