Scalable Reactive Molecular Dynamics Simulations for Computational Synthesis
Ying Li, Ken-ichi Nomura, Joseph A. Insley, Vitali Morozov, Kalyan Kumaran, Nichols A. Romero, William A. Goddard III, Rajiv K. Kalia, Aiichiro Nakano, Priya Vashishta
Abstract
Reactive molecular dynamics (MD) simulation is a powerful research tool for describing chemical reactions. We eliminate the speed-limiting charge iteration in MD with a novel extended-Lagrangian scheme. The extended-Lagrangian reactive MD (XRMD) code drastically improves energy conservation while substantially reducing time-to-solution. Furthermore, we introduce a new polarizable charge equilibration (PQEq) model to accurately predict atomic charges and polarization. The XRMD code based on hybrid message passing+multithreading achieves a weak-scaling parallel efficiency of 0.977 on 786 432 IBM Blue Gene/Q cores for a 67.6 billion-atom system. The performance is portable to the second-generation Intel Xeon Phi, Knights Landing. Blue Gene/Q simulations for the computational synthesis of materials via novel exfoliation mechanisms for synthesizing atomically thin transition metal dichalcogenide layers will dominate nanomaterials science in this century.
Group Members
Li, Y., Nomura, K., Insley, J. A., Morozov, V., Kumaran, K., Romero, N. A., III, W. A. G., Kalia, R. K., Nakano, A., & Vashishta, P. (2019). Scalable Reactive Molecular Dynamics Simulations for Computational Synthesis. *Computing in Science & Engineering*, *21*(5), 64-75. https://doi.org/10.1109/MCSE.2018.110150043