Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

An improved PSO algorithm for smooth path planning of mobile robots using continuous high-degree Bezier curve

Deep-reinforcement-learning-based images segmentation for quantitative analysis of gold immunochromatographic strip

This paper is concerned with the l2–l∞ output-feedback control problem for a class of two-dimensional (2-D) switched systems described by the general Fornasini–Marchesini second model under the sto...

On ℓ2–ℓ∞ output-feedback control scheduled by stochastic communication protocol for two-dimensional switched systems

As the typical unconventional reservoir, shale gas is believed to be the most promising alternative for the conventional resources in future energy patterns, attracting more and more attention thro...

Transport of Shale Gas in Microporous/Nanoporous Media: Molecular to Pore-Scale Simulations

Multi-objective optimization of energy consumption in crude oil pipeline transportation system operation based on exergy loss analysis

Thermal decomposition mechanism of some hydrocarbons by ReaxFF-based molecular dynamics and density functional theory study

Molecular dynamics simulation of the microscopic mechanisms of the dissolution, diffusion and aggregation processes for waxy crystals in crude oil mixtures

Shale gas is a multicomponent mixture stored in nanopores, which consists mainly of methane (CH4) and ethane (C2H6). The transport property of shale gas in clay nanopores is a fundamental issue not...

Qinglin Cheng

Papers

Multi-objective optimization of energy consumption in crude oil pipeline transportation system operation based on exergy loss analysis

Thermal decomposition mechanism of some hydrocarbons by ReaxFF-based molecular dynamics and density functional theory study

Molecular dynamics simulation of the microscopic mechanisms of the dissolution, diffusion and aggregation processes for waxy crystals in crude oil mixtures

Transport Property of Methane and Ethane in K-Illite Nanopores of Shale: Insights from Molecular Dynamic Simulations

Gelation of waxy crude oil system with ethylene-vinyl acetate on solid surface: A molecular dynamics study