MD_lab

Alia Lescoulie

A Molecular Dynamics Lenard-Jones model build in C++.

Building

git clone git@github.com:ALescoulie/MD_lab.git

cmake build .

make

Scripts

There are two python helper scripts in the utils directory to help setting up simulations. grid_gen.py writes an xyz file of a cubic lattice of the specified molecule and input_gen.py make a blank input file.

grid_gen.py

The arguments for grid_gen.py are in order:

1. The name of the specified atoms
2. The length in nm of the grid
3. The number of atoms per cell in the grid
4. The name of the output file, this should end in .xyz

Usage:

python utils/grid_gen.py Kr 10 10 grid.xyz

input_gen.py

The arguments for input_gen.py are in order:

1. The file name ending with .yaml

python utils/input_gen.py input.yaml

Running

This simulation only runs dispersion interactions for particles. To use generate a topology file. This can be done with grid_gen.py if you want a cubic lattice of a single atom.

To generate the input file use input_gen.py to make a blank input than fill out the specified fields. Then that file is passed to the MD_lab executable as an argument as shown below. At the moment the only tunable parameters are temperature, time step, simulation time, and time steps per frame.

./MD_lab input.yaml

Afterwards the trajectory will be returned to the specified file.