/*
   There are a total of 2 entries in the algebraic variable array.
   There are a total of 7 entries in each of the rate and state variable arrays.
   There are a total of 13 entries in the constant variable array.
 */
/*
 * VOI is time in component environment (day).
 * CONSTANTS[9] is T in component T (per_ml).
 * CONSTANTS[0] is k in component kinetic_parameters (ml_per_day).
 * CONSTANTS[1] is p in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[2] is c in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[3] is delta in component kinetic_parameters (first_order_rate_constant).
 * STATES[0] is I in component I (per_ml).
 * CONSTANTS[10] is I_0 in component I (per_ml).
 * CONSTANTS[11] is k_ in component kinetic_parameters (ml_per_day).
 * STATES[1] is E4 in component E4 (per_ml).
 * CONSTANTS[4] is VI_0 in component VI (per_ml).
 * STATES[2] is VI in component VI (per_ml).
 * ALGEBRAIC[1] is h in component Heavyside_function (dimensionless).
 * STATES[3] is VNI in component VNI (per_ml).
 * ALGEBRAIC[0] is V in component virus_total (per_ml).
 * STATES[4] is E1 in component E1 (per_ml).
 * CONSTANTS[12] is b_ in component kinetic_parameters (day).
 * STATES[5] is E2 in component E2 (per_ml).
 * STATES[6] is E3 in component E3 (per_ml).
 * CONSTANTS[5] is tau_p in component Heavyside_function (day).
 * CONSTANTS[6] is b in component kinetic_parameters (day).
 * CONSTANTS[7] is m in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[8] is n in component kinetic_parameters (dimensionless).
 * RATES[0] is d/dt I in component I (per_ml).
 * RATES[2] is d/dt VI in component VI (per_ml).
 * RATES[3] is d/dt VNI in component VNI (per_ml).
 * RATES[4] is d/dt E1 in component E1 (per_ml).
 * RATES[5] is d/dt E2 in component E2 (per_ml).
 * RATES[6] is d/dt E3 in component E3 (per_ml).
 * RATES[1] is d/dt E4 in component E4 (per_ml).
 * There are a total of 1 condition variables.
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
CONSTANTS[0] = 2.4e-5;
CONSTANTS[1] = 774;
CONSTANTS[2] = 3;
CONSTANTS[3] = 0.5;
STATES[0] = 0.1;
STATES[1] = 0;
CONSTANTS[4] = 200000;
STATES[2] = 200000;
STATES[3] = 0;
STATES[4] = 0;
STATES[5] = 0;
STATES[6] = 0;
CONSTANTS[5] = 0;
CONSTANTS[6] = 0.25;
CONSTANTS[7] = 0.01;
CONSTANTS[8] = 4;
CONSTANTS[9] = ( CONSTANTS[2]*CONSTANTS[3])/( CONSTANTS[0]*CONSTANTS[1]);
CONSTANTS[10] =  (CONSTANTS[2]/CONSTANTS[1])*CONSTANTS[4];
CONSTANTS[11] = CONSTANTS[0]/pow(1.00000+ CONSTANTS[7]*CONSTANTS[6], CONSTANTS[8]);
CONSTANTS[12] = CONSTANTS[6]/(1.00000+ CONSTANTS[7]*CONSTANTS[6]);
RATES[0] = 0.1001;
RATES[2] = 0.1001;
RATES[3] = 0.1001;
RATES[4] = 0.1001;
RATES[5] = 0.1001;
RATES[6] = 0.1001;
RATES[1] = 0.1001;
}
void
computeResiduals(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
                 double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
resid[0] = RATES[0] -  CONSTANTS[11]*CONSTANTS[9]*STATES[1] -  CONSTANTS[3]*STATES[0];
resid[1] = RATES[2] -  (1.00000 - ALGEBRAIC[1])*CONSTANTS[1]*STATES[0] -  CONSTANTS[2]*STATES[2];
resid[2] = RATES[3] -  ALGEBRAIC[1]*CONSTANTS[1]*STATES[0] -  CONSTANTS[2]*STATES[3];
resid[3] = RATES[4] - (STATES[2] - STATES[4])/CONSTANTS[12];
resid[4] = RATES[5] - (STATES[4] - STATES[5])/CONSTANTS[12];
resid[5] = RATES[6] - (STATES[5] - STATES[6])/CONSTANTS[12];
resid[6] = RATES[1] - (STATES[6] - STATES[1])/CONSTANTS[12];
}
void
computeVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[0] = STATES[2]+STATES[3];
}
void
computeEssentialVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[1] = (CONDVAR[0]<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;
SI[5] = 1.0;
SI[6] = 1.0;
}
void
computeRoots(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
             double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
CONDVAR[0] = VOI - CONSTANTS[5];
}