MD
Molecular Dynamics

MD is a C 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 problem is viewed as a coupled set of differential equations. 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 OpenMP directives to run it in parallel.

Licensing:

The computer code and data files described and made available on this web page are distributed under the GNU LGPL license.

Related Data and Programs:

FFT is a C program which demonstrates the computation of a Fast Fourier Transform, and is intended as a starting point for developing a parallel version using OpenMP.

HEATED_PLATE is a C program which solves the steady state heat equation in a 2D rectangular region, and is intended as a starting point for implementing an OpenMP parallel version.

MD is available in a C version and a C++ version and a FORTRAN77 version and a FORTRAN90 version and a MATLAB version.

MD_OPEN_MP is a C program which carries out a molecular dynamics simulation, using OpenMP for parallel execution.

MD1 is a FORTRAN90 program which carries out a molecular dynamics simulation.

MD2 is a FORTRAN90 program which carries out a molecular dynamics simulation.

MD3 is a FORTRAN90 program which carries out a molecular dynamics simulation.

MD3GLUE is a FORTRAN90 program which carries out a molecular dynamics simulation.

MDBNCH is a FORTRAN77 program which is a benchmark molecular simulation calculation.

OPEN_MP, a directory of C programs which illustrate the use of OpenMP.

Reference:

1. Matthew Allen, Dominic Tildesley,
   Computer Simulation of Liquids,
   Oxford University Press, 1987,
   ISBN: 0198556454,
   LC: QC145.2.
2. Peter Arbenz, Wesley Petersen,
   Introduction to Parallel Computing - A practical guide with examples in C,
   Oxford University Press,
   ISBN: 0-19-851576-6,
   LC: QA76.58.P47.
3. Rohit Chandra, Leonardo Dagum, Dave Kohr, Dror Maydan, Jeff McDonald, Ramesh Menon,
   Parallel Programming in OpenMP,
   Morgan Kaufmann, 2001,
   ISBN: 1-55860-671-8,
   LC: QA76.642.P32.
4. Barbara Chapman, Gabriele Jost, Ruud vanderPas, David Kuck,
   Using OpenMP: Portable Shared Memory Parallel Processing,
   MIT Press, 2007,
   ISBN13: 978-0262533027,
   LC: QA76.642.C49.
5. Furio Ercolessi,
   A Molecular Dynamics Primer,
   ercolessi.pdf
6. Philipp Janert,
   Gnuplot in Action: Understanding Data with Graphs,
   Manning, 2008,
   ISBN: 1-933988-39-8.
7. Dennis Rapaport,
   An Introduction to Interactive Molecular-Dynamics Simulation,
   Computers in Physics,
   Volume 11, Number 4, July/August 1997, pages 337-347.
8. Dennis Rapaport,
   The Art of Molecular Dynamics Simulation,
   Cambridge University Press, 2004,
   ISBN: 0521825687.

Source Code:

• md.c, the source code;
• md.sh, BASH commands to compile, link and load the program.

Examples and Tests:

• md_output.txt, the output file;

List of Routines:

• MAIN is the main program for MD.
• COMPUTE computes the forces and energies.
• DIST computes the displacement and distance between two particles.
• INITIALIZE initializes the positions, velocities, and accelerations.
• TIMESTAMP prints the current YMDHMS date as a time stamp.
• UPDATE updates positions, velocities and accelerations.

You can go up one level to the C source codes.