Possibly fixed the issues with merging the branch

src/jat/examples/ThreeBodyExample/ThreeBodyAPL.java

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+package jat.examples.ThreeBodyExample;
+
+import java.util.ArrayList;
+
+import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
+import org.apache.commons.math3.ode.FirstOrderDifferentialEquations;
+import org.apache.commons.math3.ode.sampling.StepHandler;
+import org.apache.commons.math3.ode.sampling.StepInterpolator;
+
+import jat.coreNOSA.algorithm.integrators.Printable;
+import jat.coreNOSA.cm.Constants;
+import jat.coreNOSA.cm.ThreeBody;
+import jat.coreNOSA.math.MatrixVector.data.VectorN;
+
+public class ThreeBodyAPL extends ThreeBody implements FirstOrderDifferentialEquations{
+	public ArrayList<Double> time = new ArrayList<Double>();
+	public ArrayList<Double> xsol = new ArrayList<Double>();
+	public ArrayList<Double> ysol = new ArrayList<Double>();
+	public ArrayList<Double> zsol = new ArrayList<Double>();
+
+	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
+		return 18;
+	}
+	public double[] randv() {
+		// returns the position and velocity of the three objects
+		// vector r1 is x[0], x[1], x[2]
+		// vector v1 is x[3], x[4], x[5]
+		// vector r2 is x[6], x[7], x[8]
+		// vector v2 is x[9], x[10], x[11]
+		// vector r3 is x[12], x[13], x[14]
+		// vector v3 is x[15], x[16], x[17]
+		double[] randv = new double[18];
+		randv[0] = 2.0;
+		randv[1] = 6.0;
+		randv[2] = 7.0;
+		randv[3] = 4.0;
+		randv[4] = 8.0;
+		randv[5] = 7.0;
+		randv[6] = 5.0;
+		randv[7] = 8.0;
+		randv[8] = 3.0;
+		randv[9] = 6.0;
+		randv[10] = 8.0;
+		randv[11] = 9.0;
+		randv[12] = 0.0;
+		randv[13] = 7.0;
+		randv[14] = 4.0;
+		randv[15] = 5.0;
+		randv[16] = 7.0;
+		randv[17] = 8.0;
+		return randv;
+	}
+
+	public StepHandler stepHandler = new StepHandler() {
+		public void init(double t0, double[] y0, double t) {
+		}
+
+		public void handleStep(StepInterpolator interpolator, boolean isLast) {
+			double t = interpolator.getCurrentTime();
+			double[] y = interpolator.getInterpolatedState();
+			System.out.println(t + " " + y[0] + " " + y[1]+ " " + y[2]);
+			time.add(t);
+			xsol.add(y[0]);
+			ysol.add(y[1]);
+			zsol.add(y[2]);
+		}
+	};
+
+}

src/jat/examples/ThreeBodyExample/ThreeBodyExample.java

@@ -0,0 +1,115 @@
+package jat.examples.ThreeBodyExample;
+
+import jat.core.cm.TwoBodyAPL;
+import jat.core.plot.plot.FrameView;
+import jat.core.plot.plot.Plot2DPanel;
+import jat.core.plot.plot.PlotPanel;
+import jat.core.plot.plot.plots.ScatterPlot;
+import jat.coreNOSA.math.MatrixVector.data.VectorN;
+import jat.examples.TwoBodyExample.TwoBodyExample;
+
+import java.awt.Color;
+import java.text.DecimalFormat;
+
+import javax.swing.JFrame;
+
+import org.apache.commons.lang3.ArrayUtils;
+import org.apache.commons.math3.linear.ArrayRealVector;
+import org.apache.commons.math3.linear.RealVectorFormat;
+import org.apache.commons.math3.ode.FirstOrderIntegrator;
+import org.apache.commons.math3.ode.nonstiff.DormandPrince853Integrator;
+
+public class ThreeBodyExample {
+
+	public ThreeBodyExample() {
+	}
+
+	public static void main(String[] args) {
+		// Class that solves a three body problem and plots it
+		ThreeBodyExample x = new ThreeBodyExample();
+
+		//initialize variables
+		double totalEnergy = 0;
+		// set the final time = one orbit period
+		double tf = 1.0;
+
+		// create a ThreeBody orbit using three masses and gravitational con
+		ThreeBodyAPL sat = new ThreeBodyAPL(9.87, 0.3, 1.0, 2.0);
+		//initialize VectorN elements
+		double[] y = sat.randv();
+
+		ArrayRealVector v = new ArrayRealVector(y);
+
+		DecimalFormat df2 = new DecimalFormat("#,###,###,##0.00");
+		RealVectorFormat format = new RealVectorFormat(df2);
+		System.out.println(format.format(v));
+
+		// find out the derivs of the problem
+		double[] derivs = sat.derivs(tf, y);
+
+		// set the initial time to zero
+		double t0 = 0.0;
+		// obtain center of mass
+		VectorN cm = sat.center_of_mass(y);
+
+		// obtain current energy
+		totalEnergy = sat.Energy(y);
+
+		// propagate the orbit
+		FirstOrderIntegrator dp853 = new DormandPrince853Integrator(1.0e-8, 100.0, 1.0e-10, 1.0e-10);
+		dp853.addStepHandler(sat.stepHandler);
+		// double[] y = new double[] { 7000.0, 0, 0, .0, 8, 0 }; // initial
+		// state
+
+		dp853.integrate(sat, 0.0, y, 8000, y); // now y contains final state at
+		// tf
+
+		Double[] objArray = sat.time.toArray(new Double[sat.time.size()]);
+		double[] timeArray = ArrayUtils.toPrimitive(objArray);
+		double[] xsolArray = ArrayUtils.toPrimitive(sat.xsol.toArray(new Double[sat.time.size()]));
+		double[] ysolArray = ArrayUtils.toPrimitive(sat.ysol.toArray(new Double[sat.time.size()]));
+
+		double[][] XY = new double[timeArray.length][2];
+
+		 int a=0;
+		// System.arraycopy(timeArray,0,XY[a],0,timeArray.length);
+		// System.arraycopy(ysolArray,0,XY[1],0,ysolArray.length);
+
+		for (int i = 0; i < timeArray.length; i++) {
+			XY[i][0] = xsolArray[i];
+			XY[i][1] = ysolArray[i];
+		}
+
+		Plot2DPanel p = new Plot2DPanel();
+
+		// Plot2DPanel p = new Plot2DPanel(min, max, axesScales, axesLabels);
+
+		ScatterPlot s = new ScatterPlot("orbit", Color.RED, XY);
+		// LinePlot l = new LinePlot("sin", Color.RED, XY);
+		// l.closed_curve = false;
+		// l.draw_dot = true;
+		p.addPlot(s);
+		p.setLegendOrientation(PlotPanel.SOUTH);
+		double plotSize = 10000.;
+		double[] min = { -plotSize, -plotSize };
+		double[] max = { plotSize, plotSize };
+
+		p.setFixedBounds(min, max);
+
+		// test outputs
+		// output derivatives
+		for (int i = 0; i< derivs.length; i++)
+		{
+			System.out.println(derivs[i]);
+		}
+
+		// output center of mass
+		System.out.println(cm);
+
+		// output total energy of the system
+		System.out.println(totalEnergy);
+		new FrameView(p).setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+
+		System.out.println("end");
+	}
+}