MD//lennard-jones simulation

Md_velo_verlet.py

import numpy
from forces import lennardjones

# Initialize simulations (code not shown)
temperature = 2.0
n_atoms = 100
rho = 0.01

U = initialize_positions(n_atoms, rho)
box = initialize_box(n_atoms, rho)
V = initialize_velocities(U, temperature)

# Start simulation

n_steps = 10000
dt = 0.001

(epot,F,Vir) = lennardjones(U,box)

for i in range(n_steps):
    U += V * dt + 0.5 * F * dt * dt
    F0 = F[:]

    (epot, F, Vir) = lennardjones(U, box)

    V += 0.5 * (F + F0) * dt