A new dynamical domain decomposition method for parallel molecular dynamics simulation

Жаховский, В. В.; Nishihara, Katsunobu; Fukuda, Y.; Shimojo, Shinsuke; Akiyama, T.; Miyanaga, Seiichi; Sone, Haruka; Kobayashi, Hajime; Ito, Eri; Seo, Yoshiki; Tamura, M.; Ueshima, Yutaka

doi:10.1109/ccgrid.2005.1558650

Cited by 24 publications

(22 citation statements)

References 5 publications

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“…In this research for hydrodynamic simulations the Lagrangian mesh-free SPH method [6,7] is used. Atomistic simulations are performed with an autobalancing parallel MD code (MD-MPD 3 [8]) based on dynamical domain decomposition of samples with highly-nonuniform density distributions into dynamical Voronoi polyhedrons.…”

Section: Introductionmentioning

confidence: 99%

Ejecta from shocked metals: Comparative simulations using molecular dynamics and smoothed particle hydrodynamics

Dyachkov

Паршиков

Zhakhovsky

2017

AIP Conference Proceedings

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Abstract. Experimental methods of observation of early stage of shock-induced ejecta from metal surface with micrometer-sized perturbations are still limited in terms of following a complete sequence of processes having microscale dimensions and nanoscale times. To get an insight into micro-jet formation the ejecting from tin and copper samples is simulated in detail by smoothed particle hydrodynamics (SPH) and molecular dynamics (MD) methods. Such a comparative study shows, with some exception, a good similarity between material flows in nanometer-and micrometer-sized samples. We demonstrate that the jet velocity profiles and mass distributions obtained by both methods are similar, even for a MD sample with the linear size of 100 nm. It is shown that the bigger MD sample is simulated, the better agreement with SPH results is achieved for spike velocities of liquid jets due to decrease of surface tension effect. The calculated ejecta masses do nonetheless agree well for all sizes of interest. Material strength effect is also discussed in our comparative MD and SPH study. At relatively weak shock loading the plastic flow and jet formation is strongly arrested in MD sample due to a higher yield strength of solid at very high strain rates evolving on MD scale. In such conditions MD results are not scaled well to SPH results obtained at several order less strain rates.

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Section: Introductionmentioning

confidence: 99%

Ejecta from shocked metals: Comparative simulations using molecular dynamics and smoothed particle hydrodynamics

Dyachkov

Паршиков

Zhakhovsky

2017

AIP Conference Proceedings

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“…The grey continuous curve separates non-ejecting ( the blue circles) and ejecting cases ( the red circles). We see that the simulations rather satisfactory correspond to the experiments Main new achievement used in the paper here (relative to the previous work [ 22]) is addition of the Monte-Carlo (MC) algorithm to the molecular dynamics (MD) algorithm [ 27]. The sense of the MC modeling is the following.…”

Section: Figmentioning

confidence: 91%

Solitary Nanostructures Produced by Ultrashort Laser Pulse

Inogamov¹,

Zhakhovsky²,

Хохлов³

et al. 2017

Nano Online

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which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. AbstractLaser-produced surface nanostructures show considerable promise for many applications while fundamental questions concerning the corresponding mechanisms of structuring are still debated. Here, we present a simple physical model describing those mechanisms happened in a thin metal film on dielectric substrate irradiated by a tightly focused ultrashort laser pulse. The main ingredients included into the model are (i) the film-substrate hydrodynamic interaction, melting and separation of the film from substrate with velocity increasing with increase of absorbed fluence; (ii) the capillary forces decelerating expansion of the expanding flying film; and (iii) rapid freezing into a solid state if the rate of solidification is comparable or larger than hydrodynamic velocities. The developed model and performed simulations explain appearance of microbump inside the focal spot on the film surface. The model follows experimental findings about gradual transformation of the bump from small parabolic to a conical shape and to the bump with a jet on its tip with increasing fluence. Disruption of the bump as a result of thinning down the liquid film to a few interatomic distances or due to mechanical break-off of solid film is described together with the jetting and formation of one or many droplets. Developed theory opens door for optimizing laser parameters for intended nanostructuring in applications.

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“…Zhakhovskii et al [1] introduced a decomposition scheme that divides the simulation domain into Voronoi regions, whose size and shape are varied during the simulation to alleviate the imbalances in processor runtimes. Even though Voronoi decomposition is an elegant way of subdivision, it comes with the drawback of dealing with the complicated nature of 3D Voronoi regions, which have to be updated gradually.…”

Section: Related Workmentioning

confidence: 99%

Parallel load‐balanced simulation for short‐range interaction particle methods with hierarchical particle grouping based on orthogonal recursive bisection

Fleißner

Eberhard

2007

Numerical Meth Engineering

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SUMMARYWe describe an efficient load-balancing algorithm for parallel simulations of particle-based discretization methods such as the discrete element method or smoothed particle hydrodynamics. Our approach is based on an orthogonal recursive bisection of the simulation domain that is the basis for recursive particle grouping and assignment of particle groups to the parallel processors. Particle grouping is carried out based on sampled discrete particle distribution functions. For interaction detection and computation, which is the core part of particle simulations, we employ a hierarchical pruning algorithm for an efficient exclusion of non-interacting particles via the detection of non-overlapping bounding boxes. Load balancing is based on a hierarchical PI-controller approach, where the differences of processor per time step waiting times serve as controller input.

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A new dynamical domain decomposition method for parallel molecular dynamics simulation

Cited by 24 publications

References 5 publications

Ejecta from shocked metals: Comparative simulations using molecular dynamics and smoothed particle hydrodynamics

Ejecta from shocked metals: Comparative simulations using molecular dynamics and smoothed particle hydrodynamics

Solitary Nanostructures Produced by Ultrashort Laser Pulse

Parallel load‐balanced simulation for short‐range interaction particle methods with hierarchical particle grouping based on orthogonal recursive bisection

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