/*
   There are a total of 3 entries in the algebraic variable array.
   There are a total of 2 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 (day).
 * CONSTANTS[0] is s in component uninfected (per_day_mm3).
 * CONSTANTS[1] is p in component uninfected (per_day).
 * CONSTANTS[2] is gamma in component uninfected (per_day).
 * CONSTANTS[13] is beta in component uninfected (dimensionless).
 * CONSTANTS[3] is N in component free_virus_particle (dimensionless).
 * CONSTANTS[4] is k_1 in component latently_infected (mm3_per_day).
 * CONSTANTS[5] is k_2 in component actively_infected (per_day).
 * CONSTANTS[6] is k_3 in component latently_infected (per_day).
 * CONSTANTS[7] is mu_V in component free_virus_particle (per_day).
 * STATES[0] is T_1 in component latently_infected (per_mm3).
 * CONSTANTS[8] is mu_b in component actively_infected (per_day).
 * STATES[1] is T in component uninfected (per_mm3).
 * CONSTANTS[9] is k_4 in component latently_infected (per_day).
 * CONSTANTS[10] is T_0 in component latently_infected (per_mm3).
 * CONSTANTS[11] is V_0 in component latently_infected (per_mm3).
 * CONSTANTS[12] is t_min in component latently_infected (day).
 * ALGEBRAIC[0] is T_1_t in component latently_infected (per_mm3).
 * ALGEBRAIC[1] is T_2 in component actively_infected (per_mm3).
 * ALGEBRAIC[2] is V in component free_virus_particle (per_mm3).
 * RATES[1] is d/dt T in component uninfected (per_mm3).
 * RATES[0] is d/dt T_1 in component latently_infected (per_mm3).
 * There are a total of 1 condition variables.
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
CONSTANTS[0] = 10;
CONSTANTS[1] = 0.01;
CONSTANTS[2] = 2E-5;
CONSTANTS[3] = 1000;
CONSTANTS[4] = 2.4E-5;
CONSTANTS[5] = 3E-3;
CONSTANTS[6] = 0.023;
CONSTANTS[7] = 2.4;
STATES[0] = 0;
CONSTANTS[8] = 0.24;
STATES[1] = 1000;
CONSTANTS[9] = 2.424;
CONSTANTS[10] = 1000;
CONSTANTS[11] = 1E-3;
CONSTANTS[12] = 2;
CONSTANTS[13] =  (CONSTANTS[2]/CONSTANTS[6])*(1.00000+CONSTANTS[5]/CONSTANTS[8]);
RATES[1] = 0.1001;
RATES[0] = 0.1001;
}
void
computeResiduals(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
                 double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
resid[0] = RATES[1] - ((CONSTANTS[0]+ CONSTANTS[1]*STATES[1]) -  CONSTANTS[2]*pow(STATES[1], 2.00000)) -  ( CONSTANTS[6]*CONSTANTS[13]+( CONSTANTS[3]*CONSTANTS[4]*CONSTANTS[5])/( CONSTANTS[4]*STATES[1]+CONSTANTS[7]))*STATES[1]*STATES[0];
resid[1] = RATES[0] - (CONDVAR[0]<=0.00000 ? ALGEBRAIC[0] :  (( CONSTANTS[3]*CONSTANTS[4]*CONSTANTS[5])/( CONSTANTS[4]*STATES[1]+CONSTANTS[7]))*STATES[1]*STATES[0] -  CONSTANTS[6]*STATES[0]);
}
void
computeVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[1] = ( CONSTANTS[5]*STATES[0])/CONSTANTS[8];
ALGEBRAIC[2] = ( CONSTANTS[3]*CONSTANTS[5]*STATES[0])/( CONSTANTS[4]*STATES[1]+CONSTANTS[7]);
}
void
computeEssentialVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[0] =  (( CONSTANTS[4]*CONSTANTS[10]*CONSTANTS[11])/(CONSTANTS[9] - CONSTANTS[6]))*(exp( - CONSTANTS[6]*VOI) - exp( - CONSTANTS[9]*VOI));
}
void
getStateInformation(double* SI)
{
SI[0] = 1.0;
SI[1] = 1.0;
}
void
computeRoots(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
             double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
CONDVAR[0] = VOI - CONSTANTS[12];
}