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 particles are not constrained by any walls; if particles meet, they simply pass through each other.

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.

Note that this program exhibits a remarkable speedup if we simply compile it with the "-O2" optimization option.

Usage:

md nd np step_num dt

• nd is the spatial dimension (2 or 3);
• np is the number of particles (500, for instance);
• step_num is the number of time steps (500, for instance).
• dt is the time step size (0.1, for instance).

Licensing:

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

Languages:

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

Related Data and Programs:

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

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

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

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

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

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

MXM_SERIAL, a C program which sets up a matrix multiplication problem A=B*C, intended as a starting point for implementing a parallel version.

OPENMP, C programs which illustrate the use of OpenMP.

POISSON_SERIAL, a C 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 C 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 C program which approximates an integral using a quadrature rule, and is intended as a starting point for parallelization exercises.

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
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_local.sh, commands to compile, load and run the program locally.
• md_local.txt, the output file;
• md_newriver.sh, commands to compile, load and run the program on the ARC NewRiver cluster.
• md_newriver.txt, the output file;

List of Routines:

• MAIN is the main program for MD.
• COMPUTE computes the forces and energies.
• CPU_TIME reports the total CPU time for a program.
• DIST computes the displacement (and its norm) between two particles.
• INITIALIZE initializes the positions, velocities, and accelerations.
• R8MAT_UNIFORM_AB returns a scaled pseudorandom R8MAT.
• 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.