README.md

LJMD Project

This package contains simplified MD code for simulating atoms with a Lennard-Jones potential.

Contents

The bundled makefiles are set up to compile the executable once in serial and once with MPI with each build placing the various object files in separate directories.

The examples directory contains 3 sets of example input decks and the reference directory the corresponding outputs.

Build instructions:

Compile everything:

make

Remove all compiled objects

make clean

What does the program do?

1. Read in parameters, initial position and velocities of atoms and compute what is missing
2. Integrate equations of motion with velocity verlet for a given number of steps
   • Propagate all velocities for half a step
   • Propagate all positions for a full step
   • Compute forces on all atoms to get accelerations
   • Propagate all velocities for half a step
   • Output intermediate results if needed

Instructions

1. Use OpenMP to parallelize the most time consuming operations in the serial program
2. Create a simple MPI parallelization by using replicated data (each MPI process has all information)
3. Document the changes in speedup and efficiency for each version of your code