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Accelerating dissipative particle dynamics simulations for soft matter systems

Trung Dac Nguyen, Steven J. Plimpton
2015 Computational materials science  
Dissipative particle dynamics (DPD) is a coarse-grained particle-based simulation method that offers microscopicscale insights into soft matter systems.  ...  We present an efficient implementation of a DPD model for graphical processing units (GPUs).  ...  Introduction Dissipative particle dynamics (DPD) was first proposed by Hoogerbrugge and Koelman in 1992 as a particle-based method for studying hydrodynamic phenomena [1] .  ... 
doi:10.1016/j.commatsci.2014.10.068 fatcat:voa2tgcrbffbhizpmyuhc2pun4

Efficient mesoscale hydrodynamics: Multiparticle collision dynamics with massively parallel GPU acceleration

Michael P. Howard, Athanassios Z. Panagiotopoulos, Arash Nikoubashman
2018 Computer Physics Communications  
We present an efficient open-source implementation of the multiparticle collision dynamics (MPCD) algorithm that scales to run on hundreds of graphics processing units (GPUs).  ...  We especially focus on optimizations for modern GPU architectures and communication patterns between multiple GPUs.  ...  Acknowledgements This research is part of the Blue Waters sustained-petascale computing project, which is supported by the  ... 
doi:10.1016/j.cpc.2018.04.009 fatcat:7mdnhg63vng5vmy7i4dy2b5oxm

Strong scaling of general-purpose molecular dynamics simulations on GPUs

Jens Glaser, Trung Dac Nguyen, Joshua A. Anderson, Pak Lui, Filippo Spiga, Jaime A. Millan, David C. Morse, Sharon C. Glotzer
2015 Computer Physics Communications  
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587).  ...  We are able to demonstrate equivalent or superior scaling on up to 3,375 GPUs in Lennard-Jones and dissipative particle dynamics (DPD) simulations of up to 108 million particles.  ...  This research is part of the Blue Waters sustained-petascale computing project, which is supported by the National Science Foundation (award number ACI 1238993) and the state of Illinois.  ... 
doi:10.1016/j.cpc.2015.02.028 fatcat:xweqlkq7gna3tfdcmwo6jpd52e

A "vortex in cell" model for quasi-geostrophic, shallow water dynamics on the sphere

A. Mohammadian, John Marshall
2010 Ocean Modelling  
The vortex in cell (VIC) method has been found to be an attractive computational choice for solving a number of fluid dynamical problems.  ...  The Lagrangian advection of particles leads to stability of the method even for long time steps.  ...  Acknowledgements We thank the Physical Oceanography program of the US National Science Foundation for support of this study. It is part of our contribution to the DIMES experiment.  ... 
doi:10.1016/j.ocemod.2010.01.001 fatcat:gudiiiod3ve4fd3fgdgrfvymai

A parallel algorithm for 3D particle tracking and Lagrangian trajectory reconstruction

Douglas Barker, Jonathan Lifflander, Anshu Arya, Yuanhui Zhang
2011 Measurement science and technology  
The parallel tracking algorithm was evaluated with three data sets including the particle image velocimetry standard 3D images data set #352, a uniform data set for optimal parallel performance and a computational-fluid-dynamics-generated  ...  The parallel algorithm is adaptable and could be easily modified to use any sequential tracking algorithm, which inputs frames of 3D particle location data and outputs particle trajectories.  ...  Acknowledgments We gratefully acknowledge the use of the Turing cluster maintained and operated by the Computational Science and Engineering Program at the University of Illinois.  ... 
doi:10.1088/0957-0233/23/2/025301 fatcat:77u265tynfegnhsjwlsif2btuu

Abstracts for the June 27-29 Princeton Conference: Discrete Models for Fluid Mechanics [article]

Yue-Hong Qian
1994 arXiv   pre-print
Submitted by the authors for the June 27-29 Princeton Conference. Questions should be directed to: qian@cfd.princeton.edu  ...  , extensive random number generators for probabilistic boundary conditions, transpose buffers for supporting a bit-serial word-parallel organization and address sequences optimized for efficient DRAM page-mode  ...  A small number of random bits at each site produce random walks, and simple synchronous update rules permit highly efficient implementation using multispin coding techniques and/or massively parallel machines  ... 
arXiv:comp-gas/9405007v1 fatcat:4pupm2oilbfwnopv7olkcdqnx4

Free-Surface Flow Simulations with Smoothed Particle Hydrodynamics Method using High-Performance Computing [chapter]

Corrado Altomare, Giacomo Viccione, Bonaventura Tagliafierro, Vittorio Bovolin, José Manuel Domínguez, Alejandro Jacobo Cabrera Crespo
2018 Computational Fluid Dynamics - Basic Instruments and Applications in Science  
SPH is a meshless particle method based on Lagrangian formulation by which the fluid domain is discretized as a collection of computing fluid particles.  ...  However, taking the advantage of GPU's parallel computing techniques, simulations involving up to 10 9 particles can be achieved.  ...  Part of the computations was carried within the high-performance computing for Environmental Fluid Mechanics (HPCEFM17) project.  ... 
doi:10.5772/intechopen.71362 fatcat:gj6o6yevkrerrkhldzggqpgxu4

Progress in particle-based multiscale and hybrid methods for flow applications

Tom-Robin Teschner, László Könözsy, Karl W. Jenkins
2016 Microfluidics and Nanofluidics  
Acknowledgments This work has been supported by the Centre of Fluid Mechanics and Computational Science, EEB6001R.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution  ...  Dissipative particle dynamics method Dissipative particle dynamics (DPD) is a particle-based method and has high resemblance to MD which can be regarded as a coarse-grained version of it.  ... 
doi:10.1007/s10404-016-1729-y fatcat:z7l5bu4o3fea3mcg5cznlodppu

Parallel computing works!

Marcin Paprzycki
1996 IEEE Parallel & Distributed Technology Systems & Applications  
sub-domains have roughly equal numbers of particles.  ...  Dynamic load baiancing is accomplished by repartitioning the simulations domain into sub-domains with roughly equal particle numbers when the CHAPTER 9.  ...  The data available for the tracking task consist, essentially, of line of sight measurements from various sensing platforms to individual objects in the target ensemble at (fairly) regular time intervals  ... 
doi:10.1109/mpdt.1996.7102339 fatcat:r6x46zu2pfd4rin4qpzt7ftqqq

Monte Carlo methods for massively parallel computers [article]

Martin Weigel
2017 arXiv   pre-print
We discuss important algorithmic requirements for such highly parallel simulations, such as the challenges of random-number generation for such cases, and outline a number of general design principles  ...  polymers and particle systems.  ...  of threads for generating these random numbers.  ... 
arXiv:1709.04394v1 fatcat:l25zmj2rcfej3ew4xh6mv5ul3u

Direct Simulation Monte Carlo for astrophysical flows – I. Motivation and methodology

Martin D. Weinberg
2014 Monthly notices of the Royal Astronomical Society  
This project is motivated by the need to understand the controlling dynamics at interfaces between gases of widely differing densities and temperature, i.e. multiphase media.  ...  We describe a hybrid Direct Simulation Monte Carlo (DSMC) code for simultaneously solving the collisional Boltzmann equation for gas and the collisionless Boltzmann equation for stars and dark matter for  ...  To simplify the parallel domain decomposition and exploit the typical cluster topology, we use a two-level nested tree as follows.  ... 
doi:10.1093/mnras/stt2406 fatcat:ctddkc24hbatnmiooeusmfik2m

Novel fluid detail enhancement based on multi-layer depth regression analysis and FLIP fluid simulation

Yuxing Qiu, Lipeng Yang, Shuai Li, Qing Xia, Hong Qin, Aimin Hao
2016 Computer Animation and Virtual Worlds  
First, we capture the depth buffer of the fluid surface dynamically from the top of scene.  ...  The core of our method is the organic of multi-layer depth image regression analysis and fluid implicit particle fluid simulation of which the regression analysis induces the criterion where the fluid  ...  We also thank the anonymous reviewers for their constructive critiques.  ... 
doi:10.1002/cav.1741 fatcat:bjklafrmrjhttillkxzek7xd7q

Simulating cosmic structure formation with the GADGET-4 code [article]

Volker Springel, Rüdiger Pakmor, Oliver Zier, Martin Reinecke
2021 arXiv   pre-print
adapted to high dynamic range zoom-calculations with extreme variability of the particle number density in the simulated volume.  ...  MPI/shared-memory parallelization and communication strategy, and a more-sophisticated domain decomposition algorithm.  ...  that were instrumental for the test simulations of this paper.  ... 
arXiv:2010.03567v2 fatcat:5a4skp2vfzemnh4wkdp3cwhfae

Simulating cosmic structure formation with the GADGET-4 code

Volker Springel, Rüdiger Pakmor, Oliver Zier, Martin Reinecke
2021 Monthly notices of the Royal Astronomical Society  
adapted to high dynamic range zoom-calculations with extreme variability of the particle number density in the simulated volume.  ...  MPI/shared-memory parallelization and communication strategy, and a more-sophisticated domain decomposition algorithm.  ...  that were instrumental for the test simulations of this paper.  ... 
doi:10.1093/mnras/stab1855 fatcat:xlfwvefqxjfmvki5v4uzgmekdq

GPU accelerated population annealing algorithm

Lev Yu. Barash, Martin Weigel, Michal Borovský, Wolfhard Janke, Lev N. Shchur
2017 Computer Physics Communications  
much more suitable for massively parallel computing.  ...  While it appears to provide algorithmic capabilities for the simulation of such systems that are roughly comparable to those of more established approaches such as parallel tempering, it is intrinsically  ...  To create sufficient parallel work for the GPU devices it turns out to be useful to combine the replica-level parallelism with an additional domain decomposition, thus exploiting also spin-level parallelism  ... 
doi:10.1016/j.cpc.2017.06.020 fatcat:o4pwqbdbdfbozgdq6rqbvuximq
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