/*
   There are a total of 3 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 12 entries in the constant variable array.
 */
/*
 * VOI is time in component environment (day).
 * CONSTANTS[0] is s in component uninfected (per_day_mm3).
 * CONSTANTS[1] is r in component uninfected (per_day).
 * CONSTANTS[2] is T_max in component uninfected (per_mm3).
 * CONSTANTS[3] is mu_T in component uninfected (per_day).
 * CONSTANTS[4] is theta in component uninfected (per_mm3).
 * CONSTANTS[5] is k_1 in component latently_infected (mm3_per_day).
 * STATES[0] is T_1 in component latently_infected (per_mm3).
 * STATES[1] is T_2 in component actively_infected (per_mm3).
 * STATES[2] is V in component free_virus_particle (per_mm3).
 * ALGEBRAIC[0] is s_V in component uninfected (per_day_mm3).
 * STATES[3] is T in component uninfected (per_mm3).
 * CONSTANTS[6] is k_2 in component actively_infected (per_day).
 * CONSTANTS[7] is mu_b in component actively_infected (per_day).
 * CONSTANTS[8] is mu_V in component free_virus_particle (per_day).
 * ALGEBRAIC[2] is N in component AZT (dimensionless).
 * ALGEBRAIC[1] is T_tot in component T_cell_population (per_mm3).
 * CONSTANTS[9] is tau in component AZT (day).
 * CONSTANTS[10] is N_initial in component AZT (dimensionless).
 * CONSTANTS[11] is N_AZT in component AZT (dimensionless).
 * RATES[3] is d/dt T in component uninfected (per_mm3).
 * RATES[0] is d/dt T_1 in component latently_infected (per_mm3).
 * RATES[1] is d/dt T_2 in component actively_infected (per_mm3).
 * RATES[2] is d/dt V in component free_virus_particle (per_mm3).
 * There are a total of 2 condition variables.
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
CONSTANTS[0] = 10;
CONSTANTS[1] = 0.03;
CONSTANTS[2] = 1500;
CONSTANTS[3] = 0.02;
CONSTANTS[4] = 1;
CONSTANTS[5] = 2.4E-5;
STATES[0] = 0;
STATES[1] = 0;
STATES[2] = 1.0E-3;
STATES[3] = 1000;
CONSTANTS[6] = 3E-3;
CONSTANTS[7] = 0.24;
CONSTANTS[8] = 2.4;
CONSTANTS[9] = 1096;
CONSTANTS[10] = 1400;
CONSTANTS[11] = 1050;
RATES[3] = 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[3] - ((ALGEBRAIC[0] -  CONSTANTS[3]*STATES[3])+ CONSTANTS[1]*STATES[3]*(1.00000 - (STATES[3]+STATES[0]+STATES[1])/CONSTANTS[2])) -  CONSTANTS[5]*STATES[2]*STATES[3];
resid[1] = RATES[0] - ( CONSTANTS[5]*STATES[2]*STATES[3] -  CONSTANTS[3]*STATES[0]) -  CONSTANTS[6]*STATES[0];
resid[2] = RATES[1] -  CONSTANTS[6]*STATES[0] -  CONSTANTS[7]*STATES[1];
resid[3] = RATES[2] - ( ALGEBRAIC[2]*CONSTANTS[7]*STATES[1] -  CONSTANTS[5]*STATES[2]*STATES[3]) -  CONSTANTS[8]*STATES[2];
}
void
computeVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[1] = STATES[3]+STATES[0]+STATES[1];
}
void
computeEssentialVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[0] = ( CONSTANTS[4]*CONSTANTS[0])/(CONSTANTS[4]+STATES[2]);
ALGEBRAIC[2] = (CONDVAR[0]<0.00000 ? CONSTANTS[10] : CONDVAR[1]>=0.00000 ? CONSTANTS[11] : 0.0/0.0);
}
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 - CONSTANTS[9];
CONDVAR[1] = VOI - CONSTANTS[9];
}