/*
   There are a total of 4 entries in the algebraic variable array.
   There are a total of 4 entries in each of the rate and state variable arrays.
   There are a total of 14 entries in the constant variable array.
 */
/*
 * VOI is time in component environment (minute).
 * STATES[0] is r in component r (nanomolar).
 * ALGEBRAIC[0] is Ir in component r (flux).
 * CONSTANTS[0] is k6 in component r (first_order_rate_constant).
 * STATES[1] is s in component s (nanomolar).
 * ALGEBRAIC[3] is Is in component model_parameters (flux).
 * CONSTANTS[1] is k7 in component model_parameters (first_order_rate_constant).
 * STATES[2] is f in component f (dimensionless).
 * CONSTANTS[2] is k1 in component f (second_order_rate_constant).
 * CONSTANTS[3] is k2 in component f (first_order_rate_constant).
 * CONSTANTS[4] is k3 in component f (first_order_rate_constant).
 * ALGEBRAIC[1] is phi_b_s in component f (dimensionless).
 * CONSTANTS[5] is sb in component f (dimensionless).
 * CONSTANTS[6] is delta_b in component f (dimensionless).
 * CONSTANTS[7] is c in component model_parameters (nanomolar).
 * STATES[3] is h in component h (nanomolar).
 * CONSTANTS[8] is k4 in component h (first_order_rate_constant).
 * CONSTANTS[9] is k5 in component h (first_order_rate_constant).
 * ALGEBRAIC[2] is phi_r_s in component h (dimensionless).
 * CONSTANTS[10] is sr in component h (dimensionless).
 * CONSTANTS[11] is delta_r in component h (dimensionless).
 * CONSTANTS[12] is k8 in component model_parameters (first_order_rate_constant).
 * CONSTANTS[13] is j1 in component model_parameters (dimensionless).
 * RATES[0] is d/dt r in component r (nanomolar).
 * RATES[1] is d/dt s in component s (nanomolar).
 * RATES[2] is d/dt f in component f (dimensionless).
 * RATES[3] is d/dt h in component h (nanomolar).
 * There are a total of 40 condition variables.
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
STATES[0] = 0.0;
CONSTANTS[0] = 5.0;
STATES[1] = 0.0;
CONSTANTS[1] = 5.0;
STATES[2] = 0.3;
CONSTANTS[2] = 0.1;
CONSTANTS[3] = 0.002;
CONSTANTS[4] = 0.018;
CONSTANTS[5] = 0.029;
CONSTANTS[6] = 0.3;
CONSTANTS[7] = 0.01;
STATES[3] = 0.0;
CONSTANTS[8] = 9.0;
CONSTANTS[9] = 71.0;
CONSTANTS[10] = -0.56;
CONSTANTS[11] = 0.3;
CONSTANTS[12] = 0.07;
CONSTANTS[13] = 10;
RATES[0] = 0.1001;
RATES[1] = 0.1001;
RATES[2] = 0.1001;
RATES[3] = 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[0] -  CONSTANTS[0]*STATES[0];
resid[1] = RATES[1] - ALGEBRAIC[3] -  CONSTANTS[1]*STATES[1];
resid[2] = RATES[2] - - ( CONSTANTS[2]*(STATES[0]+CONSTANTS[7])*STATES[2])+ (CONSTANTS[3]+ CONSTANTS[4]*ALGEBRAIC[1])*(1.00000 - STATES[2]);
resid[3] = RATES[3] -  CONSTANTS[13]*( (CONSTANTS[8]+ CONSTANTS[9]*(1.00000 - ALGEBRAIC[2]))*( (STATES[0]+CONSTANTS[7])*STATES[2]) -  CONSTANTS[12]*STATES[3]);
}
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] = (CONDVAR[0]>=0.00000&&CONDVAR[1]<=0.00000 ? 0.00000 : CONDVAR[2]>=0.00000&&CONDVAR[3]<=0.00000 ? 10.0000 : CONDVAR[4]>=0.00000&&CONDVAR[5]<=0.00000 ? 0.00000 : CONDVAR[6]>=0.00000&&CONDVAR[7]<=0.00000 ? 10.0000 : CONDVAR[8]>=0.00000&&CONDVAR[9]<=0.00000 ? 0.00000 : CONDVAR[10]>=0.00000&&CONDVAR[11]<=0.00000 ? 10.0000 : CONDVAR[12]>=0.00000&&CONDVAR[13]<=0.00000 ? 0.00000 : CONDVAR[14]>=0.00000&&CONDVAR[15]<=0.00000 ? 10.0000 : CONDVAR[16]>=0.00000&&CONDVAR[17]<=0.00000 ? 0.00000 : CONDVAR[18]>=0.00000&&CONDVAR[19]<=0.00000 ? 10.0000 : CONDVAR[20]>=0.00000&&CONDVAR[21]<=0.00000 ? 0.00000 : CONDVAR[22]>=0.00000&&CONDVAR[23]<=0.00000 ? 10.0000 : CONDVAR[24]>=0.00000&&CONDVAR[25]<=0.00000 ? 0.00000 : CONDVAR[26]>=0.00000&&CONDVAR[27]<=0.00000 ? 10.0000 : CONDVAR[28]>=0.00000&&CONDVAR[29]<=0.00000 ? 0.00000 : CONDVAR[30]>=0.00000&&CONDVAR[31]<=0.00000 ? 10.0000 : 0.00000);
ALGEBRAIC[1] = 1.00000/(1.00000+exp(- (arbitrary_log( 1.00000*STATES[1], 10) - CONSTANTS[5])/CONSTANTS[6]));
ALGEBRAIC[2] = 1.00000/(1.00000+exp(- (arbitrary_log( 1.00000*STATES[1], 10) - CONSTANTS[10])/CONSTANTS[11]));
ALGEBRAIC[3] = (CONDVAR[32]>0.00000&&CONDVAR[33]<=0.00000 ? 10.0000 : CONDVAR[34]>0.00000&&CONDVAR[35]<=0.00000 ? 0.00000 : CONDVAR[36]>0.00000&&CONDVAR[37]<=0.00000 ? 10.0000 : CONDVAR[38]>0.00000&&CONDVAR[39]<=0.00000 ? 0.00000 : 0.00000);
}
void
getStateInformation(double* SI)
{
SI[0] = 1.0;
SI[1] = 1.0;
SI[2] = 1.0;
SI[3] = 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 - 90.0000;
CONDVAR[2] = VOI - 91.0000;
CONDVAR[3] = VOI - 92.0000;
CONDVAR[4] = VOI - 93.0000;
CONDVAR[5] = VOI - 113.000;
CONDVAR[6] = VOI - 114.000;
CONDVAR[7] = VOI - 115.000;
CONDVAR[8] = VOI - 116.000;
CONDVAR[9] = VOI - 136.000;
CONDVAR[10] = VOI - 137.000;
CONDVAR[11] = VOI - 138.000;
CONDVAR[12] = VOI - 139.000;
CONDVAR[13] = VOI - 159.000;
CONDVAR[14] = VOI - 160.000;
CONDVAR[15] = VOI - 161.000;
CONDVAR[16] = VOI - 162.000;
CONDVAR[17] = VOI - 252.000;
CONDVAR[18] = VOI - 253.000;
CONDVAR[19] = VOI - 254.000;
CONDVAR[20] = VOI - 255.000;
CONDVAR[21] = VOI - 275.000;
CONDVAR[22] = VOI - 276.000;
CONDVAR[23] = VOI - 277.000;
CONDVAR[24] = VOI - 278.000;
CONDVAR[25] = VOI - 298.000;
CONDVAR[26] = VOI - 299.000;
CONDVAR[27] = VOI - 300.000;
CONDVAR[28] = VOI - 301.000;
CONDVAR[29] = VOI - 321.000;
CONDVAR[30] = VOI - 322.000;
CONDVAR[31] = VOI - 323.000;
CONDVAR[32] = VOI - 0.00000;
CONDVAR[33] = VOI - 90.0000;
CONDVAR[34] = VOI - 90.0000;
CONDVAR[35] = VOI - 180.000;
CONDVAR[36] = VOI - 180.000;
CONDVAR[37] = VOI - 270.000;
CONDVAR[38] = VOI - 270.000;
CONDVAR[39] = VOI - 360.000;
}