/*
   There are a total of 4 entries in the algebraic variable array.
   There are a total of 10 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).
 * STATES[0] is S in component S (dimensionless).
 * CONSTANTS[0] is r in component S (first_order_rate_constant).
 * CONSTANTS[1] is epsilon in component S (dimensionless).
 * ALGEBRAIC[0] is H in component S (dimensionless).
 * CONSTANTS[2] is d in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[3] is g in component memory_duration (first_order_rate_constant).
 * CONSTANTS[4] is beta_1 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[5] is beta_2 in component kinetic_parameters (first_order_rate_constant).
 * STATES[1] is R_1 in component R1 (dimensionless).
 * STATES[2] is R_2 in component R2 (dimensionless).
 * STATES[3] is R_12 in component R12 (dimensionless).
 * STATES[4] is P_1 in component P1 (dimensionless).
 * STATES[5] is P_2 in component P2 (dimensionless).
 * STATES[6] is I_1 in component I1 (dimensionless).
 * STATES[7] is I_2 in component I2 (dimensionless).
 * STATES[8] is I_12 in component I12 (dimensionless).
 * STATES[9] is I_21 in component I21 (dimensionless).
 * ALGEBRAIC[1] is P in component S (dimensionless).
 * CONSTANTS[6] is a_1 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[7] is alpha_1 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[8] is a_2 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[9] is alpha_2 in component kinetic_parameters (first_order_rate_constant).
 * CONSTANTS[10] is k_1 in component P1 (first_order_rate_constant).
 * CONSTANTS[11] is u in component kinetic_parameters (first_order_rate_constant).
 * ALGEBRAIC[2] is log_P1 in component P1 (dimensionless).
 * CONSTANTS[12] is k_2 in component P2 (first_order_rate_constant).
 * ALGEBRAIC[3] is log_P2 in component P2 (dimensionless).
 * CONSTANTS[13] is G in component memory_duration (dimensionless).
 * RATES[0] is d/dt S in component S (dimensionless).
 * RATES[6] is d/dt I_1 in component I1 (dimensionless).
 * RATES[7] is d/dt I_2 in component I2 (dimensionless).
 * RATES[8] is d/dt I_12 in component I12 (dimensionless).
 * RATES[9] is d/dt I_21 in component I21 (dimensionless).
 * RATES[1] is d/dt R_1 in component R1 (dimensionless).
 * RATES[2] is d/dt R_2 in component R2 (dimensionless).
 * RATES[3] is d/dt R_12 in component R12 (dimensionless).
 * RATES[4] is d/dt P_1 in component P1 (dimensionless).
 * RATES[5] is d/dt P_2 in component P2 (dimensionless).
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
STATES[0] = 100;
CONSTANTS[0] = 0.5;
CONSTANTS[1] = 0.1;
CONSTANTS[2] = 0.01;
CONSTANTS[3] = 0.01;
CONSTANTS[4] = 1;
CONSTANTS[5] = 1;
STATES[1] = 0;
STATES[2] = 0;
STATES[3] = 0;
STATES[4] = 1;
STATES[5] = 1;
STATES[6] = 0;
STATES[7] = 0;
STATES[8] = 0;
STATES[9] = 0;
CONSTANTS[6] = 0.03;
CONSTANTS[7] = 0.1;
CONSTANTS[8] = 1;
CONSTANTS[9] = 0.1;
CONSTANTS[10] = 1;
CONSTANTS[11] = 0.5;
CONSTANTS[12] = 1;
CONSTANTS[13] = 1.00000/CONSTANTS[3];
}
void
computeRates(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
RATES[6] = ( CONSTANTS[4]*STATES[0]*STATES[4] -  CONSTANTS[6]*STATES[6]) -  CONSTANTS[7]*STATES[6];
RATES[7] = ( CONSTANTS[5]*STATES[0]*STATES[5] -  CONSTANTS[8]*STATES[7]) -  CONSTANTS[9]*STATES[7];
RATES[8] = ( CONSTANTS[5]*STATES[1]*STATES[5] -  CONSTANTS[8]*STATES[8]) -  CONSTANTS[9]*STATES[8];
RATES[9] = ( CONSTANTS[4]*STATES[2]*STATES[4] -  CONSTANTS[6]*STATES[9]) -  CONSTANTS[7]*STATES[9];
RATES[1] = (( CONSTANTS[7]*STATES[6] -  CONSTANTS[2]*STATES[1]) -  CONSTANTS[3]*STATES[1]) -  CONSTANTS[5]*STATES[1]*STATES[5];
RATES[2] = (( CONSTANTS[9]*STATES[7] -  CONSTANTS[2]*STATES[2]) -  CONSTANTS[3]*STATES[2]) -  CONSTANTS[4]*STATES[2]*STATES[4];
RATES[3] = (( CONSTANTS[9]*STATES[8]+ CONSTANTS[7]*STATES[9]) -  CONSTANTS[2]*STATES[3]) -  CONSTANTS[3]*STATES[3];
RATES[4] =  CONSTANTS[10]*(STATES[6]+STATES[9]) -  CONSTANTS[11]*STATES[4];
RATES[5] =  CONSTANTS[12]*(STATES[7]+STATES[8]) -  CONSTANTS[11]*STATES[5];
ALGEBRAIC[0] = STATES[0]+STATES[6]+STATES[1]+STATES[7]+STATES[2]+STATES[8]+STATES[9]+STATES[3];
RATES[0] = (((( CONSTANTS[0]*ALGEBRAIC[0])/( CONSTANTS[1]*ALGEBRAIC[0]+1.00000) -  CONSTANTS[2]*STATES[0]) -  CONSTANTS[4]*STATES[0]*STATES[4]) -  CONSTANTS[5]*STATES[0]*STATES[5])+ CONSTANTS[3]*(STATES[1]+STATES[2]+STATES[3]);
}
void
computeVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[0] = STATES[0]+STATES[6]+STATES[1]+STATES[7]+STATES[2]+STATES[8]+STATES[9]+STATES[3];
ALGEBRAIC[1] = STATES[4]+STATES[5];
ALGEBRAIC[2] = arbitrary_log(STATES[4], 10);
ALGEBRAIC[3] = arbitrary_log(STATES[5], 10);
}