/*
   There are a total of 9 entries in the algebraic variable array.
   There are a total of 21 entries in each of the rate and state variable arrays.
   There are a total of 38 entries in the constant variable array.
 */
/*
 * VOI is time in component environment (minute).
 * ALGEBRAIC[0] is x1 in component x1 (molar).
 * STATES[0] is x2 in component x2 (molar).
 * CONSTANTS[0] is k1 in component reaction_constants (second_order_rate_constant).
 * CONSTANTS[1] is k_minus1 in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[22] is k4 in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[2] is k_minus4 in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[23] is k_minus3 in component reaction_constants (second_order_rate_constant).
 * STATES[1] is x3 in component x3 (molar).
 * STATES[2] is x5 in component x5 (molar).
 * STATES[3] is x6 in component x6 (molar).
 * ALGEBRAIC[1] is PTP in component reaction_constants (molar).
 * CONSTANTS[3] is k3 in component reaction_constants (first_order_rate_constant).
 * STATES[4] is x4 in component x4 (molar).
 * CONSTANTS[24] is k2 in component reaction_constants (second_order_rate_constant).
 * CONSTANTS[25] is k_minus2 in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[4] is k4b in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[5] is k_minus4b in component reaction_constants (first_order_rate_constant).
 * STATES[5] is x7 in component x7 (molar).
 * STATES[6] is x8 in component x8 (molar).
 * ALGEBRAIC[3] is k5 in component reaction_constants (rate).
 * CONSTANTS[6] is k_minus5 in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[7] is k6 in component reaction_constants (second_order_rate_constant).
 * STATES[7] is x9 in component x9 (molar).
 * CONSTANTS[8] is k7 in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[26] is k_minus7 in component reaction_constants (second_order_rate_constant).
 * CONSTANTS[27] is k7b in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[35] is k_minus7b in component reaction_constants (first_order_rate_constant).
 * STATES[8] is x10 in component x10 (molar).
 * STATES[9] is x10a in component x10a (molar).
 * CONSTANTS[9] is IRp in component reaction_constants (molar).
 * ALGEBRAIC[2] is PKC in component reaction_constants (dimensionless).
 * CONSTANTS[28] is k8 in component reaction_constants (second_order_rate_constant).
 * CONSTANTS[10] is k_minus8 in component reaction_constants (first_order_rate_constant).
 * STATES[10] is x11 in component x11 (molar).
 * STATES[11] is x12 in component x12 (molar).
 * STATES[12] is x13 in component x13 (percentage).
 * ALGEBRAIC[4] is k9 in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[29] is k_minus9 in component reaction_constants (second_order_rate_constant).
 * CONSTANTS[30] is k10 in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[11] is k_minus10 in component reaction_constants (second_order_rate_constant).
 * STATES[13] is x14 in component x14 (percentage).
 * STATES[14] is x15 in component x15 (percentage).
 * CONSTANTS[12] is PTEN in component reaction_constants (molar).
 * CONSTANTS[13] is SHIP in component reaction_constants (molar).
 * STATES[15] is x16 in component x16 (percentage).
 * ALGEBRAIC[5] is k11 in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[31] is k_minus11 in component reaction_constants (first_order_rate_constant).
 * STATES[16] is x17 in component x17 (percentage).
 * STATES[17] is x18 in component x18 (percentage).
 * ALGEBRAIC[6] is k12 in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[32] is k_minus12 in component reaction_constants (first_order_rate_constant).
 * STATES[18] is x19 in component x19 (percentage).
 * STATES[19] is x20 in component x20 (percentage).
 * CONSTANTS[33] is k13 in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[14] is k_minus13 in component reaction_constants (first_order_rate_constant).
 * ALGEBRAIC[8] is k13b in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[34] is k14 in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[15] is k_minus14 in component reaction_constants (first_order_rate_constant).
 * STATES[20] is x21 in component x21 (percentage).
 * CONSTANTS[16] is V_max in component reaction_constants (dimensionless).
 * CONSTANTS[17] is K_d in component reaction_constants (dimensionless).
 * CONSTANTS[18] is n in component reaction_constants (dimensionless).
 * CONSTANTS[19] is tau in component reaction_constants (minute).
 * CONSTANTS[36] is k9_basal in component reaction_constants (first_order_rate_constant).
 * CONSTANTS[20] is k9_stimulated in component reaction_constants (first_order_rate_constant).
 * ALGEBRAIC[7] is effect in component reaction_constants (dimensionless).
 * CONSTANTS[21] is APequil in component reaction_constants (dimensionless).
 * CONSTANTS[37] is PI3K in component reaction_constants (molar).
 * RATES[0] is d/dt x2 in component x2 (molar).
 * RATES[1] is d/dt x3 in component x3 (molar).
 * RATES[4] is d/dt x4 in component x4 (molar).
 * RATES[2] is d/dt x5 in component x5 (molar).
 * RATES[3] is d/dt x6 in component x6 (molar).
 * RATES[5] is d/dt x7 in component x7 (molar).
 * RATES[6] is d/dt x8 in component x8 (molar).
 * RATES[7] is d/dt x9 in component x9 (molar).
 * RATES[8] is d/dt x10 in component x10 (molar).
 * RATES[9] is d/dt x10a in component x10a (molar).
 * RATES[10] is d/dt x11 in component x11 (molar).
 * RATES[11] is d/dt x12 in component x12 (molar).
 * RATES[12] is d/dt x13 in component x13 (percentage).
 * RATES[13] is d/dt x14 in component x14 (percentage).
 * RATES[14] is d/dt x15 in component x15 (percentage).
 * RATES[15] is d/dt x16 in component x16 (percentage).
 * RATES[16] is d/dt x17 in component x17 (percentage).
 * RATES[17] is d/dt x18 in component x18 (percentage).
 * RATES[18] is d/dt x19 in component x19 (percentage).
 * RATES[19] is d/dt x20 in component x20 (percentage).
 * RATES[20] is d/dt x21 in component x21 (percentage).
 * There are a total of 4 condition variables.
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
STATES[0] = 9e-13;
CONSTANTS[0] = 6e7;
CONSTANTS[1] = 0.2;
CONSTANTS[2] = 0.003;
STATES[1] = 0;
STATES[2] = 0;
STATES[3] = 1e-13;
CONSTANTS[3] = 2500;
STATES[4] = 0;
CONSTANTS[4] = 2.1e-3;
CONSTANTS[5] = 2.1e-4;
STATES[5] = 0;
STATES[6] = 0;
CONSTANTS[6] = 1.67e-18;
CONSTANTS[7] = 0.461;
STATES[7] = 1e-12;
CONSTANTS[8] = 4.16;
STATES[8] = 0;
STATES[9] = 0;
CONSTANTS[9] = 8.97e-13;
CONSTANTS[10] = 10;
STATES[10] = 1e-13;
STATES[11] = 2.54e-15;
STATES[12] = 0.31;
CONSTANTS[11] = 2.77;
STATES[13] = 99.4;
STATES[14] = 0.29;
CONSTANTS[12] = 1;
CONSTANTS[13] = 1;
STATES[15] = 100;
STATES[16] = 0;
STATES[17] = 100;
STATES[18] = 0;
STATES[19] = 96;
CONSTANTS[14] = 0.167;
CONSTANTS[15] = 0.001155;
STATES[20] = 4;
CONSTANTS[16] = 20;
CONSTANTS[17] = 12;
CONSTANTS[18] = 4;
CONSTANTS[19] = 1.5;
CONSTANTS[20] = 1.39;
CONSTANTS[21] = 9.09;
CONSTANTS[22] = CONSTANTS[2]/9.00000;
CONSTANTS[23] = CONSTANTS[1]/1.00000;
CONSTANTS[24] = CONSTANTS[0];
CONSTANTS[25] =  100.000*CONSTANTS[1];
CONSTANTS[26] =  (2.50000/7.45000)*CONSTANTS[8];
CONSTANTS[27] = log(2.00000)/2.00000;
CONSTANTS[28] =  (( CONSTANTS[10]*5.00000)/70.7750)*1.00000e+12;
CONSTANTS[29] =  (94.0000/3.10000)*CONSTANTS[20];
CONSTANTS[30] =  (3.10000/2.90000)*CONSTANTS[11];
CONSTANTS[31] =  10.0000*log(2.00000)*1.00000;
CONSTANTS[32] =  10.0000*log(2.00000)*1.00000;
CONSTANTS[33] =  (4.00000/96.0000)*CONSTANTS[14];
CONSTANTS[34] = CONSTANTS[15]/96.0000;
CONSTANTS[35] = ( (( CONSTANTS[27]*2.50000)/7.45000)*3.70000e-13)/(6.27000e-13 -  (2.50000/7.45000)*3.70000e-13);
CONSTANTS[36] =  (0.310000/99.4000)*CONSTANTS[29];
CONSTANTS[37] = ( CONSTANTS[28]*3.70000e-13*1.00000e-13)/( CONSTANTS[28]*3.70000e-13+CONSTANTS[10]);
RATES[0] = 0.1001;
RATES[1] = 0.1001;
RATES[4] = 0.1001;
RATES[2] = 0.1001;
RATES[3] = 0.1001;
RATES[5] = 0.1001;
RATES[6] = 0.1001;
RATES[7] = 0.1001;
RATES[8] = 0.1001;
RATES[9] = 0.1001;
RATES[10] = 0.1001;
RATES[11] = 0.1001;
RATES[12] = 0.1001;
RATES[13] = 0.1001;
RATES[14] = 0.1001;
RATES[15] = 0.1001;
RATES[16] = 0.1001;
RATES[17] = 0.1001;
RATES[18] = 0.1001;
RATES[19] = 0.1001;
RATES[20] = 0.1001;
}
void
computeResiduals(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
                 double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
resid[0] = RATES[0] - ( CONSTANTS[1]*STATES[1]+ CONSTANTS[23]*ALGEBRAIC[1]*STATES[2]+ CONSTANTS[2]*STATES[3]) - ( CONSTANTS[0]*ALGEBRAIC[0]*STATES[0]+ CONSTANTS[22]*STATES[0]);
resid[1] = RATES[1] -  CONSTANTS[0]*ALGEBRAIC[0]*STATES[0] - ( CONSTANTS[1]*STATES[1]+ CONSTANTS[3]*STATES[1]);
resid[2] = RATES[4] - ( CONSTANTS[24]*ALGEBRAIC[0]*STATES[2]+ CONSTANTS[5]*STATES[5]) - ( CONSTANTS[25]*STATES[4]+ CONSTANTS[4]*STATES[4]);
resid[3] = RATES[2] - ( CONSTANTS[3]*STATES[1]+ CONSTANTS[25]*STATES[4]+ CONSTANTS[5]*STATES[6]) - ( CONSTANTS[24]*ALGEBRAIC[0]*STATES[2]+ CONSTANTS[23]*ALGEBRAIC[1]*STATES[2]+ CONSTANTS[4]*STATES[2]);
resid[4] = RATES[3] - (ALGEBRAIC[3]+ CONSTANTS[7]*ALGEBRAIC[1]*(STATES[5]+STATES[6])+ CONSTANTS[22]*STATES[0]) - ( CONSTANTS[6]*STATES[3]+ CONSTANTS[2]*STATES[3]);
resid[5] = RATES[5] -  CONSTANTS[4]*STATES[4] - ( CONSTANTS[5]*STATES[5]+ CONSTANTS[7]*ALGEBRAIC[1]*STATES[5]);
resid[6] = RATES[6] -  CONSTANTS[4]*STATES[2] - ( CONSTANTS[5]*STATES[6]+ CONSTANTS[7]*ALGEBRAIC[1]*STATES[6]);
resid[7] = RATES[7] - (( CONSTANTS[26]*ALGEBRAIC[1]*STATES[8] - ( CONSTANTS[8]*STATES[7]*(STATES[4]+STATES[2]))/CONSTANTS[9])+ CONSTANTS[35]*STATES[9]) -  CONSTANTS[27]*ALGEBRAIC[2]*STATES[7];
resid[8] = RATES[8] - (( CONSTANTS[8]*STATES[7]*(STATES[4]+STATES[2]))/CONSTANTS[9]+ CONSTANTS[10]*STATES[11]) -  ( CONSTANTS[26]*ALGEBRAIC[1]+ CONSTANTS[28]*STATES[10])*STATES[8];
resid[9] = RATES[9] -  CONSTANTS[27]*ALGEBRAIC[2]*STATES[7] -  CONSTANTS[35]*STATES[9];
resid[10] = RATES[10] -  CONSTANTS[10]*STATES[11] -  CONSTANTS[28]*STATES[8]*STATES[10];
resid[11] = RATES[11] -  CONSTANTS[28]*STATES[8]*STATES[10] -  CONSTANTS[10]*STATES[11];
resid[12] = RATES[12] - ( ALGEBRAIC[4]*STATES[13]+ CONSTANTS[30]*STATES[14]) -  ( CONSTANTS[29]*CONSTANTS[12]+ CONSTANTS[11]*CONSTANTS[13])*STATES[12];
resid[13] = RATES[13] -  CONSTANTS[29]*CONSTANTS[12]*STATES[12] -  ALGEBRAIC[4]*STATES[13];
resid[14] = RATES[14] -  CONSTANTS[11]*CONSTANTS[13]*STATES[12] -  CONSTANTS[30]*STATES[14];
resid[15] = RATES[15] -  CONSTANTS[31]*STATES[16] -  ALGEBRAIC[5]*STATES[15];
resid[16] = RATES[16] -  ALGEBRAIC[5]*STATES[15] -  CONSTANTS[31]*STATES[16];
resid[17] = RATES[17] -  CONSTANTS[32]*STATES[18] -  ALGEBRAIC[6]*STATES[17];
resid[18] = RATES[18] -  ALGEBRAIC[6]*STATES[17] -  CONSTANTS[32]*STATES[18];
resid[19] = RATES[19] - ( CONSTANTS[14]*STATES[20]+CONSTANTS[34]) - ( (CONSTANTS[33]+ALGEBRAIC[8])*STATES[19]+ CONSTANTS[15]*STATES[19]);
resid[20] = RATES[20] -  - CONSTANTS[14]*STATES[20]+ (CONSTANTS[33]+ALGEBRAIC[8])*STATES[19];
}
void
computeVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
}
void
computeEssentialVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[0] = (CONDVAR[0]<0.00000 ? 1.00000e-07 : 0.00000);
ALGEBRAIC[1] = (CONDVAR[1]<=0.00000||CONDVAR[2]>=0.00000 ? 1.00000 - ( 0.250000*STATES[16])/(100.000/11.0000) : 0.00000);
ALGEBRAIC[2] = ( CONSTANTS[16]*pow(STATES[18], CONSTANTS[18]))/(pow(CONSTANTS[17], CONSTANTS[18])+pow(STATES[18], CONSTANTS[18]));
ALGEBRAIC[3] = (CONDVAR[3]>0.00000 ?  10.0000*CONSTANTS[6] :  60.0000*CONSTANTS[6]);
ALGEBRAIC[4] = ( (CONSTANTS[20] - CONSTANTS[36])*STATES[11])/CONSTANTS[37]+CONSTANTS[36];
ALGEBRAIC[5] = ( 0.100000*CONSTANTS[31]*(STATES[12] - 0.310000))/(3.10000 - 0.310000);
ALGEBRAIC[6] = ( 0.100000*CONSTANTS[32]*(STATES[12] - 0.310000))/(3.10000 - 0.310000);
ALGEBRAIC[7] = ( 0.200000*STATES[16]+ 0.800000*STATES[18])/CONSTANTS[21];
ALGEBRAIC[8] =  (40.0000/60.0000 - 4.00000/96.0000)*CONSTANTS[14]*ALGEBRAIC[7];
}
void
getStateInformation(double* SI)
{
SI[0] = 1.0;
SI[1] = 1.0;
SI[2] = 1.0;
SI[3] = 1.0;
SI[4] = 1.0;
SI[5] = 1.0;
SI[6] = 1.0;
SI[7] = 1.0;
SI[8] = 1.0;
SI[9] = 1.0;
SI[10] = 1.0;
SI[11] = 1.0;
SI[12] = 1.0;
SI[13] = 1.0;
SI[14] = 1.0;
SI[15] = 1.0;
SI[16] = 1.0;
SI[17] = 1.0;
SI[18] = 1.0;
SI[19] = 1.0;
SI[20] = 1.0;
}
void
computeRoots(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
             double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
CONDVAR[0] = VOI - 15.0000;
CONDVAR[1] = STATES[16] - 400.000/11.0000;
CONDVAR[2] = ALGEBRAIC[0] - 1.00000e-07;
CONDVAR[3] = (STATES[3]+STATES[5]+STATES[6]) - 1.00000e-13;
}