Verlet Algorithm 3. Relevant Methods in Java Code

//Performs one timestep increment in the Verlet algorithm

public void doStep(double tStep) {

atomIterator.reset();

while(atomIterator.hasNext()) { //zero forces on all atoms

((Agent)atomIterator.next().ia).force.E(0.0); //integratorVerlet.Agent keeps a force Vector

}

pairIterator.allPairs(forceSum); //sum forces on all pairs

double t2 = tStep*tStep;

atomIterator.reset();

while(atomIterator.hasNext()) { //loop over all atoms, moving according to Verlet

Atom a = atomIterator.next();

Agent agent = (Agent)a.ia;

Space.Vector r = a.position(); //current position of the atom

temp.E(r); //save it

r.TE(2.0); //2*r

r.ME(agent.rLast); //2*r-rLast

agent.force.TE(a.rm()*t2); // f/m dt^2

r.PE(agent.force); //2*r - rLast + f/m dt^2

agent.rLast.E(temp); //rLast gets present r

}

return;

}

public class IntegratorVerlet extends Integrator