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Title: Scalable Reactive Molecular Dynamics Simulations for Computational Synthesis

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.

Authors:
; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1593152
DOE Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article
Journal Name:
Computing in Science and Engineering
Additional Journal Information:
Journal Volume: 21; Journal Issue: 5
Country of Publication:
United States
Language:
English
Subject:
Simulation, Modeling, Performance, and Visualization

Citation Formats

Li, Ying, Nomura, Ken-ichi, Insley, Joseph, Morozov, Vitali, Kumaran, Kalyan, Romero, Nichols A., Goddard, William, Kalia, Rajiv, Nakano, Aiichiro, and Vashishta, Priya. Scalable Reactive Molecular Dynamics Simulations for Computational Synthesis. United States: N. p., 2019. Web. doi:10.1109/MCSE.2018.110150043.
Li, Ying, Nomura, Ken-ichi, Insley, Joseph, Morozov, Vitali, Kumaran, Kalyan, Romero, Nichols A., Goddard, William, Kalia, Rajiv, Nakano, Aiichiro, & Vashishta, Priya. Scalable Reactive Molecular Dynamics Simulations for Computational Synthesis. United States. doi:10.1109/MCSE.2018.110150043.
Li, Ying, Nomura, Ken-ichi, Insley, Joseph, Morozov, Vitali, Kumaran, Kalyan, Romero, Nichols A., Goddard, William, Kalia, Rajiv, Nakano, Aiichiro, and Vashishta, Priya. Sun . "Scalable Reactive Molecular Dynamics Simulations for Computational Synthesis". United States. doi:10.1109/MCSE.2018.110150043.
@article{osti_1593152,
title = {Scalable Reactive Molecular Dynamics Simulations for Computational Synthesis},
author = {Li, Ying and Nomura, Ken-ichi and Insley, Joseph and Morozov, Vitali and Kumaran, Kalyan and Romero, Nichols A. and Goddard, William and Kalia, Rajiv and Nakano, Aiichiro and Vashishta, Priya},
abstractNote = {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.},
doi = {10.1109/MCSE.2018.110150043},
journal = {Computing in Science and Engineering},
number = 5,
volume = 21,
place = {United States},
year = {2019},
month = {9}
}