/*
   There are a total of 5 entries in the algebraic variable array.
   There are a total of 11 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[2] is J_pump in component SERCA_pump_kinetics (flux).
 * ALGEBRAIC[3] 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).
 * STATES[7] is k1_on in component Calcium_buffering (second_order_rate_constant).
 * STATES[8] is k1_off in component Calcium_buffering (first_order_rate_constant).
 * STATES[9] is k2_on in component Calcium_buffering (second_order_rate_constant).
 * STATES[10] 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[4] 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).
 * There are a total of 1 condition variables.
 */
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]);
STATES[7] = 0.1001;
STATES[8] = 0.1001;
STATES[9] = 0.1001;
STATES[10] = 0.1001;
RATES[0] = 0.1001;
RATES[1] = 0.1001;
RATES[2] = 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[2]*(STATES[0] - CONSTANTS[3]));
resid[1] = RATES[1] -  CONSTANTS[5]*(ALGEBRAIC[1]+- ALGEBRAIC[2]+ALGEBRAIC[3])+CONSTANTS[27];
resid[2] = RATES[2] -  CONSTANTS[10]*(CONSTANTS[9] -  STATES[2]*(STATES[1]+CONSTANTS[9]));
resid[3] = CONSTANTS[14] - - ( STATES[7]*STATES[1]*STATES[3])+ STATES[8]*STATES[5];
resid[4] = CONSTANTS[15] - - ( STATES[9]*STATES[1]*STATES[4])+ STATES[10]*STATES[6];
resid[5] = CONSTANTS[16] - STATES[8]/STATES[7];
resid[6] = CONSTANTS[17] - STATES[10]/STATES[9];
resid[7] = RATES[3] - CONSTANTS[31];
resid[8] = RATES[5] - CONSTANTS[32];
resid[9] = RATES[4] - CONSTANTS[33];
resid[10] = RATES[6] - CONSTANTS[34];
}
void
computeVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[0] =  CONSTANTS[0]*exp( - CONSTANTS[1]*VOI);
ALGEBRAIC[4] = (CONDVAR[0]>0.00000 ?  CONSTANTS[30]*(STATES[1] - CONSTANTS[26]) : 0.00000);
}
void
computeEssentialVariables(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[2] =  CONSTANTS[11]*(pow(STATES[1], 2.00000)/(pow(STATES[1], 2.00000)+pow(CONSTANTS[12], 2.00000)));
ALGEBRAIC[3] =  CONSTANTS[13]*(1.00000 - STATES[1]/CONSTANTS[4]);
}
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] = 0.0;
SI[8] = 0.0;
SI[9] = 0.0;
SI[10] = 0.0;
}
void
computeRoots(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
             double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
CONDVAR[0] = STATES[1] - CONSTANTS[26];
}