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The Molecular Dynamics Replicated Data Model implements a parallel computer program that uses a 3D Lennard-Jones potential truncated at a distance of three molecular diameters. Each thread computes a portion of the force on each atom and these contributions are summed to compute the total acceleration using the Verlet ODE algorithm. Allocating memory for each thread's avoids the problem of parallel threads simultaneously writing to array elements.
The Molecular Dynamics Replicated Data Model was developed using the Easy Java Simulations (EJS) modeling tool. It is distributed as a ready-to-run (compiled) Java archive.
Published August 30, 2013
Last Modified June 10, 2014
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The source code zip archive contains an XML representation of the Molecular Dynamics Replicated Data Model. Unzip this archive in your Ejs workspace to compile and run this model using EJS.
Last Modified August 30, 2013