Development of Simulation Software for NPT-MD

Report No. ARL-CR-554
Authors: Andrew Scott
Date/Pages: November 2004; 20 pages
Abstract: This report details the development of simulation software for the Common High Performance Computing Software Support Initiative Project: Visual eXtensible Molecular Dynamics. The software was designed for use in the NPT Ensemble of the Message Passing Interface-based program ?Novice-MD.? NPT assumes a fixed number of particles, N, constant pressure, P, and temperature, T. Thus, the corresponding change in volume due to system behavior causes the simulation cells to change shape. From a computational perspective, however, the external boundaries of simulation cells (two- and three-dimensional) must remain mutually perpendicular to maintain numerical stability. Algorithms were developed to convert strained, shape changed, simulation cells into equivalent ?rectangularized? cells at each time-step in the dynamic simulation, for both Runge- Kutta and Leap-Frog-Verlet integrators. The conversions at each step are tracked throughout the simulation, thereby enabling conversion to the original coordinate system at any intermediate step, and at the conclusion of the simulation. The software was written in Fortran 90 (f90), and interwoven as necessary with the existing Novice-MD code. The capabilities were successfully implemented and tested on the SGI Origin system at the U.S. Army Research Laboratory Major Shared Resource Center. Additionally, the Novice-MD code was ported and tested on a CRAY SV-1 vector platform.
Distribution: Approved for public release
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Last Update / Reviewed: November 1, 2004