Molecular Modeling Projects

This repository contains three Python object-oriented projects developed as part of the Molecular Modeling course at the University of Warsaw.

Molecular Dynamics of Random Walk

The Molecular Dynamics of Random Walk project simulates the behavior of particles in a box with periodic boundary conditions and a thermostat. The particles undergo random walks within the box, and the thermostat ensures temperature control. This project provides insights into the diffusion behavior of particles in confined environments.

• Molecular dynamics simulation using the leapfrog integration scheme.
• Periodic boundary conditions to simulate an infinite system.
• Calculation of interatomic forces using Lennard-Jones potential.
• Energy calculations including kinetic energy, potential energy, and total energy.
• Trajectory plotting and animation.
• Exporting simulation frames to create an animation.

Planet-Sun System Simulation

The Planet-Sun system simulation project focuses on simulating the motion of a planet around a central sun using different integrative algorithms: Verlet, Leap-Frog, and Euler. Each algorithm is implemented as a separate Python class. The resulting figures provide visual comparisons of the trajectories generated by each algorithm.

• Verlet Algorithm: A symplectic integrator commonly used in molecular dynamics simulations.
• Leap-Frog Algorithm: A second-order numerical integration method known for its stability and accuracy.
• Euler Algorithm: A simple but less accurate integration method commonly used for educational purposes.

Ising Model Simulation

The Ising model simulation project aims to model the behavior of a 2D Ising model using Monte Carlo methods. The code implements the Metropolis algorithm to simulate the evolution of spins on a lattice. The resulting figure visualizes the magnetization of the system as a function of temperature.

Each project is implemented in Python, following an object-oriented programming paradigm, making it easy to understand, modify, and extend.

Requirements

• Python 3.x
• NumPy
• Matplotlib
• tqdm (for progress bars)

Usage

Each project directory contains the Python script for running the simulation and generating the figures. Simply navigate to the desired project directory and execute the script using a Python interpreter.

python ising_model_simulation.py
python planet_sun_simulation.py
python molecular_dynamics_random_walk.py

License

This project is licensed under the GNU General Public License - see the LICENSE file for details.