Tutorial: How to simulate interacting particle systems
This tutorial explains how the molecular dynamics simulations on this channel were made. We will talk about the equations of motion, their numerical integration, how to use a thermostat, choices of initial state, different types of interactions, boundary conditions, and adding moving obstacles. We will also briefly discuss how to model chemical reactions, and how to simplify the coding using composite variables known as structures in C.
Intro: 0:00
Examples: 1:00
Equations of motion: 4:48
Numerical integration: 9:54
Hashgrid: 15:08
Thermostat: 20:17
Initial state: 26:44
Other interactions: 28:50
Boundary conditions: 35:00
Adding obstacles: 40:56
Chemical reactions: 44:52
Structures in C: 49:10
Last examples: 54:27
Playlist of interacting particle simulations: • Molecular dynamics
Crystal formation: • Crystal formation: particles interact...
Increasing gravity: • Lennard-Jones particles in increasing...
Rocket comparison: • Rocket comparison 14: Bell-shaped vs ...
Temperature cycling with a thermostat: • Grain boundary dynamics under tempera...
Particles with spins: • Interacting particles with spins
Interactions with pentagonal symmetry: • Molecular dynamics with pentagonal sy...
Liquid crystals: • Liquid crystals
Dipoles on a torus: • Grain boundary dynamics under tempera...
Klein bottle boundary conditions: • Crystal formation on a topological Kl...
Brownian motion on a surface of genus 2: • Brownian particles on a surface of ge...
Breaking dam with moving bricks: • An example of simulation gone wrong: ...
Polymerization: • More periodic oscillations in a modif...
Brusselator: • More periodic oscillations in a modif...
Carnot cycle: • A Carnot cycle
A tribute to Sir John Lennard-Jones: • Video #700: A tribute to John Lennard...
Reference on thermostat: Leimkuhler, B., Noorizadeh, E. & Theil, F. A Gentle Stochastic Thermostat for Molecular Dynamics. J Stat Phys 135, 261–277 (2009)
https://doi.org/10.1007/s10955-009-97...
http://www.maths.warwick.ac.uk/~theil...
#Lennard_Jones #molecular_dynamics #simulation #interacting_particles
