Molecular Dynamics Simulation

A Fortran-based molecular dynamics simulation program for simulating Lennard-Jones particles, with Python-based analysis tools.

Project Structure

.
├── bin/           # Compiled executables
├── obj/           # Object files and module files
├── output/        # Simulation output files
├── src/           # Source files
│   ├── parameters.f90    # Simulation parameters and constants
│   ├── particles.f90     # Particle system and RDF calculations
│   ├── forces.f90        # Force calculations
│   ├── integrator.f90    # Time integration
│   ├── io.f90           # Input/output operations
│   └── main.f90         # Main program
├── analyze_results.py    # Analysis and visualization script
├── Makefile             # Build system
└── README.md            # This file

Features

• Lennard-Jones potential for particle interactions
• Velocity Verlet integration
• Optional Berendsen thermostat for temperature control
• Neighbor list optimization for force calculations
• Periodic boundary conditions
• Radial Distribution Function (RDF) calculation
• Real-time energy, temperature, and pressure monitoring
• Trajectory output in XYZ format
• Interactive visualization and analysis tools

Requirements

Compilation

• Fortran compiler (gfortran recommended)
• Make build system

Analysis

• Python 3.x
• NumPy
• Matplotlib

Building the Project

To compile the simulation program:

make

This will create the executable bin/md_sim.exe and all necessary object files in the obj/ directory.

Running the Simulation

To run the simulation:

make run

This will execute the simulation and store all output files in the output/ directory:

• simulation_info.txt: Contains all simulation parameters
• energies.dat: Time evolution of energies, temperature, and pressure
• trajectory.xyz: Particle positions in XYZ format
• rdf_*.dat: Radial distribution function at different time steps

Analysis

To analyze the simulation results:

python analyze_results.py

This will:

1. Display statistical analysis of the simulation
2. Show interactive plots of:
   • Energy evolution (potential, kinetic, total)
   • Temperature evolution
   • Pressure evolution
   • Energy conservation
   • Radial Distribution Function (initial vs final)

Output Files

simulation_info.txt

Contains all simulation parameters including:

• Number of particles
• Box size
• Temperature
• Time step
• Number of steps
• Lennard-Jones parameters
• Thermostat settings
• Neighbor list parameters
• RDF calculation parameters

energies.dat

Tab-separated file with columns:

1. Time step
2. Potential energy
3. Kinetic energy
4. Total energy
5. Temperature
6. Pressure

trajectory.xyz

Standard XYZ format containing:

• Number of particles
• Comment line with step number, total energy, temperature, and pressure
• Particle positions (x, y, z)

rdf_*.dat

Radial distribution function data with columns:

1. Distance (r)
2. g(r)

Cleaning Up

To clean all compiled files and simulation outputs:

make clean

This will remove:

• All object files (obj/*.o)
• All module files (obj/*.mod)
• The executable (bin/md_sim.exe)
• All output files (output/*)

Notes

• The simulation uses reduced units where σ = ε = m = 1
• Periodic boundary conditions are applied in all directions
• The neighbor list is updated based on particle displacements
• The RDF is calculated and output at specified intervals
• All output files are automatically saved in the output/ directory