/*
   There are a total of 9 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 35 entries in the constant variable array.
 */
/*
 * VOI is time in component environment (second).
 * STATES[0] is IP3 in component IP3_dynamics (micromolar).
 * ALGEBRAIC[0] is j_IP3 in component IP3_dynamics (micromolar_micrometre_per_second).
 * CONSTANTS[0] is J_IP3 in component IP3_dynamics (micromolar_micrometre_per_second).
 * CONSTANTS[1] is k_0 in component IP3_dynamics (first_order_rate_constant).
 * CONSTANTS[2] is k_degr in component IP3_dynamics (first_order_rate_constant).
 * CONSTANTS[3] is IP3_0 in component IP3_dynamics (micromolar).
 * CONSTANTS[4] is Ca_ER in component ER (micromolar).
 * STATES[1] is Ca in component Calcium_dynamics (micromolar).
 * CONSTANTS[5] is alpha in component Calcium_dynamics (dimensionless).
 * ALGEBRAIC[1] is J_channel in component Channel_kinetics (flux).
 * ALGEBRAIC[7] is J_pump in component SERCA_pump_kinetics (flux).
 * ALGEBRAIC[8] is J_leak in component Leak (flux).
 * CONSTANTS[27] is R_buffering in component Calcium_buffering (flux).
 * CONSTANTS[6] is J_max in component Channel_kinetics (flux).
 * STATES[2] is h in component Channel_kinetics (dimensionless).
 * CONSTANTS[7] is K_act in component Channel_kinetics (micromolar).
 * CONSTANTS[8] is K_IP3 in component Channel_kinetics (micromolar).
 * CONSTANTS[9] is K_inh in component Channel_kinetics (micromolar).
 * CONSTANTS[10] is k_on in component Channel_kinetics (second_order_rate_constant).
 * CONSTANTS[11] is V_max in component SERCA_pump_kinetics (flux).
 * CONSTANTS[12] is K_p in component SERCA_pump_kinetics (micromolar).
 * CONSTANTS[13] is L in component Leak (flux).
 * CONSTANTS[14] is R1 in component Calcium_buffering (flux).
 * CONSTANTS[15] is R2 in component Calcium_buffering (flux).
 * STATES[3] is B1 in component Calcium_buffering (micromolar).
 * STATES[4] is B2 in component Calcium_buffering (micromolar).
 * STATES[5] is CaB1 in component Calcium_buffering (micromolar).
 * STATES[6] is CaB2 in component Calcium_buffering (micromolar).
 * ALGEBRAIC[2] is k1_on in component Calcium_buffering (second_order_rate_constant).
 * ALGEBRAIC[3] is k1_off in component Calcium_buffering (first_order_rate_constant).
 * ALGEBRAIC[4] is k2_on in component Calcium_buffering (second_order_rate_constant).
 * ALGEBRAIC[5] is k2_off in component Calcium_buffering (first_order_rate_constant).
 * CONSTANTS[16] is K1 in component Calcium_buffering (micromolar).
 * CONSTANTS[17] is K2 in component Calcium_buffering (micromolar).
 * CONSTANTS[18] is soma_or_neurite in component Plasma_membrane_extrusion_mechanisms (dimensionless).
 * ALGEBRAIC[6] is j_Ca in component Plasma_membrane_extrusion_mechanisms (micromolar_micrometre_per_second).
 * CONSTANTS[19] is gamma_0 in component Plasma_membrane_extrusion_mechanisms (micrometre_per_second).
 * CONSTANTS[30] is gamma in component Plasma_membrane_extrusion_mechanisms (micrometre_per_second).
 * CONSTANTS[28] is gamma_s in component Plasma_membrane_extrusion_mechanisms (micrometre_per_second).
 * CONSTANTS[29] is gamma_n in component Plasma_membrane_extrusion_mechanisms (micrometre_per_second).
 * CONSTANTS[20] is delta in component Plasma_membrane_extrusion_mechanisms (dimensionless).
 * CONSTANTS[21] is sigma in component Plasma_membrane_extrusion_mechanisms (per_micrometre).
 * CONSTANTS[22] is w_n in component Plasma_membrane_extrusion_mechanisms (dimensionless).
 * CONSTANTS[23] is w_s in component Plasma_membrane_extrusion_mechanisms (dimensionless).
 * CONSTANTS[24] is sigma_soma_2D in component Plasma_membrane_extrusion_mechanisms (per_micrometre).
 * CONSTANTS[25] is sigma_neurite_2D in component Plasma_membrane_extrusion_mechanisms (per_micrometre).
 * CONSTANTS[26] is Ca_c in component Plasma_membrane_extrusion_mechanisms (micromolar).
 * RATES[0] is d/dt IP3 in component IP3_dynamics (micromolar).
 * RATES[1] is d/dt Ca in component Calcium_dynamics (micromolar).
 * RATES[2] is d/dt h in component Channel_kinetics (dimensionless).
 * RATES[3] is d/dt B1 in component Calcium_buffering (micromolar).
 * RATES[5] is d/dt CaB1 in component Calcium_buffering (micromolar).
 * RATES[4] is d/dt B2 in component Calcium_buffering (micromolar).
 * RATES[6] is d/dt CaB2 in component Calcium_buffering (micromolar).
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
STATES[0] = 3.0;
CONSTANTS[0] = 20.86;
CONSTANTS[1] = 1.188;
CONSTANTS[2] = 0.14;
CONSTANTS[3] = 0.16;
CONSTANTS[4] = 400.0;
STATES[1] = 0.05;
CONSTANTS[5] = 0.0;
CONSTANTS[6] = 3500.0;
STATES[2] = 0.8;
CONSTANTS[7] = 0.3;
CONSTANTS[8] = 0.8;
CONSTANTS[9] = 0.2;
CONSTANTS[10] = 2.7;
CONSTANTS[11] = 3.75;
CONSTANTS[12] = 0.27;
CONSTANTS[13] = 0.1;
CONSTANTS[14] = 0.1;
CONSTANTS[15] = 0.1;
STATES[3] = 450.0;
STATES[4] = 75.0;
STATES[5] = 0;
STATES[6] = 0;
CONSTANTS[16] = 10.0;
CONSTANTS[17] = 0.24;
CONSTANTS[18] = -1;
CONSTANTS[19] = 8.0;
CONSTANTS[20] = 1.45;
CONSTANTS[21] = 0.263;
CONSTANTS[22] = 0.377;
CONSTANTS[23] = 0.623;
CONSTANTS[24] = 0.132;
CONSTANTS[25] = 0.479;
CONSTANTS[26] = 0.2;
CONSTANTS[27] = CONSTANTS[14]+CONSTANTS[15];
CONSTANTS[28] = ( CONSTANTS[19]*CONSTANTS[21])/( CONSTANTS[20]*CONSTANTS[25]*CONSTANTS[22]+ CONSTANTS[24]*CONSTANTS[23]);
CONSTANTS[31] = CONSTANTS[14];
CONSTANTS[32] = - CONSTANTS[14];
CONSTANTS[33] = CONSTANTS[15];
CONSTANTS[34] = - CONSTANTS[15];
CONSTANTS[29] = ( CONSTANTS[19]*CONSTANTS[21]*CONSTANTS[20])/( CONSTANTS[20]*CONSTANTS[25]*CONSTANTS[22]+ CONSTANTS[24]*CONSTANTS[23]);
CONSTANTS[30] = (CONSTANTS[18]<=0.00000 ? CONSTANTS[28] : CONSTANTS[29]);
}
void
computeRates(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
RATES[3] = CONSTANTS[31];
RATES[5] = CONSTANTS[32];
RATES[4] = CONSTANTS[33];
RATES[6] = CONSTANTS[34];
RATES[0] = - ( CONSTANTS[2]*(STATES[0] - CONSTANTS[3]));
RATES[2] =  CONSTANTS[10]*(CONSTANTS[9] -  STATES[2]*(STATES[1]+CONSTANTS[9]));
ALGEBRAIC[1] =  CONSTANTS[6]*pow( (STATES[0]/(STATES[0]+CONSTANTS[8]))*(STATES[1]/(STATES[1]+CONSTANTS[7]))*STATES[2], 3.00000)*(1.00000 - STATES[1]/CONSTANTS[4]);
ALGEBRAIC[7] =  CONSTANTS[11]*(pow(STATES[1], 2.00000)/(pow(STATES[1], 2.00000)+pow(CONSTANTS[12], 2.00000)));
ALGEBRAIC[8] =  CONSTANTS[13]*(1.00000 - STATES[1]/CONSTANTS[4]);
RATES[1] =  CONSTANTS[5]*(ALGEBRAIC[1]+- ALGEBRAIC[7]+ALGEBRAIC[8])+CONSTANTS[27];
}
void
computeVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[1] =  CONSTANTS[6]*pow( (STATES[0]/(STATES[0]+CONSTANTS[8]))*(STATES[1]/(STATES[1]+CONSTANTS[7]))*STATES[2], 3.00000)*(1.00000 - STATES[1]/CONSTANTS[4]);
ALGEBRAIC[7] =  CONSTANTS[11]*(pow(STATES[1], 2.00000)/(pow(STATES[1], 2.00000)+pow(CONSTANTS[12], 2.00000)));
ALGEBRAIC[8] =  CONSTANTS[13]*(1.00000 - STATES[1]/CONSTANTS[4]);
ALGEBRAIC[0] =  CONSTANTS[0]*exp( - CONSTANTS[1]*VOI);
rootfind_0(VOI, CONSTANTS, RATES, STATES, ALGEBRAIC, pret);
rootfind_1(VOI, CONSTANTS, RATES, STATES, ALGEBRAIC, pret);
ALGEBRAIC[6] = (STATES[1]>CONSTANTS[26] ?  CONSTANTS[30]*(STATES[1] - CONSTANTS[26]) : 0.00000);
}

void objfunc_0(double *p, double *hx, int m, int n, void *adata)
{
  struct rootfind_info* rfi = (struct rootfind_info*)adata;
#define VOI rfi->aVOI
#define CONSTANTS rfi->aCONSTANTS
#define RATES rfi->aRATES
#define STATES rfi->aSTATES
#define ALGEBRAIC rfi->aALGEBRAIC
#define pret rfi->aPRET
  ALGEBRAIC[2] = p[0];
  ALGEBRAIC[3] = p[1];
  hx[0] = CONSTANTS[14] - (- ( ALGEBRAIC[2]*STATES[1]*STATES[3])+ ALGEBRAIC[3]*STATES[5]);
  hx[1] = CONSTANTS[16] - ALGEBRAIC[3]/ALGEBRAIC[2];
#undef VOI
#undef CONSTANTS
#undef RATES
#undef STATES
#undef ALGEBRAIC
#undef pret
}
void rootfind_0(double VOI, double* CONSTANTS, double* RATES,
double* STATES, double* ALGEBRAIC, int* pret)
{
  static double p[2] = {0.1,0.1};
  double bp[2], work[LM_DIF_WORKSZ(2, 2)];
  struct rootfind_info rfi;
  rfi.aVOI = VOI;
  rfi.aCONSTANTS = CONSTANTS;
  rfi.aRATES = RATES;
  rfi.aSTATES = STATES;
  rfi.aALGEBRAIC = ALGEBRAIC;
  rfi.aPRET = pret;
  do_levmar(objfunc_0, p, bp, work, pret, 2, &rfi);
  ALGEBRAIC[2] = p[0];
  ALGEBRAIC[3] = p[1];
}

void objfunc_1(double *p, double *hx, int m, int n, void *adata)
{
  struct rootfind_info* rfi = (struct rootfind_info*)adata;
#define VOI rfi->aVOI
#define CONSTANTS rfi->aCONSTANTS
#define RATES rfi->aRATES
#define STATES rfi->aSTATES
#define ALGEBRAIC rfi->aALGEBRAIC
#define pret rfi->aPRET
  ALGEBRAIC[4] = p[0];
  ALGEBRAIC[5] = p[1];
  hx[0] = CONSTANTS[15] - (- ( ALGEBRAIC[4]*STATES[1]*STATES[4])+ ALGEBRAIC[5]*STATES[6]);
  hx[1] = CONSTANTS[17] - ALGEBRAIC[5]/ALGEBRAIC[4];
#undef VOI
#undef CONSTANTS
#undef RATES
#undef STATES
#undef ALGEBRAIC
#undef pret
}
void rootfind_1(double VOI, double* CONSTANTS, double* RATES,
double* STATES, double* ALGEBRAIC, int* pret)
{
  static double p[2] = {0.1,0.1};
  double bp[2], work[LM_DIF_WORKSZ(2, 2)];
  struct rootfind_info rfi;
  rfi.aVOI = VOI;
  rfi.aCONSTANTS = CONSTANTS;
  rfi.aRATES = RATES;
  rfi.aSTATES = STATES;
  rfi.aALGEBRAIC = ALGEBRAIC;
  rfi.aPRET = pret;
  do_levmar(objfunc_1, p, bp, work, pret, 2, &rfi);
  ALGEBRAIC[4] = p[0];
  ALGEBRAIC[5] = p[1];
}