MD, a MATLAB program which carries out a molecular dynamics simulation.
The computation involves following the paths of particles which exert a distance-dependent force on each other. The particles are not constrained by any walls; if particles meet, they simply pass through each other.The problem is treated as a coupled set of differential equations. The system of differential equation is discretized by choosing a discrete time step. Given the position and velocity of each particle at one time step, the algorithm estimates these values at the next time step.
To compute the next position of each particle requires the evaluation of the right hand side of its corresponding differential equation. Since each of these calculations is independent, there is a potential speedup if the program can take advantage of parallel computing.
This version of the program is intended as a starting point; students are asked to examine the program and add the appropriate parallel MATLAB modifications to run it in parallel.
md ( nd, np, step_num, dt )where
The computer code and data files described and made available on this web page are distributed under the GNU LGPL license.
MD is available in a C version and a C++ version and a FORTRAN90 version and a MATLAB version and a Python version.
FFT_SERIAL, a MATLAB program which demonstrates the computation of a Fast Fourier Transform, and is intended as a starting point for implementing a parallel version.
HEATED_PLATE, a MATLAB program which solves the steady (time independent) heat equation in a 2D rectangular region, and is intended as a starting point for implementing a parallel version.
MD_FAST, a MATLAB program which carries out a molecular dynamics simulation; it is a version of MD that has been revised to take advantage of MATLAB's vector abilities.
MD_PARFOR, a MATLAB program which carries out a molecular dynamics simulation; it runs in parallel using MATLAB's "parfor" facility, and includes instructions on how to run the job, via MATLAB's BATCH facility, on a remote system such as Virginia Tech's ITHACA cluster.
POISSON_SERIAL, a MATLAB program which computes an approximate solution to the Poisson equation in a rectangle, and is intended as the starting point for the creation of a parallel version.
PRIME_SERIAL, a MATLAB program which counts the number of primes between 1 and N, intended as a starting point for the creation of a parallel version.
QUAD_SERIAL, a MATLAB program which approximates an integral using a quadrature rule, and is intended as a starting point for parallelization exercises.