/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000001.xml diagram  at 2008.03.20 15:03:06
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000001 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_React0 = comp1*(kf_0*(x[2]/comp1) - kr_0*(x[9]/comp1));
        rate_React1 = comp1*(kf_1*(x[9]/comp1) - kr_1*(x[3]/comp1));
        rate_React10 = comp1*(kf_10*(x[8]/comp1) - kr_10*(x[11]/comp1));
        rate_React11 = comp1*(kf_11*(x[1]/comp1) - kr_11*(x[7]/comp1));
        rate_React12 = comp1*(kf_12*(x[4]/comp1) - kr_12*(x[10]/comp1));
        rate_React13 = comp1*(kf_13*(x[10]/comp1) - kr_13*(x[5]/comp1));
        rate_React14 = comp1*(kf_14*(x[6]/comp1) - kr_14*(x[4]/comp1));
        rate_React15 = comp1*(kf_15*(x[11]/comp1) - kr_15*(x[10]/comp1));
        rate_React16 = comp1*(kf_16*(x[7]/comp1) - kr_16*(x[5]/comp1));
        rate_React2 = comp1*(kf_2*(x[3]/comp1) - kr_2*(x[1]/comp1));
        rate_React3 = comp1*(kf_3*(x[0]/comp1) - kr_3*(x[8]/comp1));
        rate_React4 = comp1*(kf_4*(x[8]/comp1) - kr_4*(x[1]/comp1));
        rate_React5 = comp1*(kf_5*(x[2]/comp1) - kr_5*(x[0]/comp1));
        rate_React6 = comp1*(kf_6*(x[9]/comp1) - kr_6*(x[8]/comp1));
        rate_React7 = comp1*(kf_7*(x[6]/comp1) - kr_7*(x[11]/comp1));
        rate_React8 = comp1*(kf_8*(x[11]/comp1) - kr_8*(x[7]/comp1));
        rate_React9 = comp1*(kf_9*(x[0]/comp1) - kr_9*(x[6]/comp1));
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        comp1 = 1.0E-16; // initial value of $comp1
        kf_0 = 3000.0; // initial value of kf_0
        kf_1 = 1500.0; // initial value of kf_1
        kf_10 = 19.85; // initial value of kf_10
        kf_11 = 20.0; // initial value of kf_11
        kf_12 = 3000.0; // initial value of kf_12
        kf_13 = 1500.0; // initial value of kf_13
        kf_14 = 0.05; // initial value of kf_14
        kf_15 = 0.05; // initial value of kf_15
        kf_16 = 0.05; // initial value of kf_16
        kf_2 = 30000.0; // initial value of kf_2
        kf_3 = 3000.0; // initial value of kf_3
        kf_4 = 1500.0; // initial value of kf_4
        kf_5 = 0.54; // initial value of kf_5
        kf_6 = 130.0; // initial value of kf_6
        kf_7 = 3000.0; // initial value of kf_7
        kf_8 = 1500.0; // initial value of kf_8
        kf_9 = 19.7; // initial value of kf_9
        kr_0 = 8000.0; // initial value of kr_0
        kr_1 = 16000.0; // initial value of kr_1
        kr_10 = 1.74; // initial value of kr_10
        kr_11 = 0.81; // initial value of kr_11
        kr_12 = 4.0; // initial value of kr_12
        kr_13 = 8.0; // initial value of kr_13
        kr_14 = 0.0012; // initial value of kr_14
        kr_15 = 0.0012; // initial value of kr_15
        kr_16 = 0.0012; // initial value of kr_16
        kr_2 = 700.0; // initial value of kr_2
        kr_3 = 8.64; // initial value of kr_3
        kr_4 = 17.28; // initial value of kr_4
        kr_5 = 10800.0; // initial value of kr_5
        kr_6 = 2740.0; // initial value of kr_6
        kr_7 = 4.0; // initial value of kr_7
        kr_8 = 8.0; // initial value of kr_8
        kr_9 = 3.74; // initial value of kr_9
        t2 = 20.0; // initial value of t2
    }

    /*
     * Model variables initial values
     */
    protected double rate_React0;
    protected double rate_React1;
    protected double rate_React10;
    protected double rate_React11;
    protected double rate_React12;
    protected double rate_React13;
    protected double rate_React14;
    protected double rate_React15;
    protected double rate_React16;
    protected double rate_React2;
    protected double rate_React3;
    protected double rate_React4;
    protected double rate_React5;
    protected double rate_React6;
    protected double rate_React7;
    protected double rate_React8;
    protected double rate_React9;
    protected double comp1;
    protected double kf_0;
    protected double kf_1;
    protected double kf_10;
    protected double kf_11;
    protected double kf_12;
    protected double kf_13;
    protected double kf_14;
    protected double kf_15;
    protected double kf_16;
    protected double kf_2;
    protected double kf_3;
    protected double kf_4;
    protected double kf_5;
    protected double kf_6;
    protected double kf_7;
    protected double kf_8;
    protected double kf_9;
    protected double kr_0;
    protected double kr_1;
    protected double kr_10;
    protected double kr_11;
    protected double kr_12;
    protected double kr_13;
    protected double kr_14;
    protected double kr_15;
    protected double kr_16;
    protected double kr_2;
    protected double kr_3;
    protected double kr_4;
    protected double kr_5;
    protected double kr_6;
    protected double kr_7;
    protected double kr_8;
    protected double kr_9;
    protected double t2;
    protected double time;

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


        double[] y = new double[20];
        y[0] = x[0];
        y[1] = x[1];
        y[2] = x[2];
        y[3] = x[3];
        y[4] = x[4];
        y[5] = x[5];
        y[6] = x[6];
        y[7] = x[7];
        y[8] = x[8];
        y[9] = x[9];
        y[10] = x[10];
        y[11] = x[11];
        y[12] = kf_0;
        y[13] = kf_1;
        y[14] = kf_12;
        y[15] = kf_13;
        y[16] = kf_3;
        y[17] = kf_4;
        y[18] = kf_7;
        y[19] = kf_8;
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[12];
        this.time = 0.0;
        x[0] = 0.0; // - $"comp1.A"
        x[1] = 0.0; // - $"comp1.ALL"
        x[2] = 1.66057788110262E-21; // - $"comp1.B"
        x[3] = 0.0; // - $"comp1.BLL"
        x[4] = 0.0; // - $"comp1.D"
        x[5] = 0.0; // - $"comp1.DLL"
        x[6] = 0.0; // - $"comp1.I"
        x[7] = 0.0; // - $"comp1.ILL"
        x[8] = 0.0; // - $comp1.AL
        x[9] = 0.0; // - $comp1.BL
        x[10] = 0.0; // - $comp1.DL
        x[11] = 0.0; // - $comp1.IL

        __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 'BIOMD0000000001.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_React3+rate_React5-rate_React9;
        result[1] = -rate_React11+rate_React2+rate_React4;
        result[2] = -rate_React0-rate_React5;
        result[3] = +rate_React1-rate_React2;
        result[4] = -rate_React12+rate_React14;
        result[5] = +rate_React13+rate_React16;
        result[6] = -rate_React14-rate_React7+rate_React9;
        result[7] = +rate_React11-rate_React16+rate_React8;
        result[8] = -rate_React10+rate_React3-rate_React4+rate_React6;
        result[9] = +rate_React0-rate_React1-rate_React6;
        result[10] = +rate_React12-rate_React13+rate_React15;
        result[11] = +rate_React10-rate_React15+rate_React7-rate_React8;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[12];
        __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 );
    }

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

        __internalRateVarInitFunc_0(time, x);

        double [] flags = new double[1];
        flags[0] = (time > t2) ? +1 : -1; //RemovalACh
        return flags;
    }

    public void processEvent(int __internalVar12060037864530, double time, double[] x)
    {
        this.time = time;
        if ( __internalVar12060037864530 == 0) //RemovalACh
        {
            kf_0 = 0.0;
            kf_3 = 0.0;
            kf_7 = 0.0;
            kf_12 = 0.0;
            kf_1 = 0.0;
            kf_4 = 0.0;
            kf_8 = 0.0;
            kf_13 = 0.0;
        }
    }

} // class ...