/*
   There are a total of 16 entries in the algebraic variable array.
   There are a total of 9 entries in each of the rate and state variable arrays.
   There are a total of 16 entries in the constant variable array.
 */
/*
 * VOI is time in component environment (hour).
 * STATES[0] is A in component A (molecules).
 * ALGEBRAIC[0] is RXN1 in component RXN1 (flux).
 * ALGEBRAIC[1] is RXN2 in component RXN2 (flux).
 * ALGEBRAIC[4] is RXN5 in component RXN5 (flux).
 * ALGEBRAIC[10] is RXN11 in component RXN11 (flux).
 * ALGEBRAIC[5] is RXN6 in component RXN6 (flux).
 * ALGEBRAIC[9] is RXN10 in component RXN10 (flux).
 * ALGEBRAIC[11] is RXN12 in component RXN12 (flux).
 * STATES[1] is C in component C (molecules).
 * ALGEBRAIC[2] is RXN3 in component RXN3 (flux).
 * STATES[2] is DA in component DA (molecules).
 * ALGEBRAIC[6] is RXN7 in component RXN7 (flux).
 * STATES[3] is DAp in component DAp (molecules).
 * ALGEBRAIC[7] is RXN8 in component RXN8 (flux).
 * STATES[4] is DR in component DR (molecules).
 * ALGEBRAIC[12] is RXN13 in component RXN13 (flux).
 * STATES[5] is DRP in component DRP (molecules).
 * ALGEBRAIC[13] is RXN14 in component RXN14 (flux).
 * STATES[6] is MA in component MA (molecules).
 * ALGEBRAIC[8] is RXN9 in component RXN9 (flux).
 * STATES[7] is MR in component MR (molecules).
 * ALGEBRAIC[14] is RXN15 in component RXN15 (flux).
 * ALGEBRAIC[15] is RXN16 in component RXN16 (flux).
 * STATES[8] is R in component R (molecules).
 * ALGEBRAIC[3] is RXN4 in component RXN4 (flux).
 * CONSTANTS[0] is Gamma_1 in component RXN1 (second_order_rate).
 * CONSTANTS[1] is Delta_1 in component RXN2 (first_order_rate).
 * CONSTANTS[2] is Delta_2 in component RXN3 (first_order_rate).
 * CONSTANTS[3] is Delta_3 in component RXN4 (first_order_rate).
 * CONSTANTS[4] is Gamma_2 in component RXN5 (second_order_rate).
 * CONSTANTS[5] is Thetha_1 in component RXN6 (first_order_rate).
 * CONSTANTS[6] is Alpha_1 in component RXN7 (first_order_rate).
 * CONSTANTS[7] is Alpha_2 in component RXN8 (first_order_rate).
 * CONSTANTS[8] is Delta_4 in component RXN9 (first_order_rate).
 * CONSTANTS[9] is BetaA_1 in component RXN10 (first_order_rate).
 * CONSTANTS[10] is Gamma_3 in component RXN11 (second_order_rate).
 * CONSTANTS[11] is Theta_2 in component RXN12 (first_order_rate).
 * CONSTANTS[12] is Alpha_3 in component RXN13 (first_order_rate).
 * CONSTANTS[13] is Alpha_4 in component RXN14 (first_order_rate).
 * CONSTANTS[14] is Delta_5 in component RXN15 (first_order_rate).
 * CONSTANTS[15] is BetaR_1 in component RXN16 (first_order_rate).
 * RATES[0] is d/dt A in component A (molecules).
 * RATES[1] is d/dt C in component C (molecules).
 * RATES[2] is d/dt DA in component DA (molecules).
 * RATES[3] is d/dt DAp in component DAp (molecules).
 * RATES[4] is d/dt DR in component DR (molecules).
 * RATES[5] is d/dt DRP in component DRP (molecules).
 * RATES[6] is d/dt MA in component MA (molecules).
 * RATES[7] is d/dt MR in component MR (molecules).
 * RATES[8] is d/dt R in component R (molecules).
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
STATES[0] = 0.0;
STATES[1] = 0.0;
STATES[2] = 1;
STATES[3] = 0.0;
STATES[4] = 1;
STATES[5] = 1;
STATES[6] = 0.0;
STATES[7] = 0.0;
STATES[8] = 0.0;
CONSTANTS[0] = 2;
CONSTANTS[1] = 1;
CONSTANTS[2] = 1;
CONSTANTS[3] = 0.2;
CONSTANTS[4] = 1;
CONSTANTS[5] = 50;
CONSTANTS[6] = 50;
CONSTANTS[7] = 500;
CONSTANTS[8] = 10;
CONSTANTS[9] = 50;
CONSTANTS[10] = 1;
CONSTANTS[11] = 100;
CONSTANTS[12] = 0.01;
CONSTANTS[13] = 50;
CONSTANTS[14] = 0.5;
CONSTANTS[15] = 5;
}
void
computeRates(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[0] =  STATES[0]*STATES[8]*CONSTANTS[0];
ALGEBRAIC[2] =  STATES[1]*CONSTANTS[2];
RATES[1] =  (1.00000/1.00000)*( - 1.00000*ALGEBRAIC[2]+ALGEBRAIC[0]);
ALGEBRAIC[4] =  STATES[0]*STATES[2]*CONSTANTS[4];
ALGEBRAIC[5] =  STATES[3]*CONSTANTS[5];
ALGEBRAIC[6] =  STATES[2]*CONSTANTS[6];
RATES[2] =  (1.00000/1.00000)*( -1.00000*ALGEBRAIC[4]+ -1.00000*ALGEBRAIC[6]+ALGEBRAIC[5]+ALGEBRAIC[6]);
ALGEBRAIC[7] =  STATES[3]*CONSTANTS[7];
RATES[3] =  (1.00000/1.00000)*( -1.00000*ALGEBRAIC[5]+ -1.00000*ALGEBRAIC[7]+ALGEBRAIC[4]+ALGEBRAIC[7]);
ALGEBRAIC[9] =  STATES[6]*CONSTANTS[9];
ALGEBRAIC[8] =  STATES[6]*CONSTANTS[8];
RATES[6] =  (1.00000/1.00000)*( -1.00000*ALGEBRAIC[8]+ -1.00000*ALGEBRAIC[9]+ALGEBRAIC[6]+ALGEBRAIC[7]+ALGEBRAIC[9]);
ALGEBRAIC[1] =  STATES[0]*CONSTANTS[1];
ALGEBRAIC[10] =  STATES[0]*STATES[4]*CONSTANTS[10];
ALGEBRAIC[11] =  STATES[5]*CONSTANTS[11];
RATES[0] =  (1.00000/1.00000)*( - 1.00000*ALGEBRAIC[0]+ - 1.00000*ALGEBRAIC[1]+ - 1.00000*ALGEBRAIC[4]+ - 1.00000*ALGEBRAIC[10]+ALGEBRAIC[5]+ALGEBRAIC[9]+ALGEBRAIC[11]);
ALGEBRAIC[12] =  STATES[4]*CONSTANTS[12];
RATES[4] =  (1.00000/1.00000)*( -1.00000*ALGEBRAIC[10]+ -1.00000*ALGEBRAIC[12]+ALGEBRAIC[11]+ALGEBRAIC[12]);
ALGEBRAIC[13] =  STATES[5]*CONSTANTS[13];
RATES[5] =  (1.00000/1.00000)*( -1.00000*ALGEBRAIC[11]+ -1.00000*ALGEBRAIC[13]+ALGEBRAIC[10]+ALGEBRAIC[13]);
ALGEBRAIC[14] =  STATES[7]*CONSTANTS[14];
ALGEBRAIC[15] =  STATES[7]*CONSTANTS[15];
RATES[7] =  (1.00000/1.00000)*( -1.00000*ALGEBRAIC[14]+ -1.00000*ALGEBRAIC[15]+ALGEBRAIC[12]+ALGEBRAIC[13]+ALGEBRAIC[15]);
ALGEBRAIC[3] =  STATES[8]*CONSTANTS[3];
RATES[8] =  (1.00000/1.00000)*( -1.00000*ALGEBRAIC[0]+ -1.00000*ALGEBRAIC[3]+ALGEBRAIC[2]+ALGEBRAIC[15]);
}
void
computeVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[0] =  STATES[0]*STATES[8]*CONSTANTS[0];
ALGEBRAIC[2] =  STATES[1]*CONSTANTS[2];
ALGEBRAIC[4] =  STATES[0]*STATES[2]*CONSTANTS[4];
ALGEBRAIC[5] =  STATES[3]*CONSTANTS[5];
ALGEBRAIC[6] =  STATES[2]*CONSTANTS[6];
ALGEBRAIC[7] =  STATES[3]*CONSTANTS[7];
ALGEBRAIC[9] =  STATES[6]*CONSTANTS[9];
ALGEBRAIC[8] =  STATES[6]*CONSTANTS[8];
ALGEBRAIC[1] =  STATES[0]*CONSTANTS[1];
ALGEBRAIC[10] =  STATES[0]*STATES[4]*CONSTANTS[10];
ALGEBRAIC[11] =  STATES[5]*CONSTANTS[11];
ALGEBRAIC[12] =  STATES[4]*CONSTANTS[12];
ALGEBRAIC[13] =  STATES[5]*CONSTANTS[13];
ALGEBRAIC[14] =  STATES[7]*CONSTANTS[14];
ALGEBRAIC[15] =  STATES[7]*CONSTANTS[15];
ALGEBRAIC[3] =  STATES[8]*CONSTANTS[3];
}