Homework1 - Homework#1(page 1 of 2 Simple MD code with...

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MSE 4270/6270: Introduction to Atomistic Simulations, Leonid Zhigilei Homework #1 (page 1 of 2) Simple MD code with Velocity Verlet algorithm Write the simplest possible one-dimensional molecular dynamics code for two particles connected by a spring (Force = k(x 2 -x 1 -x 0 )) where ' x=x 2 -x 1 is the distance between particles, x 0 is the equilibrium length of the spring. Your code can have the following structure: Define the parameters of the system (k, x 0 , m 1 , m 2 ), initial coordinates and velocities of the particles in the system (x 1 0 , x 2 0 , v 1 0 , v 2 0 ), initial time = 0, time of the simulation, and timestep of integration, ' t. Calculate initial force F init = k(x 2 0 - x 1 0 - x 0 ) F old = F init , x 1 old = x 1 0 , x 2 old = x 2 0 , v 1 old = v 1 0 , v 2 old = v 2 0 Time loop: 1. Calculate position at the current time x 1 new = x 1 old + ' t v 1 old + ' t 2 F old /2m 1 x 2 new = x 2 old + ' t v 2 old - ' t 2 F old /2m 2 2. Calculate new forces F new = k(x 2 new - x 1 new - x 0 ) 3. Calculate new velocities v 1 new = v 1 old + ' t(F old + F new )/2m 1 v 2 new = v 2 old - ' t(F old + F new )/2m 2 4. Copy new variables to old ones (actually, you do not need to store the values
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