Verlet Algorithm 3. Relevant Methods in Java Code

//(anonymous) class for incrementing the sum of the forces on each atom

forceSum = new AtomPair.Action() {

private Space.Vector f = simulation().space.makeVector();

public void action(AtomPair pair) {

PotentialSoft potential = (PotentialSoft)simulation().getPotential(pair) //identify pot’l

f.E(potential.force(pair)); //compute force of atom1 on atom2

((Agent)pair.atom1().ia).force.PE(f); //increment atom1 force

((Agent)pair.atom2().ia).force.ME(f); //increment atom2 force

}

};

//Agent class for IntegratorVerlet; stores useful quantities in each Atom

public final static class Agent implements Integrator.Agent {

public Atom atom;

public Space.Vector force; //used to accumulate the force on the atom

public Space.Vector rLast; //holds the position of the atom at the last step

public Agent(Atom a) { //constructor

atom = a;

force = atom.parentMolecule().parentPhase().parentSimulation.space.makeVector();

rLast = atom.parentMolecule().parentPhase().parentSimulation.space.makeVector();

}

public class IntegratorVerlet extends Integrator