Harmonic Potential
After initial conditions are set up, and the simulation is started. The simulation decides the motion of the atoms by their current velocities and the force interactions between other atoms, among other factors. The characterization of the interactions is converted into a mathematical model detailing force exerted as a function of distance. Such a model is called a potential. And in this simulation, we are using harmonic potentials. As the name might suggest, the atoms follow interactions and produce forces following the properties of Simple Harmonic Motion. The forces between atoms accelerate and decelerate the motion of the atoms.
An easy way to imagine how they interact is by picturing each atom attached to its neighbors by springs as they are in the Bravais Lattice. The springs are perfect harmonic springs, and they produce forces equal to displacement times spring constant .