/*
   There are a total of 9 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 20 entries in the constant variable array.
 */
/*
 * VOI is time in component environment (day).
 * CONSTANTS[0] is mu_T in component uninfected_CD4 (per_day).
 * CONSTANTS[1] is r in component uninfected_CD4 (per_day).
 * STATES[0] is T_1 in component latently_infected_CD4 (per_micro_L).
 * CONSTANTS[2] is T_max in component uninfected_CD4 (per_micro_L).
 * CONSTANTS[3] is k_1 in component HIV1 (micro_L_per_day).
 * STATES[1] is V in component HIV1 (per_micro_L).
 * CONSTANTS[4] is k_1_ in component hybrid_HIV1 (micro_L_per_day).
 * STATES[2] is V_ in component hybrid_HIV1 (per_micro_L).
 * CONSTANTS[5] is s_0 in component uninfected_CD4 (per_micro_L_day).
 * CONSTANTS[6] is theta in component uninfected_CD4 (per_micro_L).
 * ALGEBRAIC[0] is s_V in component uninfected_CD4 (per_micro_L_day).
 * STATES[3] is T in component uninfected_CD4 (per_micro_L).
 * CONSTANTS[7] is k_2 in component latently_infected_CD4 (per_day).
 * CONSTANTS[8] is k_1D in component actively_infected_CD4 (micro_L_per_day).
 * ALGEBRAIC[1] is D in component DIV (per_micro_L).
 * CONSTANTS[9] is mu_b in component actively_infected_CD4 (per_day).
 * STATES[4] is T_2 in component actively_infected_CD4 (per_micro_L).
 * CONSTANTS[10] is k_s in component actively_coinfected_CD4 (per_day).
 * CONSTANTS[11] is mu_bD in component actively_coinfected_CD4 (per_day).
 * STATES[5] is T_D2 in component actively_coinfected_CD4 (per_micro_L).
 * CONSTANTS[12] is mu_TD in component stably_coinfected_CD4 (per_day).
 * STATES[6] is T_D1 in component stably_coinfected_CD4 (per_micro_L).
 * ALGEBRAIC[4] is N_D_t in component DIV (dimensionless).
 * ALGEBRAIC[5] is pi_D_t in component DIV (per_day).
 * CONSTANTS[13] is mu_D in component DIV (per_day).
 * ALGEBRAIC[2] is N_t in component production_function (dimensionless).
 * CONSTANTS[14] is t_DIV in component DIV (day).
 * STATES[7] is D_ode in component DIV (per_micro_L).
 * CONSTANTS[15] is D_0 in component DIV (per_micro_L).
 * ALGEBRAIC[6] is N_2_t in component HIV1 (dimensionless).
 * CONSTANTS[16] is mu_V in component HIV1 (per_day).
 * ALGEBRAIC[7] is N_t_ in component hybrid_HIV1 (dimensionless).
 * ALGEBRAIC[8] is pi_t_ in component hybrid_HIV1 (per_day).
 * CONSTANTS[17] is N_0 in component production_function (dimensionless).
 * CONSTANTS[18] is gamma in component production_function (dimensionless).
 * CONSTANTS[19] is t_c in component production_function (day).
 * ALGEBRAIC[3] is T_tot in component cell_population (per_micro_L).
 * RATES[3] is d/dt T in component uninfected_CD4 (per_micro_L).
 * RATES[0] is d/dt T_1 in component latently_infected_CD4 (per_micro_L).
 * RATES[4] is d/dt T_2 in component actively_infected_CD4 (per_micro_L).
 * RATES[5] is d/dt T_D2 in component actively_coinfected_CD4 (per_micro_L).
 * RATES[6] is d/dt T_D1 in component stably_coinfected_CD4 (per_micro_L).
 * RATES[7] is d/dt D_ode in component DIV (per_micro_L).
 * RATES[1] is d/dt V in component HIV1 (per_micro_L).
 * RATES[2] is d/dt V_ in component hybrid_HIV1 (per_micro_L).
 * There are a total of 2 condition variables.
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
CONSTANTS[0] = 0.02;
CONSTANTS[1] = 0.03;
STATES[0] = 0;
CONSTANTS[2] = 1500;
CONSTANTS[3] = 2.4E-5;
STATES[1] = 1E-3;
CONSTANTS[4] = 2.4E-7;
STATES[2] = 0;
CONSTANTS[5] = 10;
CONSTANTS[6] = 1;
STATES[3] = 1000;
CONSTANTS[7] = 0.017;
CONSTANTS[8] = 2.4E-5;
CONSTANTS[9] = 0.24;
STATES[4] = 0;
CONSTANTS[10] = 0.48;
CONSTANTS[11] = 0.12;
STATES[5] = 0;
CONSTANTS[12] = 0.02;
STATES[6] = 0;
CONSTANTS[13] = 0.76;
CONSTANTS[14] = 2557;
STATES[7] = 0;
CONSTANTS[15] = 0.1;
CONSTANTS[16] = 2.4;
CONSTANTS[17] = 300;
CONSTANTS[18] = 25;
CONSTANTS[19] = 7305;
RATES[3] = 0.1001;
RATES[0] = 0.1001;
RATES[4] = 0.1001;
RATES[5] = 0.1001;
RATES[6] = 0.1001;
RATES[7] = 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[3] - (((ALGEBRAIC[0] -  CONSTANTS[0]*STATES[3])+ CONSTANTS[1]*STATES[3]*(1.00000 - (STATES[3]+STATES[0])/CONSTANTS[2])) -  CONSTANTS[3]*STATES[1]*STATES[3]) -  CONSTANTS[4]*STATES[2]*STATES[3];
resid[1] = RATES[0] - (( CONSTANTS[3]*STATES[1]*STATES[3]+ CONSTANTS[4]*STATES[2]*STATES[3]) -  CONSTANTS[0]*STATES[0]) -  CONSTANTS[7]*STATES[0];
resid[2] = RATES[4] - ( CONSTANTS[7]*STATES[0] -  CONSTANTS[8]*ALGEBRAIC[1]*STATES[4]) -  CONSTANTS[9]*STATES[4];
resid[3] = RATES[5] - ( CONSTANTS[8]*ALGEBRAIC[1]*STATES[4] -  CONSTANTS[10]*STATES[5]) -  CONSTANTS[11]*STATES[5];
resid[4] = RATES[6] -  CONSTANTS[10]*STATES[5] -  CONSTANTS[12]*STATES[6];
resid[5] = RATES[7] - (CONDVAR[1]<0.00000 ? CONSTANTS[15]/CONSTANTS[14] : ( ALGEBRAIC[4]*CONSTANTS[11]*STATES[5]+ ALGEBRAIC[5]*STATES[6]) -  CONSTANTS[13]*STATES[7]);
resid[6] = RATES[1] - (( ALGEBRAIC[2]*CONSTANTS[9]*STATES[4]+ ALGEBRAIC[6]*CONSTANTS[11]*STATES[5]) -  CONSTANTS[3]*STATES[1]*STATES[3]) -  CONSTANTS[16]*STATES[1];
resid[7] = RATES[2] - (( ALGEBRAIC[7]*CONSTANTS[11]*STATES[5]+ ALGEBRAIC[8]*STATES[6]) -  CONSTANTS[16]*STATES[2]) -  CONSTANTS[4]*STATES[3]*STATES[2];
}
void
computeVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[3] = STATES[3]+STATES[0]+STATES[4]+STATES[5]+STATES[6];
}
void
computeEssentialVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[0] = ( CONSTANTS[5]*CONSTANTS[6])/(CONSTANTS[6]+STATES[1]);
ALGEBRAIC[1] = (CONDVAR[0]<0.00000 ? 0.00000 : STATES[7]);
ALGEBRAIC[2] =  CONSTANTS[17]*(1.00000+ CONSTANTS[18]*(pow(VOI, 2.00000)/(pow(VOI, 2.00000)+pow(CONSTANTS[19], 2.00000))));
ALGEBRAIC[4] =  0.200000*ALGEBRAIC[2];
ALGEBRAIC[5] =  0.500000*CONSTANTS[9]*ALGEBRAIC[2];
ALGEBRAIC[6] =  0.100000*ALGEBRAIC[2];
ALGEBRAIC[7] =  0.100000*ALGEBRAIC[2];
ALGEBRAIC[8] =  0.0100000*CONSTANTS[9]*ALGEBRAIC[2];
}
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)
{
CONDVAR[0] = VOI - CONSTANTS[14];
CONDVAR[1] = VOI - CONSTANTS[14];
}