Comments on the code are more extensive and clear up some of the

confusion we've been having with what things are and how they work as
well as why we implemented certains classes and functions the way we did

Needs to be further updated as well

src/jat/examples/ThreeBodyExample/ThreeBodyAPL.java

@@ -18,16 +18,29 @@ public class ThreeBodyAPL extends ThreeBody implements FirstOrderDifferentialEqu
 	public ArrayList<Double> ysol = new ArrayList<Double>();
 	public ArrayList<Double> zsol = new ArrayList<Double>();
 
+	/*
+	 * Why we created the ThreeBodyAPL:
+	 * The APL is responsible for computing the derivatives used in the ThreeBodyExample and interpolating data
+	 * APL stands for Applied Physics Laboratory
+	 */
+
+	/*
+	 * What we used from existing code
+	 * The information that this class uses from the ThreeBody class are calculations for:
+	 * Masses, center of mass and energy. 
+	 * This is usefull for us because all of this is necessary for our modification
+	 */
+
 	public ThreeBodyAPL(double G, double m1, double m2, double m3) {
 		super(G, m1, m2, m3);
 	}
-
+	
 	@Override
 	public void computeDerivatives(double t, double[] y, double[] yDot) {
 		// returns the derivatives of the ThreeBody problem
 		yDot = this.derivs(t, y);
 	}
-
+	
 	@Override
 	public int getDimension() {
 		// returns a dimension of 6

src/jat/examples/ThreeBodyExample/ThreeBodyExample.java

@@ -19,6 +19,13 @@
 import org.apache.commons.math3.ode.FirstOrderIntegrator;
 import org.apache.commons.math3.ode.nonstiff.DormandPrince853Integrator;
 
+/*
+ * We modified the ThreeBodyProblem by emulating the two body problem, and expanding it to ThreeBody
+ * Elements of two body, such as the orbit calculations, were not as heavily focused on
+ * We acknowledge that some of our calculations may be a bit inaccurate because some of the math got a bit over our heads
+ * 
+ * @author Maegan and John
+ */
 public class ThreeBodyExample {
 
 	public ThreeBodyExample() {
@@ -53,8 +60,21 @@ public static void main(String[] args) {
 		VectorN cm = sat.center_of_mass(y);
 
 		// obtain current energy
+
 		totalEnergy = sat.Energy(y);
-
+		/*
+		 * Notes about the calculations:
+		 * Dormand Prince is a type of Runge-Kutta diff eq. (another method of checking diff eq)
+		 * Errors are calculated looking at 4th and 5th level differential equations
+		 * These were most likely chosen by the original creator of the project because they take the error into account fairly accurately
+		 * In relation to physics, this calculates the relative orbits for the bodies
+		 * The step handler is another type of analyzing the algorithms for each body
+		 * These provide fairly accurate results
+		 * 
+		 * In general, these equations went over our heads, but refer to the NASA site as well as 
+		 * look into other resources to get more information on 3-Body calculations
+		 * 
+		 */
 		// propagate the orbit
 		FirstOrderIntegrator dp853 = new DormandPrince853Integrator(1.0e-8, 100.0, 1.0e-10, 1.0e-10);
 		dp853.addStepHandler(sat.stepHandler);