/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000047.xml diagram  at 2008.03.20 15:04:26
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000047 extends JavaBaseModel
{

/*
 * Write rules to calculate equation parameters
 */
    private void __internalVarInitFunc_0(double time, double[] x)
    {
        n = n0*(Math.exp(-kbN*time) + kappa*(1 - Math.exp(-kbN*time)));
        p1 = p11 + p12*n/(K1 + n);
        p2 = x[0]/(K2 + x[0]);
    }


/*
 * Write rules to calculate equation parameters excluding internal variables.
 */
    public void __internalRateVarInitFunc_0(double time, double[] x)
    {
        rate_Jch = Jch_Fch_0*p1*p2*x[2];
        rate_Jleak = Jleak_Fleak;
        rate_Jpump = Jpump_Fpump_0*x[0]/(Jpump_Kpump + x[0]);
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        Jch_Fch_0 = 8.0; // initial value of Jch_Fch_0
        Jleak_Fleak = 0.5; // initial value of Jleak_Fleak
        Jpump_Fpump_0 = 2.0; // initial value of Jpump_Fpump_0
        Jpump_Kpump = 0.1; // initial value of Jpump_Kpump
        K1 = 5.0; // initial value of K1
        K2 = 0.7; // initial value of K2
        K3 = 0.7; // initial value of K3
        k31 = 0.5; // initial value of k31
        kappa = 5.0; // initial value of kappa
        kbN = 0.5; // initial value of kbN
        n = 1.0; // initial value of n
        n0 = 1.0; // initial value of n0
        p11 = 0.2; // initial value of p11
        p12 = 0.8; // initial value of p12
    }

    /*
     * Model variables initial values
     */
    protected double rate_Jch;
    protected double rate_Jleak;
    protected double rate_Jpump;
    protected double Jch_Fch_0;
    protected double Jleak_Fleak;
    protected double Jpump_Fpump_0;
    protected double Jpump_Kpump;
    protected double K1;
    protected double K2;
    protected double K3;
    protected double k31;
    protected double kappa;
    protected double kbN;
    protected double n;
    protected double n0;
    protected double p1;
    protected double p11;
    protected double p12;
    protected double p2;
    protected double time;

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

        __internalVarInitFunc_0(time, x);

        double[] y = new double[6];
        y[0] = x[0];
        y[1] = x[1];
        y[2] = n;
        y[3] = p1;
        y[4] = p2;
        y[5] = x[2];
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[3];
        this.time = 0.0;
        x[0] = 0.0; // - $"Cytosol.Ca_Cyt"
        x[1] = 0.0; // - $"Cytosol.Endoplasmic_Reticulum.CaER"
        x[2] = 0.95; // - p3

        __internalVarInitFunc_0(time, x);
        __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)
    {

        __internalVarInitFunc_0(time, x);
        __internalRateVarInitFunc_0(time, x);

    }

        /*
         * calculate dy/dt for 'BIOMD0000000047.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = +rate_Jch+rate_Jleak-rate_Jpump;
        result[1] = -rate_Jch-rate_Jleak+rate_Jpump;
        result[2] = -(k31*x[0]*x[2]) + k31*K3*(1 - x[2]);
    }
    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 ...