MASSIVELY DATA-PARALLEL MOLECULAR DYNAMICS

In light of present day data-parallel computers, an appraisal of molecular dynamics simulations of large N-particle systems, isolated or in contact with a heat-bath, is given. Special attention is focused 011 the Connection Machine CM-2. Particularly the cases of long-range potentials and impulsive hard-core interactions are discussed in detail. Data-parallel strategies including data distribution, communications and computation are presented and compared with well-known sequential approaches. The conclusion offered is that the methods described here are easy to design and offer the possibility of reasonably fast implementations for the reliable simulation of macroscopic samples of matter.

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Data-parallel molecular dynamics: 1-D hard-core fluid

Computer Physics Communications ◽

10.1016/0010-4655(92)90088-g ◽

1992 ◽

Vol 70 (1) ◽

pp. 32-40 ◽

Cited By ~ 2

Author(s):

Ernesto Bonomi ◽

Marco Tomassini

Keyword(s):

Molecular Dynamics ◽

Hard Core ◽

Data Parallel ◽

Parallel Molecular Dynamics

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Molecular Dynamics Simulations of Shock-Defect Interactions in Two-Dimensional Nonreactive Crystals

MRS Proceedings ◽

10.1557/proc-296-161 ◽

1992 ◽

Vol 296 ◽

Cited By ~ 2

Author(s):

Robert S. Sinkovits ◽

Lee Phillips ◽

Elaine S. Oran ◽

Jay P. Boris

Keyword(s):

Molecular Dynamics ◽

Hexagonal Lattice ◽

Square Lattice ◽

Two Dimensional ◽

Connection Machine ◽

Defect Sites ◽

Principal Axes ◽

Shock Motion ◽

Defect Interactions ◽

Dynamics Simulations

AbstractThe interactions of shocks with defects in two-dimensional square and hexagonal lattices of particles interacting through Lennard-Jones potentials are studied using molecular dynamics. In perfect lattices at zero temperature, shocks directed along one of the principal axes propagate through the crystal causing no permanent disruption. Vacancies, interstitials, and to a lesser degree, massive defects are all effective at converting directed shock motion into thermalized two-dimensional motion. Measures of lattice disruption quantitatively describe the effects of the different defects. The square lattice is unstable at nonzero temperatures, as shown by its tendency upon impact to reorganize into the lower-energy hexagonal state. This transition also occurs in the disordered region associated with the shock-defect interaction. The hexagonal lattice can be made arbitrarily stable even for shock-vacancy interactions through appropriate choice of potential parameters. In reactive crystals, these defect sites may be responsible for the onset of detonation. All calculations are performed using a program optimized for the massively parallel Connection Machine.

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Fracture of Nanophase Ceramics: A Molecular-Dynamics Study

MRS Proceedings ◽

10.1557/proc-457-187 ◽

1996 ◽

Vol 457 ◽

Author(s):

Aiichiro Nakano ◽

Rajiv K. Kalia ◽

Andrey Omeltchenko ◽

Kenji Tsuruta ◽

Priya Vashishta

Keyword(s):

Molecular Dynamics ◽

Silicon Nitride ◽

Load Balancing ◽

Molecular Dynamics Simulations ◽

Dynamic Fracture ◽

Parallel Computers ◽

Fracture Surfaces ◽

Affine Structures ◽

Dynamics Simulations ◽

Multiscale Algorithms

ABSTRACTNew multiscale algorithms and a load-balancing scheme are combined for molecular-dynamics simulations of nanocluster-assembled ceramics on parallel computers. Million-atom simulations of the dynamic fracture in nanophase silicon nitride reveal anisotropie self-affine structures and crossover phenomena associated with fracture surfaces.

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Parallel Molecular Dynamics with Irregular Domain Decomposition

Communications in Computational Physics ◽

10.4208/cicp.140810.021210a ◽

2011 ◽

Vol 10 (4) ◽

pp. 1071-1088 ◽

Cited By ~ 8

Author(s):

Mauro Bisson ◽

Massimo Bernaschi ◽

Simone Melchionna

Keyword(s):

Molecular Dynamics ◽

Blood Flow ◽

Input Parameter ◽

Complex Geometries ◽

Irregular Domain ◽

Irregular Domains ◽

Additional Input ◽

Parallel Molecular Dynamics ◽

Dynamics Simulations ◽

General Method

AbstractThe spatial domain of Molecular Dynamics simulations is usually a regular box that can be easily divided in subdomains for parallel processing. Recent efforts aimed at simulating complex biological systems, like the blood flow inside arteries, require the execution of Parallel Molecular Dynamics (PMD) in vessels that have, by nature, an irregular shape. In those cases, the geometry of the domain becomes an additional input parameter that directly influences the outcome of the simulation. In this paper we discuss the problems due to the parallelization of MD in complex geometries and show an efficient and general method to perform MD in irregular domains.

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