/*
   There are a total of 26 entries in the algebraic variable array.
   There are a total of 8 entries in each of the rate and state variable arrays.
   There are a total of 35 entries in the constant variable array.
 */
/*
 * CONSTANTS[0] is RNA_Device1 in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[1] is TF in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[2] is TFS in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[3] is RNA_Device2 in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[4] is IC in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[5] is PhzS in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[6] is PhzM in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[7] is PYO in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[34] is JRNA in component Template_Promoter_Constitutive (nM_per_s).
 * ALGEBRAIC[18] is JGain in component RNA_Device1_interface (nM_per_s).
 * ALGEBRAIC[0] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[2] is J in component Template_ProteinCDS (nM_per_s).
 * ALGEBRAIC[3] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[4] is J in component Template_RxR2P1Rev (nM_per_s).
 * ALGEBRAIC[19] is JGain in component TF_interface (nM_per_s).
 * CONSTANTS[8] is concentration in component S (nM).
 * ALGEBRAIC[20] is JGain in component TFS_interface (nM_per_s).
 * ALGEBRAIC[5] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[6] is JRNA in component Template_Promoter_Inductive (nM_per_s).
 * ALGEBRAIC[21] is JGain in component RNA_Device2_interface (nM_per_s).
 * ALGEBRAIC[7] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[9] is J in component Template_ProteinCDS (nM_per_s).
 * ALGEBRAIC[22] is JGain in component PhzM_interface (nM_per_s).
 * ALGEBRAIC[12] is J in component Template_RxR1P1 (nM_per_s).
 * CONSTANTS[9] is concentration in component PCA (nM).
 * ALGEBRAIC[13] is J in component Template_RxR1P1MM (nM_per_s).
 * ALGEBRAIC[23] is JGain in component IC_interface (nM_per_s).
 * ALGEBRAIC[14] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[16] is J in component Template_RxR1P1MM (nM_per_s).
 * ALGEBRAIC[11] is J in component Template_ProteinCDS (nM_per_s).
 * ALGEBRAIC[24] is JGain in component PhzS_interface (nM_per_s).
 * ALGEBRAIC[15] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[25] is JGain in component PYO_interface (nM_per_s).
 * ALGEBRAIC[17] is J in component Template_RxR1P1 (nM_per_s).
 * CONSTANTS[10] is cellVolume in component Chassis_EColi (femtoliter).
 * VOI is time in component Time (second).
 * CONSTANTS[11] is k in component ElectrEcoBluDevice1_Promoter (PoPs).
 * STATES[0] is concentration in component Template_Species (nM).
 * CONSTANTS[12] is kDecay in component Bioenvironment_Degradation_ElectrEcoBluDevice1RNA (per_s).
 * ALGEBRAIC[1] is RNARiPs in component Template_RBS (RiPsInAttoMoles).
 * CONSTANTS[13] is k in component ElectrEcoBluDevice1_RBS (RiPs).
 * STATES[1] is concentration in component Template_Species (nM).
 * CONSTANTS[14] is kDecay in component Bioenvironment_Degradation_TF (per_s).
 * CONSTANTS[15] is kf in component Bioenvironment_RxR2P1Rev_TFSFormation (per_nM_per_s).
 * CONSTANTS[16] is kb in component Bioenvironment_RxR2P1Rev_TFSFormation (per_s).
 * STATES[2] is concentration in component Template_Species (nM).
 * CONSTANTS[17] is kDecay in component Bioenvironment_Degradation_TFS (per_s).
 * CONSTANTS[18] is k in component ElectrEcoBluDevice2_Promoter (PoPs).
 * CONSTANTS[19] is Km in component ElectrEcoBluDevice2_Promoter (nM).
 * CONSTANTS[20] is n in component ElectrEcoBluDevice2_Promoter (dimensionless).
 * STATES[3] is concentration in component Template_Species (nM).
 * CONSTANTS[21] is kDecay in component Bioenvironment_Degradation_ElectrEcoBluDevice2RNA (per_s).
 * ALGEBRAIC[8] is RNARiPs in component Template_RBS (RiPsInAttoMoles).
 * CONSTANTS[22] is k in component ElectrEcoBluDevice2_RBS_PhzM (RiPs).
 * ALGEBRAIC[10] is RNARiPs in component Template_RBS (RiPsInAttoMoles).
 * CONSTANTS[23] is k in component ElectrEcoBluDevice2_RBS_PhzS (RiPs).
 * STATES[4] is concentration in component Template_Species (nM).
 * CONSTANTS[24] is kDecay in component Bioenvironment_Degradation_PhzM (per_s).
 * CONSTANTS[25] is k in component Bioenvironment_RxR1P1MM_ICFormation (per_s).
 * CONSTANTS[26] is Km in component Bioenvironment_RxR1P1MM_ICFormation (nM).
 * STATES[5] is concentration in component Template_Species (nM).
 * CONSTANTS[27] is kDecay in component Bioenvironment_Degradation_IC (per_s).
 * STATES[6] is concentration in component Template_Species (nM).
 * CONSTANTS[28] is kDecay in component Bioenvironment_Degradation_PhzS (per_s).
 * CONSTANTS[29] is k in component Bioenvironment_RxR1P1MM_PYOFormation (per_s).
 * CONSTANTS[30] is Km in component Bioenvironment_RxR1P1MM_PYOFormation (nM).
 * STATES[7] is concentration in component Template_Species (nM).
 * CONSTANTS[31] is kDecay in component Bioenvironment_Degradation_PYO (per_s).
 * CONSTANTS[32] is avogadrosConstant in component Template_Promoter_Constitutive (per_mole).
 * CONSTANTS[33] is avogadrosConstant in component Template_Promoter_Inductive (per_mole).
 * RATES[0] is d/dt concentration in component Template_Species (nM).
 * RATES[1] is d/dt concentration in component Template_Species (nM).
 * RATES[2] is d/dt concentration in component Template_Species (nM).
 * RATES[3] is d/dt concentration in component Template_Species (nM).
 * RATES[4] is d/dt concentration in component Template_Species (nM).
 * RATES[5] is d/dt concentration in component Template_Species (nM).
 * RATES[6] is d/dt concentration in component Template_Species (nM).
 * RATES[7] is d/dt concentration in component Template_Species (nM).
 * There are a total of 0 condition variables.
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
CONSTANTS[0] = 0;
CONSTANTS[1] = 8621;
CONSTANTS[2] = 0;
CONSTANTS[3] = 0;
CONSTANTS[4] = 0;
CONSTANTS[5] = 0;
CONSTANTS[6] = 0;
CONSTANTS[7] = 0;
CONSTANTS[8] = 5000;
CONSTANTS[9] = 2;
CONSTANTS[10] = 1;
CONSTANTS[11] = 1.085;
CONSTANTS[12] = 0.05;
CONSTANTS[13] = 1.4;
CONSTANTS[14] = 5.8e-3;
CONSTANTS[15] = 1e3;
CONSTANTS[16] = 4e6;
CONSTANTS[17] = 3.851e-4;
CONSTANTS[18] = 89;
CONSTANTS[19] = 15000;
CONSTANTS[20] = 1;
CONSTANTS[21] = 8e-6;
CONSTANTS[22] = 40;
CONSTANTS[23] = 1;
CONSTANTS[24] = 8e-1;
CONSTANTS[25] = 0.2;
CONSTANTS[26] = 0.1;
CONSTANTS[27] = 5e-5;
CONSTANTS[28] = 8e-1;
CONSTANTS[29] = 1;
CONSTANTS[30] = 0.1;
CONSTANTS[31] = 5e-1;
CONSTANTS[32] = 6.0221415e23;
CONSTANTS[33] = 6.0221415e23;
CONSTANTS[34] =  CONSTANTS[11]*1.00000e+09/( CONSTANTS[10]*1.00000e-15*CONSTANTS[32]);
STATES[0] = CONSTANTS[0];
STATES[1] = CONSTANTS[1];
STATES[2] = CONSTANTS[2];
STATES[3] = CONSTANTS[3];
STATES[4] = CONSTANTS[6];
STATES[5] = CONSTANTS[4];
STATES[6] = CONSTANTS[5];
STATES[7] = CONSTANTS[7];
RATES[0] = 0.1;
RATES[1] = 0.1;
RATES[2] = 0.1;
RATES[3] = 0.1;
RATES[4] = 0.1;
RATES[5] = 0.1;
RATES[6] = 0.1;
RATES[7] = 0.1;
}
void
computeResiduals(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
                 double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
resid[0] = RATES[0] - ALGEBRAIC[18];
resid[1] = RATES[1] - ALGEBRAIC[19];
resid[2] = RATES[2] - ALGEBRAIC[20];
resid[3] = RATES[3] - ALGEBRAIC[21];
resid[4] = RATES[4] - ALGEBRAIC[22];
resid[5] = RATES[5] - ALGEBRAIC[23];
resid[6] = RATES[6] - ALGEBRAIC[24];
resid[7] = RATES[7] - ALGEBRAIC[25];
}
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[12]*STATES[0];
ALGEBRAIC[18] = CONSTANTS[34] - ALGEBRAIC[0];
ALGEBRAIC[1] =  1.00000e+09*CONSTANTS[13]*STATES[0]*CONSTANTS[10]*1.00000e-15;
ALGEBRAIC[2] =  1.00000e+06*ALGEBRAIC[1]/CONSTANTS[10];
ALGEBRAIC[3] =  CONSTANTS[14]*STATES[1];
ALGEBRAIC[4] =  STATES[1]*CONSTANTS[8]*CONSTANTS[15] -  CONSTANTS[16]*STATES[2];
ALGEBRAIC[19] = ALGEBRAIC[2] - ALGEBRAIC[3] - ALGEBRAIC[4];
ALGEBRAIC[5] =  CONSTANTS[17]*STATES[2];
ALGEBRAIC[20] = ALGEBRAIC[4] - ALGEBRAIC[5];
ALGEBRAIC[6] =   CONSTANTS[18]*pow(STATES[2], CONSTANTS[20])/(pow(CONSTANTS[19], CONSTANTS[20])+pow(STATES[2], CONSTANTS[20]))*1.00000e+09/( CONSTANTS[10]*1.00000e-15*CONSTANTS[33]);
ALGEBRAIC[7] =  CONSTANTS[21]*STATES[3];
ALGEBRAIC[21] = ALGEBRAIC[6] - ALGEBRAIC[7];
ALGEBRAIC[8] =  1.00000e+09*CONSTANTS[22]*STATES[3]*CONSTANTS[10]*1.00000e-15;
ALGEBRAIC[9] =  1.00000e+06*ALGEBRAIC[8]/CONSTANTS[10];
ALGEBRAIC[12] =  CONSTANTS[24]*STATES[4];
ALGEBRAIC[22] = ALGEBRAIC[9] - ALGEBRAIC[12];
ALGEBRAIC[13] =  CONSTANTS[25]*STATES[4]*CONSTANTS[9]/(CONSTANTS[9]+CONSTANTS[26]);
ALGEBRAIC[14] =  CONSTANTS[27]*STATES[5];
ALGEBRAIC[16] =  CONSTANTS[29]*STATES[6]*STATES[5]/(STATES[5]+CONSTANTS[30]);
ALGEBRAIC[23] = ALGEBRAIC[13] - ALGEBRAIC[14] - ALGEBRAIC[16];
ALGEBRAIC[10] =  1.00000e+09*CONSTANTS[23]*STATES[3]*CONSTANTS[10]*1.00000e-15;
ALGEBRAIC[11] =  1.00000e+06*ALGEBRAIC[10]/CONSTANTS[10];
ALGEBRAIC[15] =  CONSTANTS[28]*STATES[6];
ALGEBRAIC[24] = ALGEBRAIC[11] - ALGEBRAIC[15];
ALGEBRAIC[17] =  CONSTANTS[31]*STATES[7];
ALGEBRAIC[25] = ALGEBRAIC[16] - ALGEBRAIC[17];
}
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;
}
void
computeRoots(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
             double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
}