protected override void Run()
        {
            /* When the bolded "Run Search Process" is clicked from the
             * pulldown window, this function is initiated. It can be removed
             * so that any of the included functions can be called directly, or
             * other code can fill this entire file. --> YOUR RESEARCH GOES HERE.
             */
            //  designGraph testGraph = designGraph.openGraphFromXml(settings.inputDirectory + "c1.gxml");]
            designGraph testGraph = this.seedGraph;

            /** reciprocating follower arc ***/
            //double[,] desiredPath ={{1.87,8},{2.93,8.46},{2.80,8.41},
            //                           {1.99,8.06},{0.96,7.46},{0,6.71},{-0.77,5.93},{-1.3,5.26},{-1.60,4.81},{-1.65,4.75},{-1.25,5.33},{0,6.71}};
            /** bean shape **/
            double[,] desiredPath = { {    125,    225 }, { 165.44, 217.76 }, { 189.57, 200.42 }, { 185.89, 178.49 }, { 158.65, 161.92 }, { 109.38, 135.30 }, { 57.997, 101.69 }, { 24.59, 82.07 }, { 0.33, 76.90 }, { -17.03, 91.46 },
                                      { -13.92, 129.10 }, {  -0.74, 155.01 }, {  20.73, 180.91 }, {  53.78, 205.65 }, {  88.17, 219.90 } };

            double         startAngle = 0;
            double         endAngle   = 2 * Math.PI;
            double         iOmega     = 2;
            MechSimulation ev         = new MechSimulation();

            ev.Graph = testGraph;

            ev.calculate(); //new[] { 0.0, 0.0, 6.0, 0.0, 1.874099, 7.998559, 1.73, 1 });
            var CPWD = new ComparePathWithDesired(seedCandidate, desiredPath, ev);
            var rms  = CPWD.calculate(new double[1]);

            //ev.saveParameterData(settings.outputDirectory + "outputPathC1");
            SearchIO.output("***Completed!*** RMS = " + rms, 0);
            //
            // c now needs values for the positions of the pivots unless of course it's set in the xml
            // otherwise you could set by calling calc(x).
            //
            //double[,] path = ev.returnPath();
            //
            // save double as csv or something (see Albert and Dagu).
            //
            //
            //runSearchProcessBFS();
            //runSearchProcessDFS();
            //runSearchProcessBESTFIRST();
        }
        protected override void Run()
        {
            Random r = new Random(); //1);



            //  double[,] desiredPath ={{1.87,8},{2.93,8.46},{2.80,8.41},
            //                             {1.99,8.06},{0.96,7.46},{0,6.71},{-0.77,5.93},{-1.3,5.26},{-1.60,4.81},{-1.65,4.75},{-1.25,5.33},{0,6.71}};
            double[,] desiredPath = { { 125, 225 }, { 165.44, 217.76 }, { 189.57, 200.42 }, { 185.89, 178.49 }, { 158.65, 161.92 }, { 109.38, 135.30 }, { 57.997, 101.69 }, { 24.59, 82.07 }, { 0.33, 76.90 }, { -17.03, 91.46 }, { -13.92, 129.10 }, { -0.74, 155.01 }, { 20.73, 180.91 }, { 53.78, 205.65 }, { 88.17, 219.90 } };

            double         startAngle = 0;
            double         endAngle   = 2 * Math.PI;
            double         iOmega     = 2;
            double         iAlpha     = 0;
            MechSimulation sim        = new MechSimulation();


            //Below is a relation for bounding box and also the first point
            double bb_min, bb_max;

            //   bb_min = StarMath.Min(desiredPath);
            //  bb_max = StarMath.Max(desiredPath);

            //now that min and max are obtained - we will form a bounding box using these max and min values

            bb_max = 250;
            bb_min = 250;

            sim.Graph = seedGraph;
            //  designGraph testGraph = this.seedGraph;
            //   ev.c = new candidate(testGraph, 0);
            //  ev.c = this.seedGraph;

            //bounding box - trying to contain the solutions within a particular box
            //      BoundingBox bb = new BoundingBox(sim, bb_max,bb_min);
            //   GrashofCriteria cc = new GrashofCriteria(sim, 0);

            //adding a new objective function which can be taken by the optimization program
            var pathObjFun = new ComparePathWithDesired(seedCandidate, desiredPath, sim);


            //initializing the optimization program
            var optMethod = new NelderMead();

            //var optMethod = new GradientBasedOptimization();

            optMethod.Add(new PowellMethod());
            optMethod.Add(new DSCPowell(0.00001, .5, 1000));


            //     optMethod.Add(new GoldenSection(0.001,300));
            optMethod.Add(new ArithmeticMean(0.001, 0.1, 300));

            //adding simulation
            optMethod.Add(sim);

            //adding objective function to this optimization routine
            optMethod.Add(pathObjFun);

            //we are removing this since we do not have a merit function defined
            optMethod.Add(new squaredExteriorPenalty(optMethod, 1.0));
            //      optMethod.Add(bb);
            //    optMethod.Add(cc);

            // convergence
            optMethod.Add(new MaxIterationsConvergence(100));
            //   optMethod.Add(new DeltaXConvergence(0.01));
            optMethod.Add(new ToKnownBestFConvergence(0.0, 0.1));
            optMethod.Add(new MaxSpanInPopulationConvergence(0.01));

            var n     = 6;
            var dsd   = new DesignSpaceDescription();
            var minX  = StarMath.Min(StarMath.GetColumn(0, desiredPath));
            var maxX  = StarMath.Max(StarMath.GetColumn(0, desiredPath));
            var minY  = StarMath.Min(StarMath.GetColumn(1, desiredPath));
            var maxY  = StarMath.Max(StarMath.GetColumn(1, desiredPath));
            var delta = maxX - minX;

            minX -= delta;
            maxX += delta;
            delta = maxY - minY;
            minY -= delta;
            maxY += delta;

            for (int i = 0; i < n; i++)
            {
                if (i % 2 == 0)
                {
                    dsd.Add(new VariableDescriptor(minX, maxX));
                }
                else
                {
                    dsd.Add(new VariableDescriptor(minY, maxY));
                }
            }
            // dsd.Add(new VariableDescriptor(0,300));
            var LHC        = new LatinHyperCube(dsd, VariablesInScope.BothDiscreteAndReal);
            var initPoints = LHC.GenerateCandidates(null, 100);

            //for each initPoints - generate the fstar value



            //generating random x,y values
            //double[] x0 = new double[8];
            //for (int i = 0; i < x0.GetLength(0); i++) //since I am going to assign ground pivots as they are
            //    x0[i] =  100*r.NextDouble();


            //sim.calculate(x0);

            // double[] xStar;
            // double fStar = optMethod.Run(out xStar, x0);
            //// double fStar = optMethod.Run(out xStar, 8);

            double[]        fStar1 = new double[initPoints.Count];
            List <double[]> xStar1 = new List <double[]>();


            for (int i = 0; i < fStar1.GetLength(0); i++)
            {
                double[] x0 = new double[n];
                x0 = initPoints[i];
                double[] xStar;
                double   fStar = optMethod.Run(out xStar, x0);
                fStar1[i] = fStar;
                xStar1.Add(xStar);
                SearchIO.output("LHC i: " + i);
            }

            int xstarindex;

            SearchIO.output("fStar Min=" + StarMath.Min(fStar1, out xstarindex), 0);
            SearchIO.output("Xstar Values:" + xStar1[xstarindex]);
            SearchIO.output("***Converged by" + optMethod.ConvergenceDeclaredByTypeString, 0);
            SearchIO.output("Rerunning with new x values", 0);

            //     var optMethod1 = new GradientBasedOptimization();
            //     optMethod1.Add(new FletcherReevesDirection());
            //  //   optMethod1.Add(new ArithmeticMean(0.001, 0.1, 300));

            //     optMethod1.Add(new GoldenSection(0.001, 300));
            //     optMethod1.Add(sim);
            //     optMethod1.Add(pathObjFun);
            //     optMethod1.Add(new squaredExteriorPenalty(optMethod, 1.0));
            ////     optMethod1.Add(new MaxIterationsConvergence(100));
            //     optMethod1.Add(new ToKnownBestFConvergence(0.0, 0.1));
            //   //  optMethod.Add(new MaxSpanInPopulationConvergence(0.01))

            //     double[] xStar2;
            //     double fStar2 = optMethod1.Run(out xStar2, xStar1[xstarindex]);

            //     SearchIO.output("New Fstar = " + fStar2, 0);

            //double xstarmin, xstarmax;
            //xstarmax = StarMath.Max(xStar1[xstarindex]);
            //xstarmin = StarMath.Min(xStar1[xstarindex]);

            //var dsd1 = new DesignSpaceDescription();
            //dsd1.Add(new VariableDescriptor(xstarmin, xstarmax));
            //var LHC1 = new LatinHyperCube(dsd1, VariablesInScope.BothDiscreteAndReal);
            //var initPoints1 = LHC.GenerateCandidates(null, 100);
            //double[] fstar1 = new double[initPoints1.Count];
            //List<double[]> xstar_second = new List<double[]>();
            //for (int i = 0; i < fstar1.GetLength(0); i++)
            //{
            //    double[] x0 = new double[n];
            //    x0 = initPoints[i];
            //    double[] xStar;
            //    double fStar = optMethod.Run(out xStar, x0);
            //    fstar1[i] = fStar;
            //    xstar_second.Add(xStar);
            //    SearchIO.output("LHC i: " + i);

            //}



            //SearchIO.output("New fStar = " + StarMath.Min(fstar1), 0);


            //SearchIO.output("***Converged by" + optMethod.ConvergenceDeclaredByTypeString, 0);
        }