Molecular Dynamics (MD) Simulation

Overview

This directory contains a simple molecular dynamics (MD) application designed to simulate particle interactions under gravitational and viscous forces.

The program reads input from input.dat and outputs results to output.dat. A test utility in the Test directory is available to compare output.dat files, reporting only differences above a preset tolerance value.

Installation and Building

Requirements

• Intel oneAPI (2024.0.2)

Compilation

A Makefile is provided to compile the application from the root directory:

make -j

A submit.srun file is also provided which can be used to submit a job to the backend compute node of Cirrus:

Make sure to correctly set your account code

sbatch submit.srun

Usage

To execute the program, run:

./build/md

This will read input.dat, run the molecular dynamics simulation and then produce output.dat.

Correctness Testing

The test directory contains a utility to compare output.dat files:

./test/diff-output output_original/output.dat500 output.dat500

This will report any differences exceeding a preset tolerance.