SOMA-BD: Brownian dynamics simulation for soft matter on GPU

This paper introduces a high-performance Brownian Dynamics simulation code designed for Nvidia GPUs. The code prioritizes accuracy with double-precision calculations and utilizes a bucket sort neighbor list for efficient particle interaction management. Additionally, a CUDA occupancy-aware autotuning system optimizes thread block size for diverse hardware configurations. Benchmarks demonstrate significant performance gains compared to existing tools, particularly for large-scale simulations with various interaction potentials (Lennard-Jones, Yukawa, DLVO). The software offers user-friendly configuration via JSON files and supports restarting simulations from both binary and XYZ data formats. Future work includes expanding supported interaction potentials, refining autotuning and investigating scalability. This open-source software empowers researchers in material science and related fields to conduct efficient and accurate BD simulations.