Project 1: Molecular dynamics simulation of Argon atoms

Classical dynamics of $N$ Argon atoms inside a $d$-dimensional box with periodic boundary conditions.

The atom-pair interaction is modelled as a Lennard-Jones potential and the numerical evolution can be done using the Euler method or the velocity-Verlet algorithm. The observables that can be calculated are (1) pair correlation function, (2) specific heat, (3) mean-squared displacement, (4) diffusion constant and (5) pressure.

Setup

Clone this repo and run pip install -r requirements.txt to install its dependencies.

Usage

Open main.py and specify the input parameters:

• Box and particles
  • particle_num : number of particles, always in the shape $4k^3$ with $k \in \mathbb{N}$ to completely fill the box
  • dim : dimensionality of the box (FCC lattice only implemented for dim=3)
  • lattice_const : lattice constant of the FCC in units of $\sigma$
• Temperature
  • temperature : temperature in units of $\epsilon / k_{B}$
  • temperature_error : maximum error in the temperature when rescaling in units of $\epsilon / k_{B}$
  • rescale_time : time interval between rescalings in units of $(m \sigma^2 / \epsilon )^{1/2}$
• Molecular simulation
  • run_time : run time of the simulation in units of $(m \sigma^2 / \epsilon )^{1/2}$
  • num_tsteps : number of time steps of the simulation
  • algorithm_method : algorithm used to calculate the temporal evolution (verlet or euler)
  • simulation : list of steps to do ["equilibrium", "simulation"]
• Post-processing of the simulation
  • observables : list of observables to calculate ["pair_correlation", "specific_heat", "displacement", "diffusion", "pressure"]
  • plotting : list of plots to perform ["gif", "Evst"]

For a more detailed information of the available plots (including e.g. histogram of velocities and plots of observables), see plotting.py.

Authors

• Álvaro Bermejillo Seco
• Daniel Bedialauneta Rodríguez
• Marc Serra Peralta