/*
 * This code is generated by BioUML FrameWork 
 * for BIOMD0000000090.xml diagram  at 2008.03.20 15:08:20
 */
import biouml.plugins.simulation.ae.NewtonSolver;
import biouml.plugins.simulation.java.JavaBaseModel;
import ru.biosoft.math.MathRoutines;

public class BIOMD0000000090 extends JavaBaseModel
{

/*
 * Write rules to calculate equation parameters
 */
    private void __internalVarInitFunc_0(double time, double[] x)
    {
        _c0_c1_A2c_ = Ac - x[0];
        _c0_c1_c2_A2m_ = Am - x[3];
        c0_c1_N1 = N - x[11];
        c0_c1_c2_S2 = S - x[12];
    }


/*
 * Write rules to calculate equation parameters excluding internal variables.
 */
    public void __internalRateVarInitFunc_0(double time, double[] x)
    {
        rate_v1 = c0*k_v0/(1 + Math.pow((x[5]/Kc), n));
        rate_v10 = c0*k_v10;
        rate_v11a = c0_c1_c2*k11*x[11]*x[4]/((a*x[11] + x[4])*(1 + Math.pow((x[7]/Kh), m)));
        rate_v11a2 = c0_c1_c2*k11*x[11]*x[4]/((a*x[11] + x[4])*(1 + Math.pow((x[7]/Kh), m)));
        rate_v11b = c0_c1_c2*3*k11*x[11]*x[4]/((a*x[11] + x[4])*(1 + Math.pow((x[7]/Kh), m)))*_c0_c1_c2_A2m_/(Ka + _c0_c1_c2_A2m_);
        rate_v12 = c0_c1*k12*x[0];
        rate_v13 = c0*k_v13;
        rate_v14 = c0_c1_c2*k14*x[4];
        rate_v15 = c0_c1*k15*x[1];
        rate_v16 = c0_c1_c2*k16*x[3]*_c0_c1_A2c_;
        rate_v17 = c0_c1*k17*x[7];
        rate_v18 = c0_c1*k18*x[8];
        rate_v2 = c0_c1*k2*x[10]*x[0];
        rate_v3 = c0_c1*k3*x[2]*x[0];
        rate_v4 = c0_c1*k4*x[9]*x[11];
        rate_v5 = c0_c1*k5*x[7]*x[8];
        rate_v6 = c0_c1*k6*x[5];
        rate_v7 = c0_c1*k7*x[6]*c0_c1_N1;
        rate_v8 = c0_c1_c2*k8*x[1]*c0_c1_c2_S2;
        rate_v9 = c0_c1_c2*k9*x[12]*c0_c1_N1;
        rate_vLEAK = 0;
    }

    public void Init()
    {
        initialValues = getInitialValues();
/*
 * Initialize variables
 */
        _c0_c1_A2c_ = 0.5; // initial value of $"c0.c1.A2c"
        _c0_c1_c2_A2m_ = 0.5; // initial value of $"c0.c1.c2.A2m"
        c0 = 1.0; // initial value of $c0
        c0_c1 = 1.0; // initial value of $c0.c1
        c0_c1_c2 = 1.0; // initial value of $c0.c1.c2
        c0_c1_c2_S2 = 0.5; // initial value of $c0.c1.c2.S2
        Ac = 2.0; // initial value of Ac
        Am = 2.0; // initial value of Am
        Ka = 1.0; // initial value of Ka
        Kc = 0.1; // initial value of Kc
        Kh = 0.5; // initial value of Kh
        N = 2.0; // initial value of N
        S = 2.0; // initial value of S
        a = 0.1; // initial value of a
        k11 = 10.0; // initial value of k11
        k12 = 5.0; // initial value of k12
        k14 = 10.0; // initial value of k14
        k15 = 5.0; // initial value of k15
        k16 = 10.0; // initial value of k16
        k17 = 0.02; // initial value of k17
        k18 = 1.0; // initial value of k18
        k2 = 0.2; // initial value of k2
        k3 = 0.2; // initial value of k3
        k4 = 0.2; // initial value of k4
        k5 = 0.1; // initial value of k5
        k6 = 0.12; // initial value of k6
        k7 = 10.0; // initial value of k7
        k8 = 10.0; // initial value of k8
        k9 = 10.0; // initial value of k9
        k_v0 = 1.6; // initial value of k_v0
        k_v10 = 80.0; // initial value of k_v10
        k_v13 = 4.0; // initial value of k_v13
        m = 4.0; // initial value of m
        n = 4.0; // initial value of n
    }

    /*
     * Model variables initial values
     */
    protected double _c0_c1_A2c_;
    protected double _c0_c1_PPi_;
    protected double _c0_c1_c2_A2m_;
    protected double _c0_c1_c2_H2O_;
    protected double _c0_eth_ex_;
    protected double _c0_oxy_ex_;
    protected double _c0_sul_ex_;
    protected double rate_v1;
    protected double rate_v10;
    protected double rate_v11a;
    protected double rate_v11a2;
    protected double rate_v11b;
    protected double rate_v12;
    protected double rate_v13;
    protected double rate_v14;
    protected double rate_v15;
    protected double rate_v16;
    protected double rate_v17;
    protected double rate_v18;
    protected double rate_v2;
    protected double rate_v3;
    protected double rate_v4;
    protected double rate_v5;
    protected double rate_v6;
    protected double rate_v7;
    protected double rate_v8;
    protected double rate_v9;
    protected double rate_vLEAK;
    protected double c0;
    protected double c0_c1;
    protected double c0_c1_Ho;
    protected double c0_c1_N1;
    protected double c0_c1_c2;
    protected double c0_c1_c2_C1;
    protected double c0_c1_c2_C2;
    protected double c0_c1_c2_Hm;
    protected double c0_c1_c2_S2;
    protected double Ac;
    protected double Am;
    protected double Ka;
    protected double Kc;
    protected double Kh;
    protected double N;
    protected double S;
    protected double a;
    protected double k11;
    protected double k12;
    protected double k14;
    protected double k15;
    protected double k16;
    protected double k17;
    protected double k18;
    protected double k2;
    protected double k3;
    protected double k4;
    protected double k5;
    protected double k6;
    protected double k7;
    protected double k8;
    protected double k9;
    protected double k_v0;
    protected double k_v10;
    protected double k_v13;
    protected double m;
    protected double n;

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

        __internalVarInitFunc_0(time, x);

        double[] y = new double[17];
        y[0] = _c0_c1_A2c_;
        y[1] = x[0];
        y[2] = x[1];
        y[3] = x[2];
        y[4] = _c0_c1_c2_A2m_;
        y[5] = x[3];
        y[6] = x[4];
        y[7] = x[5];
        y[8] = x[6];
        y[9] = x[7];
        y[10] = x[8];
        y[11] = x[9];
        y[12] = x[10];
        y[13] = c0_c1_N1;
        y[14] = x[11];
        y[15] = x[12];
        y[16] = c0_c1_c2_S2;
        return y;
    }
    public double[] getInitialValues()
    {
        double [] x = new double[13];
        this.time = 0.0;
        x[0] = 1.5; // - $"c0.c1.A3c"
        x[1] = 0.3; // - $"c0.c1.aco"
        x[2] = 0.5; // - $"c0.c1.aps"
        x[3] = 1.5; // - $"c0.c1.c2.A3m"
        x[4] = 7.0; // - $"c0.c1.c2.oxy"
        x[5] = 0.3; // - $"c0.c1.cys"
        x[6] = 4.0; // - $"c0.c1.eth"
        x[7] = 0.5; // - $"c0.c1.hyd"
        x[8] = 1.5; // - $"c0.c1.oah"
        x[9] = 0.4; // - $"c0.c1.pap"
        x[10] = 0.4; // - $"c0.c1.sul"
        x[11] = 2.0; // - $c0.c1.N2
        x[12] = 1.5; // - $c0.c1.c2.S1

        __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 'BIOMD0000000090.xml' model
         */
    public void __internalDyDt_0(double time, double [] x, double[] result)
    {
        result[0] = -rate_v12+rate_v16-rate_v2-rate_v3;
        result[1] = -rate_v15+rate_v7-rate_v8;
        result[2] = +rate_v2-rate_v3;
        result[3] = +rate_v11b-rate_v16;
        result[4] = +rate_v10-rate_v11a2-rate_v14;
        result[5] = +rate_v5-rate_v6;
        result[6] = +rate_v13-rate_v7;
        result[7] = -rate_v17+rate_v4-rate_v5;
        result[8] = +rate_v15-rate_v18-rate_v5;
        result[9] = +rate_v3-rate_v4;
        result[10] = +rate_v1-rate_v2;
        result[11] = -rate_v11a-rate_v4*3+rate_v7*2+rate_v9*4;
        result[12] = +rate_v8-rate_v9;
    }
    protected double [] calculateResult(double time, double[] x)
    {
        double[] result = new double[13];
        __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 ...