This repositry contains the code produced for the High Performance Computing project looking at Parallel Molecular Dynamics with Short Ranged Potentials.
Molecular dynamics models use the Lennard-Jones potential, and use Verlet integration.
The serial code is contained in the notebook Serial_Code.ipynb. This produces an animation and plots of the kinetic, potential and total energy.
The full parallel code used is contained in the folder Parallel_Code. Instructions to run this code are contained in the folder.
The benchmarks.py file just produces outputs based on the benchmarks obtained in the parallel full model. The output is five plots.
The parallel lattice model is comtained in the Lattice Method folder.
You must first run precompute.py to make the local file of pre-computed forces.
Them run Lattice_Spyder_MPI.py, following the same steps as used to run the Parallel Full model.