Classical molecular dynamics

Classical (molecular) dynamics proceeds by solving the dynamics for a system governed by a classical Hamiltonian containing the kinetic energy of the particles and a potential energy function:

\[H = \frac{P^2}{2M} + V(R)\]

To integrate the equations we use the VelocityVerlet() algorithm from DifferentialEquations.jl, which is one of the most widely used algorithms for molecular dynamics.

Example

We can create two particles with mass = 1 and attach a DiatomicHarmonic interaction which provides a harmonic interatomic potential.

Note

Recall that the constructor for Simulation(...) when called without a type parameter as below defaults to Simulation{Classical}(...).

using NQCDynamics
using Plots

sim = Simulation(Atoms([1, 1]), DiatomicHarmonic())
v = rand(3, 2)
u0 = DynamicsVariables(sim, zeros(3, 2), hcat(randn(3), randn(3).+1))

traj = run_dynamics(sim, (0.0, 10.0), u0; dt=0.1, output=OutputPosition)

plot(traj, :OutputPosition)