/*
   There are a total of 25 entries in the algebraic variable array.
   There are a total of 7 entries in each of the rate and state variable arrays.
   There are a total of 30 entries in the constant variable array.
 */
/*
 * CONSTANTS[0] is concentration in component Subtilin (nM).
 * CONSTANTS[1] is RNA1 in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[2] is RNA2 in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[3] is spaK in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[4] is spaR in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[5] is spaKactive in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[6] is spaRactive in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[7] is GFP in component SpeciesInitialConcentrations (nM).
 * CONSTANTS[29] is JRNA in component Template_Promoter_Constitutive (nM_per_s).
 * ALGEBRAIC[18] is JGain in component RNA1_interface (nM_per_s).
 * ALGEBRAIC[0] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[4] is J in component Template_ProteinCDS (nM_per_s).
 * ALGEBRAIC[10] is J in component Template_RxR2P1 (nM_per_s).
 * ALGEBRAIC[7] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[5] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[6] is J in component Template_RxR2P1 (nM_per_s).
 * ALGEBRAIC[19] is JGain in component spaK_interface (nM_per_s).
 * ALGEBRAIC[8] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[20] is JGain in component spaKactive_interface (nM_per_s).
 * ALGEBRAIC[2] is J in component Template_ProteinCDS (nM_per_s).
 * ALGEBRAIC[9] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[11] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[21] is JGain in component spaR_interface (nM_per_s).
 * ALGEBRAIC[12] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[22] is JGain in component spaRactive_interface (nM_per_s).
 * ALGEBRAIC[13] is JRNA in component Template_Promoter_Inductive (nM_per_s).
 * ALGEBRAIC[23] is JGain in component RNA2_interface (nM_per_s).
 * ALGEBRAIC[14] is J in component Template_RxR1P1 (nM_per_s).
 * ALGEBRAIC[16] is J in component Template_ProteinCDS (nM_per_s).
 * ALGEBRAIC[24] is JGain in component GFP_interface (nM_per_s).
 * ALGEBRAIC[17] is J in component Template_RxR1P1 (nM_per_s).
 * CONSTANTS[8] is cellVolume in component Chassis_Bacillus (femtoliter).
 * VOI is time in component Time (second).
 * CONSTANTS[9] is k in component Bugbuster_Promoter1 (PoPs).
 * STATES[0] is concentration in component Template_Species (nM).
 * CONSTANTS[10] is kDecay in component Bioenvironment_Degradation_BugbusterRNA1 (per_s).
 * ALGEBRAIC[1] is RNARiPs in component Template_RBS (RiPsInAttoMoles).
 * CONSTANTS[11] is k in component Bugbuster_RBS_spaR (RiPs).
 * ALGEBRAIC[3] is RNARiPs in component Template_RBS (RiPsInAttoMoles).
 * CONSTANTS[12] is k in component Bugbuster_RBS_spaK (RiPs).
 * STATES[1] is concentration in component Template_Species (nM).
 * CONSTANTS[13] is kDecay in component Bioenvironment_Degradation_spaK (per_s).
 * CONSTANTS[14] is k in component Bioenvironment_RxR2P1_spaKActivation (per_nM_per_s).
 * STATES[2] is concentration in component Template_Species (nM).
 * CONSTANTS[15] is k in component Bioenvironment_Dephosphorylation_spaKactive (per_s).
 * CONSTANTS[16] is kDecay in component Bioenvironment_Degradation_spaKactive (per_s).
 * STATES[3] is concentration in component Template_Species (nM).
 * CONSTANTS[17] is kDecay in component Bioenvironment_Degradation_spaR (per_s).
 * CONSTANTS[18] is k in component Bioenvironment_RxR2P1_spaRActivation (per_nM_per_s).
 * STATES[4] is concentration in component Template_Species (nM).
 * CONSTANTS[19] is k in component Bioenvironment_Dephosphorylation_spaRactive (per_s).
 * CONSTANTS[20] is kDecay in component Bioenvironment_Degradation_spaRactive (per_s).
 * CONSTANTS[21] is k in component Bugbuster_Promoter2 (PoPs).
 * CONSTANTS[22] is n in component Bugbuster_Promoter2 (dimensionless).
 * CONSTANTS[23] is Km in component Bugbuster_Promoter2 (nM).
 * STATES[5] is concentration in component Template_Species (nM).
 * CONSTANTS[24] is kDecay in component Bioenvironment_Degradation_BugbusterRNA2 (per_s).
 * ALGEBRAIC[15] is RNARiPs in component Template_RBS (RiPsInAttoMoles).
 * CONSTANTS[25] is k in component Bugbuster_RBS_GFP (RiPs).
 * STATES[6] is concentration in component Template_Species (nM).
 * CONSTANTS[26] is kDecay in component Bioenvironment_Degradation_GFP (per_s).
 * CONSTANTS[27] is avogadrosConstant in component Template_Promoter_Constitutive (per_mole).
 * CONSTANTS[28] 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).
 * There are a total of 0 condition variables.
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
CONSTANTS[0] = 1000;
CONSTANTS[1] = 0;
CONSTANTS[2] = 0;
CONSTANTS[3] = 0;
CONSTANTS[4] = 0;
CONSTANTS[5] = 0;
CONSTANTS[6] = 0;
CONSTANTS[7] = 0;
CONSTANTS[8] = 1;
CONSTANTS[9] = 0.04;
CONSTANTS[10] = 0.0058;
CONSTANTS[11] = 0.1;
CONSTANTS[12] = 0.1818;
CONSTANTS[13] = 0.0012;
CONSTANTS[14] = 1e-4;
CONSTANTS[15] = 0.1;
CONSTANTS[16] = 0.0012;
CONSTANTS[17] = 0.0012;
CONSTANTS[18] = 1e-4;
CONSTANTS[19] = 0.1;
CONSTANTS[20] = 0.0012;
CONSTANTS[21] = 0.04;
CONSTANTS[22] = 2;
CONSTANTS[23] = 320;
CONSTANTS[24] = 0.0058;
CONSTANTS[25] = 0.145;
CONSTANTS[26] = 0.0012;
CONSTANTS[27] = 6.0221415e23;
CONSTANTS[28] = 6.0221415e23;
CONSTANTS[29] =  CONSTANTS[9]*1.00000e+09/( CONSTANTS[8]*1.00000e-15*CONSTANTS[27]);
STATES[0] = CONSTANTS[1];
STATES[1] = CONSTANTS[3];
STATES[2] = CONSTANTS[5];
STATES[3] = CONSTANTS[4];
STATES[4] = CONSTANTS[6];
STATES[5] = CONSTANTS[2];
STATES[6] = 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;
}
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];
}
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[10]*STATES[0];
ALGEBRAIC[18] = CONSTANTS[29] - ALGEBRAIC[0];
ALGEBRAIC[3] =  1.00000e+09*CONSTANTS[12]*STATES[0]*CONSTANTS[8]*1.00000e-15;
ALGEBRAIC[4] =  1.00000e+06*ALGEBRAIC[3]/CONSTANTS[8];
ALGEBRAIC[10] =  STATES[2]*STATES[3]*CONSTANTS[18];
ALGEBRAIC[7] =  CONSTANTS[15]*STATES[2];
ALGEBRAIC[5] =  CONSTANTS[13]*STATES[1];
ALGEBRAIC[6] =  CONSTANTS[0]*STATES[1]*CONSTANTS[14];
ALGEBRAIC[19] = ALGEBRAIC[4]+ALGEBRAIC[10]+ALGEBRAIC[7] - (ALGEBRAIC[6]+ALGEBRAIC[5]);
ALGEBRAIC[8] =  CONSTANTS[16]*STATES[2];
ALGEBRAIC[20] = ALGEBRAIC[6] - ALGEBRAIC[8]+ALGEBRAIC[7]+ALGEBRAIC[10];
ALGEBRAIC[1] =  1.00000e+09*CONSTANTS[11]*STATES[0]*CONSTANTS[8]*1.00000e-15;
ALGEBRAIC[2] =  1.00000e+06*ALGEBRAIC[1]/CONSTANTS[8];
ALGEBRAIC[9] =  CONSTANTS[17]*STATES[3];
ALGEBRAIC[11] =  CONSTANTS[19]*STATES[4];
ALGEBRAIC[21] = ALGEBRAIC[2]+ALGEBRAIC[11] - (ALGEBRAIC[9]+ALGEBRAIC[10]);
ALGEBRAIC[12] =  CONSTANTS[20]*STATES[4];
ALGEBRAIC[22] = ALGEBRAIC[10] - ALGEBRAIC[12]+ALGEBRAIC[11];
ALGEBRAIC[13] =   CONSTANTS[21]*pow(STATES[4], CONSTANTS[22])/(pow(CONSTANTS[23], CONSTANTS[22])+pow(STATES[4], CONSTANTS[22]))*1.00000e+09/( CONSTANTS[8]*1.00000e-15*CONSTANTS[28]);
ALGEBRAIC[14] =  CONSTANTS[24]*STATES[5];
ALGEBRAIC[23] = ALGEBRAIC[13] - ALGEBRAIC[14];
ALGEBRAIC[15] =  1.00000e+09*CONSTANTS[25]*STATES[5]*CONSTANTS[8]*1.00000e-15;
ALGEBRAIC[16] =  1.00000e+06*ALGEBRAIC[15]/CONSTANTS[8];
ALGEBRAIC[17] =  CONSTANTS[26]*STATES[6];
ALGEBRAIC[24] = 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;
}
void
computeRoots(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
             double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
}