/*
   There are a total of 34 entries in the algebraic variable array.
   There are a total of 16 entries in each of the rate and state variable arrays.
   There are a total of 47 entries in the constant variable array.
 */
/*
 * VOI is time in component environment (minute).
 * ALGEBRAIC[0] is v1 in component v1 (flux).
 * CONSTANTS[0] is Vmax in component v1 (flux).
 * CONSTANTS[1] is Km in component v1 (umol_per_g).
 * STATES[0] is GL in component GL (umol_per_g).
 * ALGEBRAIC[1] is v2 in component v2 (flux).
 * CONSTANTS[2] is Vmax in component v2 (flux).
 * CONSTANTS[3] is Km in component v2 (umol_per_g).
 * STATES[1] is O2 in component O2 (umol_per_g).
 * ALGEBRAIC[21] is v3 in component v3 (flux).
 * CONSTANTS[4] is Vmax in component v3 (first_order_rate_constant).
 * ALGEBRAIC[8] is k3 in component v3 (first_order_rate_constant).
 * STATES[2] is FA in component FA (umol_per_g).
 * ALGEBRAIC[5] is PS in component PS (dimensionless).
 * CONSTANTS[5] is PS0 in component PS0 (dimensionless).
 * ALGEBRAIC[22] is v4 in component v4 (flux).
 * CONSTANTS[6] is Vmax in component v4 (first_order_rate_constant).
 * ALGEBRAIC[9] is k4 in component v4 (first_order_rate_constant).
 * CONSTANTS[7] is epsilon in component v4 (dimensionless).
 * ALGEBRAIC[4] is RS in component RS (dimensionless).
 * CONSTANTS[8] is RS0 in component RS0 (dimensionless).
 * ALGEBRAIC[6] is AF in component AF (dimensionless).
 * CONSTANTS[9] is AF0 in component AF0 (dimensionless).
 * ALGEBRAIC[23] is v5 in component v5 (flux).
 * CONSTANTS[10] is Vmax in component v5 (first_order_rate_constant).
 * ALGEBRAIC[10] is k5 in component v5 (first_order_rate_constant).
 * CONSTANTS[11] is epsilon in component v5 (dimensionless).
 * STATES[3] is GP in component GP (umol_per_g).
 * ALGEBRAIC[24] is v6 in component v6 (flux).
 * CONSTANTS[12] is Vmax in component v6 (first_order_rate_constant).
 * ALGEBRAIC[11] is k6 in component v6 (first_order_rate_constant).
 * CONSTANTS[13] is epsilon in component v6 (dimensionless).
 * ALGEBRAIC[3] is CS in component CS (dimensionless).
 * CONSTANTS[14] is CS0 in component CS0 (dimensionless).
 * ALGEBRAIC[25] is v7 in component v7 (flux).
 * CONSTANTS[15] is Vmax in component v7 (first_order_rate_constant).
 * ALGEBRAIC[12] is k7 in component v7 (first_order_rate_constant).
 * CONSTANTS[16] is epsilon in component v7 (dimensionless).
 * STATES[4] is GY in component GY (umol_per_g).
 * ALGEBRAIC[2] is v8 in component v8 (flux).
 * CONSTANTS[17] is Vmax in component v8 (first_order_rate_constant).
 * CONSTANTS[45] is k8 in component v8 (first_order_rate_constant).
 * STATES[5] is TG in component TG (umol_per_g).
 * ALGEBRAIC[26] is v9 in component v9 (flux).
 * CONSTANTS[18] is Vmax in component v9 (first_order_rate_constant).
 * ALGEBRAIC[13] is k9 in component v9 (first_order_rate_constant).
 * STATES[6] is PY in component PY (umol_per_g).
 * ALGEBRAIC[27] is v10 in component v10 (flux).
 * CONSTANTS[19] is Vmax in component v10 (first_order_rate_constant).
 * ALGEBRAIC[14] is k10 in component v10 (first_order_rate_constant).
 * CONSTANTS[20] is epsilon in component v10 (dimensionless).
 * ALGEBRAIC[28] is v11 in component v11 (flux).
 * CONSTANTS[21] is Vmax in component v11 (first_order_rate_constant).
 * ALGEBRAIC[15] is k11 in component v11 (first_order_rate_constant).
 * STATES[7] is LA in component LA (umol_per_g).
 * ALGEBRAIC[29] is v12 in component v12 (flux).
 * CONSTANTS[22] is Vmax in component v12 (first_order_rate_constant).
 * ALGEBRAIC[16] is k12 in component v12 (first_order_rate_constant).
 * CONSTANTS[23] is epsilon in component v12 (dimensionless).
 * STATES[8] is AC in component AC (umol_per_g).
 * ALGEBRAIC[30] is v13 in component v13 (flux).
 * CONSTANTS[24] is Vmax in component v13 (first_order_rate_constant).
 * ALGEBRAIC[17] is k13 in component v13 (first_order_rate_constant).
 * STATES[9] is CR in component CR (umol_per_g).
 * ALGEBRAIC[31] is v14 in component v14 (flux).
 * CONSTANTS[25] is Vmax in component v14 (first_order_rate_constant).
 * ALGEBRAIC[18] is k14 in component v14 (first_order_rate_constant).
 * STATES[10] is PC in component PC (umol_per_g).
 * ALGEBRAIC[32] is v15 in component v15 (flux).
 * CONSTANTS[26] is Vmax in component v15 (first_order_rate_constant).
 * ALGEBRAIC[19] is k15 in component v15 (first_order_rate_constant).
 * CONSTANTS[27] is epsilon in component v15 (dimensionless).
 * STATES[11] is CoA_pool in component CoA_pool (umol_per_g).
 * STATES[12] is FC in component FC (umol_per_g).
 * CONSTANTS[28] is FC0 in component FC0 (umol_per_g).
 * ALGEBRAIC[33] is v16 in component v16 (flux).
 * CONSTANTS[29] is Vmax in component v16 (first_order_rate_constant).
 * ALGEBRAIC[20] is k16 in component v16 (first_order_rate_constant).
 * CONSTANTS[30] is epsilon in component v16 (dimensionless).
 * CONSTANTS[46] is v17 in component v17 (flux).
 * CONSTANTS[31] is Vmax in component v17 (first_order_rate_constant).
 * CONSTANTS[44] is k17 in component v17 (first_order_rate_constant).
 * CONSTANTS[32] is ATP in component ATP (umol_per_g).
 * CONSTANTS[33] is aGL in component GL (umol_per_ml).
 * CONSTANTS[34] is sigmaGL in component GL (g_per_ml).
 * ALGEBRAIC[7] is F in component model_parameters (ml_per_g_min).
 * CONSTANTS[35] is aFA in component FA (umol_per_ml).
 * CONSTANTS[36] is sigmaFA in component FA (g_per_ml).
 * CONSTANTS[37] is aLA in component LA (umol_per_ml).
 * CONSTANTS[38] is sigmaLA in component LA (g_per_ml).
 * CONSTANTS[39] is aO2 in component O2 (umol_per_ml).
 * CONSTANTS[40] is sigmaO2 in component O2 (g_per_ml).
 * STATES[13] is CO2 in component CO2 (umol_per_g).
 * CONSTANTS[41] is aCO2 in component CO2 (umol_per_ml).
 * CONSTANTS[42] is sigmaCO2 in component CO2 (g_per_ml).
 * STATES[14] is NAD in component NAD (umol_per_g).
 * STATES[15] is ADP in component ADP (umol_per_g).
 * CONSTANTS[43] is NADH in component NADH (umol_per_g).
 * RATES[0] is d/dt GL in component GL (umol_per_g).
 * RATES[2] is d/dt FA in component FA (umol_per_g).
 * RATES[3] is d/dt GP in component GP (umol_per_g).
 * RATES[4] is d/dt GY in component GY (umol_per_g).
 * RATES[5] is d/dt TG in component TG (umol_per_g).
 * RATES[6] is d/dt PY in component PY (umol_per_g).
 * RATES[7] is d/dt LA in component LA (umol_per_g).
 * RATES[8] is d/dt AC in component AC (umol_per_g).
 * RATES[12] is d/dt FC in component FC (umol_per_g).
 * RATES[11] is d/dt CoA_pool in component CoA_pool (umol_per_g).
 * RATES[1] is d/dt O2 in component O2 (umol_per_g).
 * RATES[13] is d/dt CO2 in component CO2 (umol_per_g).
 * RATES[14] is d/dt NAD in component NAD (umol_per_g).
 * RATES[15] is d/dt ADP in component ADP (umol_per_g).
 * RATES[10] is d/dt PC in component PC (umol_per_g).
 * RATES[9] is d/dt CR in component CR (umol_per_g).
 * There are a total of 2 condition variables.
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
CONSTANTS[0] = 5.90;
CONSTANTS[1] = 0.05;
STATES[0] = 0.998;
CONSTANTS[2] = 67.6;
CONSTANTS[3] = 0.01;
STATES[1] = 0.963;
CONSTANTS[4] = 4.90;
STATES[2] = 0.021;
CONSTANTS[5] = 0.2;
CONSTANTS[6] = 21.3;
CONSTANTS[7] = 0.6;
CONSTANTS[8] = 0.111;
CONSTANTS[9] = 0.523;
CONSTANTS[10] = 2.82;
CONSTANTS[11] = 0.254;
STATES[3] = 0.171;
CONSTANTS[12] = 3.14;
CONSTANTS[13] = 0.5;
CONSTANTS[14] = 1.0;
CONSTANTS[15] = 0.0162;
CONSTANTS[16] = 0.5;
STATES[4] = 33.0;
CONSTANTS[17] = 0.005;
STATES[5] = 3.96;
CONSTANTS[18] = 1.8;
STATES[6] = 0.20;
CONSTANTS[19] = 12.6;
CONSTANTS[20] = 0.98;
CONSTANTS[21] = 0.96;
STATES[7] = 1.98;
CONSTANTS[22] = 695.7;
CONSTANTS[23] = 0.75;
STATES[8] = 0.0046;
CONSTANTS[24] = 0.455;
STATES[9] = 3.5;
CONSTANTS[25] = 0.455;
STATES[10] = 8.80;
CONSTANTS[26] = 626.1;
CONSTANTS[27] = 0.669;
STATES[11] = 0.043;
STATES[12] = 0.0088;
CONSTANTS[28] = 0.0088;
CONSTANTS[29] = 67.0;
CONSTANTS[30] = 0.775;
CONSTANTS[31] = 7.76;
CONSTANTS[32] = 4.5;
CONSTANTS[33] = 4.0;
CONSTANTS[34] = 3.76;
CONSTANTS[35] = 0.5;
CONSTANTS[36] = 13.2;
CONSTANTS[37] = 1.8;
CONSTANTS[38] = 0.51;
CONSTANTS[39] = 6.53;
CONSTANTS[40] = 1.0;
STATES[13] = 20.0;
CONSTANTS[41] = 15.5;
CONSTANTS[42] = 1.0;
STATES[14] = 1.81;
STATES[15] = 0.90;
CONSTANTS[43] = 0.19;
CONSTANTS[44] = CONSTANTS[31];
CONSTANTS[45] = CONSTANTS[17];
CONSTANTS[46] =  CONSTANTS[44]*CONSTANTS[32];
RATES[0] = 0.1001;
RATES[2] = 0.1001;
RATES[3] = 0.1001;
RATES[4] = 0.1001;
RATES[5] = 0.1001;
RATES[6] = 0.1001;
RATES[7] = 0.1001;
RATES[8] = 0.1001;
RATES[12] = 0.1001;
RATES[11] = 0.1001;
RATES[1] = 0.1001;
RATES[13] = 0.1001;
RATES[14] = 0.1001;
RATES[15] = 0.1001;
RATES[10] = 0.1001;
RATES[9] = 0.1001;
}
void
computeResiduals(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
                 double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
resid[0] = RATES[0] -  ALGEBRAIC[7]*(CONSTANTS[33] -  CONSTANTS[34]*STATES[0]) - ALGEBRAIC[0];
resid[1] = RATES[2] - ( 3.00000*ALGEBRAIC[2]+ ALGEBRAIC[7]*(CONSTANTS[35] -  CONSTANTS[36]*STATES[2])) - (ALGEBRAIC[21]+ALGEBRAIC[22]);
resid[2] = RATES[3] - (ALGEBRAIC[0]+ALGEBRAIC[25]) - (ALGEBRAIC[23]+ALGEBRAIC[24]);
resid[3] = RATES[4] - ALGEBRAIC[24] - ALGEBRAIC[25];
resid[4] = RATES[5] -  (1.00000/3.00000)*ALGEBRAIC[21] - ALGEBRAIC[2];
resid[5] = RATES[6] - ( 2.00000*ALGEBRAIC[23]+ALGEBRAIC[28]) - (ALGEBRAIC[26]+ALGEBRAIC[27]);
resid[6] = RATES[7] - (ALGEBRAIC[26]+ ALGEBRAIC[7]*(CONSTANTS[37] -  CONSTANTS[38]*STATES[7])) - ALGEBRAIC[28];
resid[7] = RATES[8] - (ALGEBRAIC[27]+ALGEBRAIC[22]) - (ALGEBRAIC[29]+ALGEBRAIC[33]);
resid[8] = RATES[12] - (ALGEBRAIC[29]+ALGEBRAIC[32]+ALGEBRAIC[33]) - (ALGEBRAIC[27]+ALGEBRAIC[22]);
resid[9] = RATES[11] - ALGEBRAIC[33] - ALGEBRAIC[32];
resid[10] = RATES[1] -  ALGEBRAIC[7]*(CONSTANTS[39] -  CONSTANTS[40]*STATES[1]) - ALGEBRAIC[1];
resid[11] = RATES[13] - ALGEBRAIC[27]+ 2.00000*ALGEBRAIC[29]+ ALGEBRAIC[7]*(CONSTANTS[41] -  CONSTANTS[42]*STATES[13]);
resid[12] = RATES[14] - (ALGEBRAIC[26]+ 2.00000*ALGEBRAIC[1]) - ( 2.00000*ALGEBRAIC[23]+ALGEBRAIC[27]+ALGEBRAIC[28]+ (11.0000/3.00000)*ALGEBRAIC[29]+ (35.0000/3.00000)*ALGEBRAIC[22]);
resid[13] = RATES[15] - (ALGEBRAIC[0]+ALGEBRAIC[24]+ 2.00000*ALGEBRAIC[22]+ 2.00000*ALGEBRAIC[21]+ALGEBRAIC[30]+CONSTANTS[46]) - ( 3.00000*ALGEBRAIC[23]+ALGEBRAIC[29]+ 6.00000*ALGEBRAIC[1]+ALGEBRAIC[31]);
resid[14] = RATES[10] - ALGEBRAIC[30] - ALGEBRAIC[31];
resid[15] = RATES[9] - ALGEBRAIC[31] - ALGEBRAIC[30];
}
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] =  CONSTANTS[0]*(STATES[0]/(CONSTANTS[1]+STATES[0]));
ALGEBRAIC[1] =  CONSTANTS[2]*(STATES[1]/(CONSTANTS[3]+STATES[1]));
ALGEBRAIC[2] =  CONSTANTS[45]*STATES[5];
ALGEBRAIC[7] = (CONDVAR[0]>0.00000&&CONDVAR[1]<0.00000 ? 1.00000 : 0.400000);
ALGEBRAIC[5] = STATES[15]/CONSTANTS[32];
ALGEBRAIC[8] =  CONSTANTS[4]*(pow(ALGEBRAIC[5], -1.00000)/(pow(CONSTANTS[5], -1.00000)+pow(ALGEBRAIC[5], -1.00000)));
ALGEBRAIC[21] =  ALGEBRAIC[8]*STATES[2];
ALGEBRAIC[4] = CONSTANTS[43]/STATES[14];
ALGEBRAIC[6] = STATES[8]/STATES[12];
ALGEBRAIC[9] =  CONSTANTS[6]*( CONSTANTS[7]*(pow(ALGEBRAIC[6], -1.00000)/(pow(CONSTANTS[9], -1.00000)+pow(ALGEBRAIC[6], -1.00000)))+ (1.00000 - CONSTANTS[7])*(pow(ALGEBRAIC[4], -1.00000)/(pow(CONSTANTS[8], -1.00000)+pow(ALGEBRAIC[4], -1.00000))));
ALGEBRAIC[22] =  ALGEBRAIC[9]*STATES[2];
ALGEBRAIC[10] =  CONSTANTS[10]*( CONSTANTS[11]*(ALGEBRAIC[5]/(CONSTANTS[5]+ALGEBRAIC[5]))+ (1.00000 - CONSTANTS[11])*(pow(ALGEBRAIC[4], -1.00000)/(pow(CONSTANTS[8], -1.00000)+pow(ALGEBRAIC[4], -1.00000))));
ALGEBRAIC[23] =  ALGEBRAIC[10]*STATES[3];
ALGEBRAIC[3] = STATES[9]/STATES[10];
ALGEBRAIC[11] =  CONSTANTS[12]*( CONSTANTS[13]*(pow(ALGEBRAIC[5], -1.00000)/(pow(CONSTANTS[5], -1.00000)+pow(ALGEBRAIC[5], -1.00000)))+ (1.00000 - CONSTANTS[13])*pow(pow(ALGEBRAIC[3], -1.00000)/(pow(CONSTANTS[14], -1.00000)+pow(ALGEBRAIC[3], -1.00000)), 2.00000));
ALGEBRAIC[24] =  ALGEBRAIC[11]*STATES[3];
ALGEBRAIC[12] =  CONSTANTS[15]*( CONSTANTS[16]*(ALGEBRAIC[5]/(CONSTANTS[5]+ALGEBRAIC[5]))+ (1.00000 - CONSTANTS[16])*pow(ALGEBRAIC[3]/(CONSTANTS[14]+ALGEBRAIC[3]), 2.00000));
ALGEBRAIC[25] =  ALGEBRAIC[12]*STATES[4];
ALGEBRAIC[13] =  CONSTANTS[18]*(ALGEBRAIC[4]/(CONSTANTS[8]+ALGEBRAIC[4]));
ALGEBRAIC[26] =  ALGEBRAIC[13]*STATES[6];
ALGEBRAIC[14] =  CONSTANTS[19]*( CONSTANTS[20]*(pow(ALGEBRAIC[4], -1.00000)/(pow(CONSTANTS[8], -1.00000)+pow(ALGEBRAIC[4], -1.00000)))+ (1.00000 - CONSTANTS[20])*(pow(ALGEBRAIC[6], -1.00000)/(pow(CONSTANTS[9], -1.00000)+pow(ALGEBRAIC[6], -1.00000))));
ALGEBRAIC[27] =  ALGEBRAIC[14]*STATES[6];
ALGEBRAIC[15] =  CONSTANTS[21]*(pow(ALGEBRAIC[4], -1.00000)/(pow(CONSTANTS[8], -1.00000)+pow(ALGEBRAIC[4], -1.00000)));
ALGEBRAIC[28] =  ALGEBRAIC[15]*STATES[7];
ALGEBRAIC[16] =  CONSTANTS[22]*( CONSTANTS[23]*(pow(ALGEBRAIC[4], -1.00000)/(pow(CONSTANTS[8], -1.00000)+pow(ALGEBRAIC[4], -1.00000)))+ (1.00000 - CONSTANTS[23])*(ALGEBRAIC[5]/(CONSTANTS[5]+ALGEBRAIC[5])));
ALGEBRAIC[29] =  ALGEBRAIC[16]*STATES[8];
ALGEBRAIC[17] =  CONSTANTS[24]*(pow(ALGEBRAIC[5], -1.00000)/(pow(CONSTANTS[5], -1.00000)+pow(ALGEBRAIC[5], -1.00000)));
ALGEBRAIC[30] =  ALGEBRAIC[17]*STATES[9];
ALGEBRAIC[18] =  CONSTANTS[25]*(ALGEBRAIC[5]/(CONSTANTS[5]+ALGEBRAIC[5]));
ALGEBRAIC[31] =  ALGEBRAIC[18]*STATES[10];
ALGEBRAIC[19] =  CONSTANTS[26]*( CONSTANTS[27]*(pow(ALGEBRAIC[4], -1.00000)/(pow(CONSTANTS[8], -1.00000)+pow(ALGEBRAIC[4], -1.00000)))+ (1.00000 - CONSTANTS[27])*(pow(STATES[12], -1.00000)/(pow(CONSTANTS[28], -1.00000)+pow(STATES[12], -1.00000))));
ALGEBRAIC[32] =  ALGEBRAIC[19]*STATES[11];
ALGEBRAIC[20] =  CONSTANTS[29]*( CONSTANTS[30]*(pow(ALGEBRAIC[4], -1.00000)/(pow(CONSTANTS[8], -1.00000)+pow(ALGEBRAIC[4], -1.00000)))+ (1.00000 - CONSTANTS[30])*(pow(STATES[12], -1.00000)/(pow(CONSTANTS[28], -1.00000)+pow(STATES[12], -1.00000))));
ALGEBRAIC[33] =  ALGEBRAIC[20]*STATES[8];
}
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;
}
void
computeRoots(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
             double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
CONDVAR[0] = VOI - 0.00000;
CONDVAR[1] = VOI - 5.00000;
}