/*
   There are a total of 13 entries in the algebraic variable array.
   There are a total of 6 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 (second).
 * STATES[0] is D in component equations (dimensionless).
 * STATES[1] is A_1 in component equations (dimensionless).
 * STATES[2] is A_2 in component equations (dimensionless).
 * ALGEBRAIC[0] is R_off in component equations (dimensionless).
 * CONSTANTS[0] is x_0 in component equations (dimensionless).
 * STATES[3] is x_1 in component equations (dimensionless).
 * STATES[4] is x_2 in component equations (dimensionless).
 * ALGEBRAIC[9] is g in component equations (per_second).
 * ALGEBRAIC[6] is f in component equations (per_second).
 * ALGEBRAIC[10] is h in component equations (per_second).
 * ALGEBRAIC[1] is lambda_A1 in component equations (dimensionless).
 * ALGEBRAIC[2] is lambda_A2 in component equations (dimensionless).
 * ALGEBRAIC[8] is F_t in component equations (dimensionless).
 * ALGEBRAIC[3] is E_1 in component equations (dimensionless).
 * ALGEBRAIC[4] is E_2 in component equations (dimensionless).
 * ALGEBRAIC[7] is dSL_dt in component equations (per_second).
 * STATES[5] is SL in component equations (dimensionless).
 * CONSTANTS[1] is k_on in component equations (per_second).
 * CONSTANTS[2] is k_off in component equations (per_second).
 * CONSTANTS[3] is f_r in component equations (per_second).
 * ALGEBRAIC[11] is f_prime in component equations (per_second).
 * CONSTANTS[4] is f_prime_0 in component equations (per_second).
 * CONSTANTS[5] is h_0 in component equations (per_second).
 * ALGEBRAIC[12] is h_prime in component equations (per_second).
 * CONSTANTS[6] is h_prime_0 in component equations (per_second).
 * CONSTANTS[7] is g_0 in component equations (per_second).
 * CONSTANTS[8] is nu in component equations (dimensionless).
 * ALGEBRAIC[5] is sigma in component equations (dimensionless).
 * CONSTANTS[9] is sigma_minus in component equations (dimensionless).
 * CONSTANTS[10] is sigma_plus in component equations (dimensionless).
 * CONSTANTS[11] is R_T in component equations (dimensionless).
 * CONSTANTS[12] is e_cb in component equations (dimensionless).
 * RATES[0] is d/dt D in component equations (dimensionless).
 * RATES[1] is d/dt A_1 in component equations (dimensionless).
 * RATES[2] is d/dt A_2 in component equations (dimensionless).
 * RATES[4] is d/dt x_2 in component equations (dimensionless).
 * RATES[3] is d/dt x_1 in component equations (dimensionless).
 * RATES[5] is d/dt SL in component equations (dimensionless).
 * There are a total of 4 condition variables.
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
STATES[0] = 0.005;
STATES[1] = 0.005;
STATES[2] = 0.005;
CONSTANTS[0] = 1e-16;
STATES[3] = 1e-16;
STATES[4] = 1e-16;
STATES[5] = 2;
CONSTANTS[1] = 120;
CONSTANTS[2] = 50;
CONSTANTS[3] = 50;
CONSTANTS[4] = 400;
CONSTANTS[5] = 8;
CONSTANTS[6] = 6;
CONSTANTS[7] = 4;
CONSTANTS[8] = 3;
CONSTANTS[9] = 1;
CONSTANTS[10] = 8;
CONSTANTS[11] = 1;
CONSTANTS[12] = 1.5;
RATES[0] = 0.1001;
RATES[1] = 0.1001;
RATES[2] = 0.1001;
RATES[4] = 0.1001;
RATES[3] = 0.1001;
RATES[5] = 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[1]*ALGEBRAIC[0]+ ALGEBRAIC[11]*STATES[1]+ ALGEBRAIC[9]*STATES[2]) -  (CONSTANTS[2]+ALGEBRAIC[6])*STATES[0];
resid[1] = RATES[1] - ( ALGEBRAIC[6]*STATES[0]+ ALGEBRAIC[12]*STATES[2]) -  (ALGEBRAIC[11]+ALGEBRAIC[10])*STATES[1];
resid[2] = RATES[2] -  ALGEBRAIC[10]*STATES[1] -  (ALGEBRAIC[12]+ALGEBRAIC[9])*STATES[2];
resid[3] = RATES[4] - (STATES[2]==0.00000 ? ALGEBRAIC[7] :  (( - ALGEBRAIC[10]*STATES[1])/STATES[2])*(STATES[4] - CONSTANTS[0])+ALGEBRAIC[7]);
resid[4] = RATES[3] - (STATES[1]==0.00000 ? ALGEBRAIC[7] :  - (( ALGEBRAIC[6]*STATES[0])/STATES[1]+( ALGEBRAIC[12]*STATES[2])/STATES[1])*STATES[3]+ALGEBRAIC[7]);
resid[5] = RATES[5] - ALGEBRAIC[7];
}
void
computeVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[3] =  CONSTANTS[12]*STATES[1];
ALGEBRAIC[4] =  CONSTANTS[12]*STATES[2];
ALGEBRAIC[8] =  ALGEBRAIC[3]*STATES[3]+ ALGEBRAIC[4]*STATES[4];
}
void
computeEssentialVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[0] = ((CONSTANTS[11] - STATES[0]) - STATES[1]) - STATES[2];
ALGEBRAIC[1] = STATES[1]/CONSTANTS[11];
ALGEBRAIC[2] = STATES[2]/CONSTANTS[11];
ALGEBRAIC[6] =  CONSTANTS[3]*pow(1.00000+ ALGEBRAIC[1]*(exp( (STATES[3]/CONSTANTS[0])*(CONSTANTS[8] - 1.00000)) - 1.00000)+ ALGEBRAIC[2]*(exp( (STATES[4]/CONSTANTS[0])*(CONSTANTS[8] - 1.00000)) - 1.00000), 2.00000);
ALGEBRAIC[7] = (CONDVAR[2]>0.00000&&CONDVAR[3]<0.00000 ? 21.2000 : 0.00000);
ALGEBRAIC[5] = (CONDVAR[0]>0.00000 ? CONSTANTS[10] : CONDVAR[1]<0.00000 ? CONSTANTS[9] : 0.00000);
ALGEBRAIC[9] =  CONSTANTS[7]*exp( ALGEBRAIC[5]*pow(STATES[4] - CONSTANTS[0], 2.00000));
ALGEBRAIC[10] =  CONSTANTS[5]*exp( ALGEBRAIC[5]*pow(STATES[3], 2.00000));
ALGEBRAIC[11] =  CONSTANTS[4]*exp( ALGEBRAIC[5]*pow(STATES[3], 2.00000));
ALGEBRAIC[12] =  CONSTANTS[6]*exp( ALGEBRAIC[5]*(pow(STATES[4], 2.00000) - pow(STATES[3], 2.00000)));
}
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;
}
void
computeRoots(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
             double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
CONDVAR[0] = STATES[4] - CONSTANTS[0];
CONDVAR[1] = STATES[4] - CONSTANTS[0];
CONDVAR[2] = VOI - 0.00100000;
CONDVAR[3] = VOI - 0.00200000;
}