/*
   There are a total of 8 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 18 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).
 * CONSTANTS[2] is T_max in component uninfected_CD4 (per_micro_L).
 * CONSTANTS[3] is s_0 in component uninfected_CD4 (per_micro_L_day).
 * CONSTANTS[4] is theta in component uninfected_CD4 (per_micro_L).
 * CONSTANTS[5] is k_1 in component HIV1 (micro_L_per_day).
 * CONSTANTS[6] is k_1_ in component hybrid_HIV1 (micro_L_per_day).
 * STATES[0] is T_1 in component latently_infected_CD4 (per_micro_L).
 * STATES[1] is V in component HIV1 (per_micro_L).
 * STATES[2] is V_ in component hybrid_HIV1 (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).
 * CONSTANTS[9] is mu_b in component actively_infected_CD4 (per_day).
 * STATES[4] is D in component DIV (per_micro_L).
 * STATES[5] 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[6] is T_D2 in component actively_coinfected_CD4 (per_micro_L).
 * CONSTANTS[12] is mu_TD in component stably_coinfected_CD4 (per_day).
 * STATES[7] is T_D1 in component stably_coinfected_CD4 (per_micro_L).
 * CONSTANTS[13] is mu_D in component DIV (per_day).
 * ALGEBRAIC[1] is N_t in component production_function (dimensionless).
 * ALGEBRAIC[3] is N_D_t in component DIV (dimensionless).
 * ALGEBRAIC[6] is pi_D_t in component DIV (per_day).
 * CONSTANTS[14] is mu_V in component HIV1 (per_day).
 * ALGEBRAIC[4] is N_2_t in component HIV1 (dimensionless).
 * ALGEBRAIC[5] is N_t_ in component hybrid_HIV1 (dimensionless).
 * ALGEBRAIC[7] is pi_t_ in component hybrid_HIV1 (per_day).
 * CONSTANTS[15] is N_0 in component production_function (dimensionless).
 * CONSTANTS[16] is gamma in component production_function (dimensionless).
 * CONSTANTS[17] is t_c in component production_function (day).
 * ALGEBRAIC[2] 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[5] is d/dt T_2 in component actively_infected_CD4 (per_micro_L).
 * RATES[6] is d/dt T_D2 in component actively_coinfected_CD4 (per_micro_L).
 * RATES[7] is d/dt T_D1 in component stably_coinfected_CD4 (per_micro_L).
 * RATES[4] is d/dt D 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).
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
CONSTANTS[0] = 0.02;
CONSTANTS[1] = 0.03;
CONSTANTS[2] = 1500;
CONSTANTS[3] = 10;
CONSTANTS[4] = 1;
CONSTANTS[5] = 2.4E-5;
CONSTANTS[6] = 2.4E-6;
STATES[0] = 0;
STATES[1] = 1E-3;
STATES[2] = 0;
STATES[3] = 1000;
CONSTANTS[7] = 0.017;
CONSTANTS[8] = 2.4E-6;
CONSTANTS[9] = 0.24;
STATES[4] = 0;
STATES[5] = 0;
CONSTANTS[10] = 0.24;
CONSTANTS[11] = 0.17;
STATES[6] = 0;
CONSTANTS[12] = 0.02;
STATES[7] = 0;
CONSTANTS[13] = 2.4;
CONSTANTS[14] = 2.4;
CONSTANTS[15] = 300;
CONSTANTS[16] = 25;
CONSTANTS[17] = 7305;
}
void
computeRates(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
RATES[0] = (( CONSTANTS[5]*STATES[1]*STATES[3]+ CONSTANTS[6]*STATES[2]*STATES[3]) -  CONSTANTS[0]*STATES[0]) -  CONSTANTS[7]*STATES[0];
RATES[5] = ( CONSTANTS[7]*STATES[0] -  CONSTANTS[8]*STATES[4]*STATES[5]) -  CONSTANTS[9]*STATES[5];
RATES[6] = ( CONSTANTS[8]*STATES[4]*STATES[5] -  CONSTANTS[10]*STATES[6]) -  CONSTANTS[11]*STATES[6];
RATES[7] =  CONSTANTS[10]*STATES[6] -  CONSTANTS[12]*STATES[7];
ALGEBRAIC[0] = ( CONSTANTS[3]*CONSTANTS[4])/(CONSTANTS[4]+STATES[1]);
RATES[3] = (((ALGEBRAIC[0] -  CONSTANTS[0]*STATES[3])+ CONSTANTS[1]*STATES[3]*(1.00000 - (STATES[3]+STATES[0])/CONSTANTS[2])) -  CONSTANTS[5]*STATES[1]*STATES[3]) -  CONSTANTS[6]*STATES[2]*STATES[3];
ALGEBRAIC[1] =  CONSTANTS[15]*(1.00000+ CONSTANTS[16]*(pow(VOI, 2.00000)/(pow(VOI, 2.00000)+pow(CONSTANTS[17], 2.00000))));
ALGEBRAIC[4] =  0.600000*ALGEBRAIC[1];
RATES[1] = (( ALGEBRAIC[1]*CONSTANTS[9]*STATES[5]+ ALGEBRAIC[4]*CONSTANTS[11]*STATES[6]) -  CONSTANTS[5]*STATES[1]*STATES[3]) -  CONSTANTS[14]*STATES[1];
ALGEBRAIC[3] =  0.200000*ALGEBRAIC[1];
ALGEBRAIC[6] =  0.300000*CONSTANTS[9]*ALGEBRAIC[1];
RATES[4] = ( ALGEBRAIC[3]*CONSTANTS[11]*STATES[6]+ ALGEBRAIC[6]*STATES[7]) -  CONSTANTS[13]*STATES[4];
ALGEBRAIC[5] =  0.200000*ALGEBRAIC[1];
ALGEBRAIC[7] =  0.100000*CONSTANTS[9]*ALGEBRAIC[1];
RATES[2] = (( ALGEBRAIC[5]*CONSTANTS[11]*STATES[6]+ ALGEBRAIC[7]*STATES[7]) -  CONSTANTS[14]*STATES[2]) -  CONSTANTS[6]*STATES[3]*STATES[2];
}
void
computeVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[0] = ( CONSTANTS[3]*CONSTANTS[4])/(CONSTANTS[4]+STATES[1]);
ALGEBRAIC[1] =  CONSTANTS[15]*(1.00000+ CONSTANTS[16]*(pow(VOI, 2.00000)/(pow(VOI, 2.00000)+pow(CONSTANTS[17], 2.00000))));
ALGEBRAIC[4] =  0.600000*ALGEBRAIC[1];
ALGEBRAIC[3] =  0.200000*ALGEBRAIC[1];
ALGEBRAIC[6] =  0.300000*CONSTANTS[9]*ALGEBRAIC[1];
ALGEBRAIC[5] =  0.200000*ALGEBRAIC[1];
ALGEBRAIC[7] =  0.100000*CONSTANTS[9]*ALGEBRAIC[1];
ALGEBRAIC[2] = STATES[3]+STATES[0]+STATES[5];
}