molDyn2D

molecular dynamics in 2D

Dependencies and Running:

This is a basic program to simulate particles in 2 dimensions under the influence of a Lennard-Jones type potential and make a movie of the molecular dynamics. It requires bash to run the control script, g++ to compile the molecular dynamics simulation, gnuplot to make the frames of the movie, and mencoder to string the frames into a movie. To run:

$>bash run.sh

Sample Output

Full Video of 256 particles, Full Video of 36 particles

Adjusting Inputs

To adjust the simulation settings you can change the values in the inputs file.

Notes on changing inputs:

• particles:

  • The simulation itself is fairly fast and can handle upwards of 1k particles. The plotting method however is very crude and as such attempting to make a movie with over 128 particles can take over 24 CPU hours.

• particles/length:

  • It's not recommended to set the density less than 1 particle per unit length^2. The Force caculation is found such that it will not calculate forces that result in numerical instabilities.

• vel0 (intial velocity)

  • vel0 is the max possible initial velocity of each particle in any given direction. It is related to the temperature of the simulation by the Bolzmann distribution. For best results keep this a positive value less than 20.

• fps (frames per second)

  • If the vel0 is low (<2.0), it's recommended to set fps higher so the movie will evolve faster. If vel0 is high (>5.0), it's recommeded to set the fps lower so you can see what's happening.