/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000040.xml diagram  at 2008.03.20 15:04:19
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000040 extends JavaBaseModel
{

/*
 * Write rules to calculate equation parameters
 */


/*
 * Write rules to calculate equation parameters excluding internal variables.
 */
    public void __internalRateVarInitFunc_0(double time, double[] x)
    {
        rate_Reaction1 = x[1]*_BZ_BrO3_*Reaction1_k1*BZ;
        rate_Reaction2 = x[1]*x[0]*Reaction2_k2*BZ;
        rate_Reaction3 = _BZ_BrO3_*x[0]*Reaction3_k3*BZ;
        rate_Reaction4 = Math.pow(x[0], 2)*Reaction4_k4*BZ;
        rate_Reaction5 = x[2]*Reaction5_k5*BZ;
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        _BZ_BrO3_ = 0.06; // initial value of $"BZ.BrO3"
        BZ = 1.0; // initial value of $BZ
        Reaction1_k1 = 1.34; // initial value of Reaction1_k1
        Reaction2_k2 = 1.6E9; // initial value of Reaction2_k2
        Reaction3_k3 = 8000.0; // initial value of Reaction3_k3
        Reaction4_k4 = 4.0E7; // initial value of Reaction4_k4
        Reaction5_k5 = 1.0; // initial value of Reaction5_k5
        f = 1.0; // initial value of f
    }

    /*
     * Model variables initial values
     */
    protected double _BZ_BrO3_;
    protected double _BZ_HOBr_;
    protected double rate_Reaction1;
    protected double rate_Reaction2;
    protected double rate_Reaction3;
    protected double rate_Reaction4;
    protected double rate_Reaction5;
    protected double BZ;
    protected double Reaction1_k1;
    protected double Reaction2_k2;
    protected double Reaction3_k3;
    protected double Reaction4_k4;
    protected double Reaction5_k5;
    protected double f;

    public double[] extendResult(double time,double [] x)
    {
        this.time = time;


        double[] y = new double[3];
        y[0] = x[0];
        y[1] = x[1];
        y[2] = x[2];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[3];
        this.time = 0.0;
        x[0] = 5.0E-11; // - $"BZ.HBrO2"
        x[1] = 1.0E-7; // - $BZ.Br
        x[2] = 0.05; // - $BZ.Ce

        __internalRateVarInitFunc_0(time, x);

        return x;
    }

/*
 * code for algebraic rules calculations
 */

/*
 * end of code for algebraic rules calculations
 */

    protected void calculateRates(double time, double[] x)
    {

        __internalRateVarInitFunc_0(time, x);

    }

        /*
         * calculate dy/dt for 'BIOMD0000000040.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = +rate_Reaction1-rate_Reaction2+rate_Reaction3*2-rate_Reaction3-rate_Reaction4*2;
        result[1] = -rate_Reaction1-rate_Reaction2+rate_Reaction5*f;
        result[2] = +rate_Reaction3-rate_Reaction5;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[3];
        __internalDyDt_0(time, x, result);
        return result;
    }
    public double[] dy_dt(double time, double[] x)
    {
        this.time = time;
        calculateRates( time,x );

        return calculateResult( time,x );
    }

} // class ...