Parallel software design of large-scale diamond-structured crystals molecular dynamics simulation

JG Liang and QQ Li and H Han and Y Fu, FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE, 166, 107694 (2025).

DOI: 10.1016/j.future.2024.107694

Molecular dynamics (MD) simulation, a crucial technique for investigating atomic structure and dynamic properties, has become a primary method for studying the thermodynamic properties of dielectric materials, such as silicon, and their low-dimensional nanostructures. Diamond-structured semiconductors exhibit unique crystallographic properties. Achieving optimal simulation performance on supercomputing platforms necessitates specialized parallel design and optimization, considering both atom spatial characteristics and platform architecture. To tackle storage challenges in large-scale simulations of diamond- structured crystals, we designed a hierarchical storage-based atom data organization and a neighbor list construction algorithm exploiting positional offsets. Furthermore, a novel "point-line-plane"communication model was implemented. This model leverages the distribution of atom neighbors and a fixed neighbor list, enhancing communication efficiency via data packing to enable scalable simulations. A numerical simulation software, Diamond-MD, was developed for simulating diamond-structured crystals, enabling simulations at the 100 million-atom scale. Benchmark results indicate that Diamond-MD achieves a 44% reduction in memory usage and a 48% improvement in computational performance compared to LAMMPS. Moreover, Diamond-MD demonstrates excellent scalability.

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