/*
   There are a total of 1 entries in the algebraic variable array.
   There are a total of 5 entries in each of the rate and state variable arrays.
   There are a total of 15 entries in the constant variable array.
 */
/*
 * VOI is time in component environment (day).
 * CONSTANTS[0] is lambda in component uninfected (per_ml_day).
 * CONSTANTS[1] is d_T in component uninfected (per_day).
 * CONSTANTS[2] is efficacy in component drug_efficacy (dimensionless).
 * CONSTANTS[3] is k in component uninfected (ml_per_day).
 * STATES[0] is V in component viral_load (per_ml).
 * STATES[1] is T in component uninfected (per_ml).
 * CONSTANTS[4] is eta in component latently_infected (dimensionless).
 * CONSTANTS[5] is d_0 in component latently_infected (per_day).
 * ALGEBRAIC[0] is f in component activated (dimensionless).
 * CONSTANTS[6] is a in component latently_infected (per_day).
 * CONSTANTS[7] is rho in component latently_infected (per_day).
 * STATES[2] is L_a in component activated (per_ml).
 * STATES[3] is L_0 in component latently_infected (per_ml).
 * CONSTANTS[8] is p in component activated (per_day).
 * CONSTANTS[9] is a_L in component activated (per_day).
 * CONSTANTS[10] is T_off in component activated (day).
 * CONSTANTS[11] is T_on in component activated (day).
 * CONSTANTS[12] is delta in component productively_infected (per_day).
 * STATES[4] is T_star in component productively_infected (per_ml).
 * CONSTANTS[13] is p_v in component viral_load (per_day).
 * CONSTANTS[14] is c in component viral_load (per_day).
 * RATES[1] is d/dt T in component uninfected (per_ml).
 * RATES[3] is d/dt L_0 in component latently_infected (per_ml).
 * RATES[2] is d/dt L_a in component activated (per_ml).
 * RATES[4] is d/dt T_star in component productively_infected (per_ml).
 * RATES[0] is d/dt V in component viral_load (per_ml).
 * There are a total of 2 condition variables.
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
CONSTANTS[0] = 1E4;
CONSTANTS[1] = 0.01;
CONSTANTS[2] = 0.85;
CONSTANTS[3] = 2.4E-8;
STATES[0] = 50;
STATES[1] = 600000;
CONSTANTS[4] = 0.001;
CONSTANTS[5] = 0.001;
CONSTANTS[6] = 0.03;
CONSTANTS[7] = 0.01;
STATES[2] = 0;
STATES[3] = 2;
CONSTANTS[8] = 1.4;
CONSTANTS[9] = 0.1;
CONSTANTS[10] = 54;
CONSTANTS[11] = 50;
CONSTANTS[12] = 1;
STATES[4] = 0.3;
CONSTANTS[13] = 2000;
CONSTANTS[14] = 23;
RATES[1] = 0.1001;
RATES[3] = 0.1001;
RATES[2] = 0.1001;
RATES[4] = 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]) -  (1.00000 - CONSTANTS[2])*CONSTANTS[3]*STATES[0]*STATES[1];
resid[1] = RATES[3] - (( CONSTANTS[4]*(1.00000 - CONSTANTS[2])*CONSTANTS[3]*STATES[0]*STATES[1] -  CONSTANTS[5]*STATES[3]) -  ALGEBRAIC[0]*CONSTANTS[6]*STATES[3])+ (1.00000 - ALGEBRAIC[0])*CONSTANTS[7]*STATES[2];
resid[2] = RATES[2] - ( ALGEBRAIC[0]*( CONSTANTS[6]*STATES[3]+ CONSTANTS[8]*STATES[2]) -  (1.00000 - ALGEBRAIC[0])*(CONSTANTS[6]+CONSTANTS[7])*STATES[2]) -  CONSTANTS[9]*STATES[2];
resid[3] = RATES[4] - ( (1.00000 - CONSTANTS[4])*(1.00000 - CONSTANTS[2])*CONSTANTS[3]*STATES[0]*STATES[1] -  1.00000*CONSTANTS[12]*STATES[4]*STATES[4])+ CONSTANTS[9]*STATES[2];
resid[4] = RATES[0] -  CONSTANTS[13]*STATES[4] -  CONSTANTS[14]*STATES[0];
}
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 ? 0.00000 : CONDVAR[1]<0.00000 ? 0.00000 : 1.00000);
}
void
getStateInformation(double* SI)
{
SI[0] = 1.0;
SI[1] = 1.0;
SI[2] = 1.0;
SI[3] = 1.0;
SI[4] = 1.0;
}
void
computeRoots(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
             double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
CONDVAR[0] = CONSTANTS[10] - VOI;
CONDVAR[1] = VOI - CONSTANTS[11];
}