Accelerating dissipative particle dynamics simulations for soft matter systems

Nguyen, Trung Dac; Plimpton, Steven J.

doi:10.1016/j.commatsci.2014.10.068

Title: Accelerating dissipative particle dynamics simulations for soft matter systems

Journal Article · Wed Nov 26 00:00:00 EST 2014 · Computational Materials Science

DOI:https://doi.org/10.1016/j.commatsci.2014.10.068· OSTI ID:1565290

Nguyen, Trung Dac ^[1]; Plimpton, Steven J. ^[2]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). National Center for Computational Sciences
Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

Dissipative particle dynamics (DPD) is a coarse-grained particle-based simulation method that offers microscopic-scale insights into soft matter systems. We present an efficient implementation of a DPD model for graphical processing units (GPUs). As implemented in the LAMMPS molecular dynamics package, it can run effectively on current-generation supercomputers which often have hybrid nodes containing multi-core CPUs and (one or more) GPUs. Using efficient communication of information between the CPUs and GPUs, DPD interactions can be computed on the GPU while other portions of a full simulation model (boundary conditions, constraints, bonded interactions, diagnostic calculations, etc.) can be performed on the CPU. Our GPU-enhanced runs show a speedup of up to 9.5× versus many-core CPU simulations, and can run scalably across thousands of compute nodes. We briefly discuss how the new GPU implementation was validated against the CPU version for thermodynamics, diffusion, and hydrodynamic behavior. We also highlight large-scale models which the faster DPD implementation has enabled, for studies of monolayer self-assembly and thin-film instabilities.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)

Sponsoring Organization:: USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1565290

Alternate ID(s):: OSTI ID: 1250303; OSTI ID: 1820891

Journal Information:: Computational Materials Science, Vol. 100, Issue PB; ISSN 0927-0256

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 35 works

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Effect of solvent quality on Poiseuille flow of polymer solutions in microchannels: A dissipative particle dynamics study Xu, Shaofeng; Lou, Yinghou; He, Ping Journal of Applied Polymer Science, Vol. 136, Issue 15 https://doi.org/10.1002/app.47345	journal	December 2018
Molecular Dynamics Simulation to Investigate the Rake Angle Effects on Nanometric Cutting of Single Crystal Ni3Al Feng, Rui-cheng; Qi, Yong-nian; Zhu, Zong-xiao International Journal of Precision Engineering and Manufacturing, Vol. 21, Issue 4 https://doi.org/10.1007/s12541-019-00249-z	journal	December 2019
A many-body dissipative particle dynamics study of nanoneedle-liquid interface Falsafi, Ali; Nejat Pishkenari, Hossein Journal of Applied Physics, Vol. 124, Issue 21 https://doi.org/10.1063/1.5051118	journal	December 2018
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