/*
   There are a total of 9 entries in the algebraic variable array.
   There are a total of 3 entries in each of the rate and state variable arrays.
   There are a total of 8 entries in the constant variable array.
 */
/*
 * VOI is time in component model (minute).
 * STATES[0] is NFATP_cyt in component model (molecule).
 * STATES[1] is NFAT_cyt in component model (molecule).
 * STATES[2] is NFAT_nuc in component model (molecule).
 * ALGEBRAIC[5] is NFAT_tot in component model (molecule).
 * CONSTANTS[0] is k1_unstim in component model (per_minute).
 * CONSTANTS[1] is k1_stim in component model (per_minute).
 * ALGEBRAIC[1] is k1 in component model (per_minute).
 * CONSTANTS[2] is k2 in component model (per_minute).
 * CONSTANTS[3] is k3 in component model (per_minute).
 * CONSTANTS[4] is k4 in component model (per_minute).
 * CONSTANTS[5] is stim_wavelength in component model (minute).
 * CONSTANTS[6] is stim_duration in component model (minute).
 * ALGEBRAIC[0] is stim_on in component model (dimensionless).
 * CONSTANTS[7] is time_before_stim in component model (minute).
 * ALGEBRAIC[2] is Jdephosphorylation in component model (molecules_per_minute).
 * ALGEBRAIC[3] is Jtranslocate in component model (molecules_per_minute).
 * ALGEBRAIC[4] is Jexport in component model (molecules_per_minute).
 * ALGEBRAIC[6] is percentage_NFAT_cyt in component model (dimensionless).
 * ALGEBRAIC[7] is percentage_NFATP_cyt in component model (dimensionless).
 * ALGEBRAIC[8] is percentage_NFAT_nuc in component model (dimensionless).
 * RATES[0] is d/dt NFATP_cyt in component model (molecule).
 * RATES[1] is d/dt NFAT_cyt in component model (molecule).
 * RATES[2] is d/dt NFAT_nuc in component model (molecule).
 * There are a total of 2 condition variables.
 */
void
initConsts(double* CONSTANTS, double* RATES, double *STATES)
{
STATES[0] = 5000;
STATES[1] = 0;
STATES[2] = 0;
CONSTANTS[0] = 0;
CONSTANTS[1] = 0.359;
CONSTANTS[2] = 0.147;
CONSTANTS[3] = 0.06;
CONSTANTS[4] = 0.035;
CONSTANTS[5] = 3;
CONSTANTS[6] = 0.5;
CONSTANTS[7] = 1;
RATES[0] = 0.1001;
RATES[1] = 0.1001;
RATES[2] = 0.1001;
}
void
computeResiduals(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
                 double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
resid[0] = RATES[0] - ALGEBRAIC[4] - ALGEBRAIC[2];
resid[1] = RATES[1] - ALGEBRAIC[2] - ALGEBRAIC[3];
resid[2] = RATES[2] - ALGEBRAIC[3] - ALGEBRAIC[4];
}
void
computeVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[5] = STATES[0]+STATES[1]+STATES[2];
ALGEBRAIC[6] = ( STATES[1]*100.000)/ALGEBRAIC[5];
ALGEBRAIC[7] = ( STATES[0]*100.000)/ALGEBRAIC[5];
ALGEBRAIC[8] = ( STATES[2]*100.000)/ALGEBRAIC[5];
}
void
computeEssentialVariables(double VOI, double* CONSTANTS, double* RATES, double* STATES, double* ALGEBRAIC)
{
ALGEBRAIC[0] = (CONDVAR[0]>=0.00000&&CONDVAR[1]<=0.00000 ? 1.00000 : 0.00000);
ALGEBRAIC[1] = (ALGEBRAIC[0]==1.00000 ? CONSTANTS[1] : CONSTANTS[0]);
ALGEBRAIC[2] =  ALGEBRAIC[1]*STATES[0] -  CONSTANTS[2]*STATES[1];
ALGEBRAIC[3] =  CONSTANTS[3]*STATES[1];
ALGEBRAIC[4] =  CONSTANTS[4]*STATES[2];
}
void
getStateInformation(double* SI)
{
SI[0] = 1.0;
SI[1] = 1.0;
SI[2] = 1.0;
}
void
computeRoots(double VOI, double* CONSTANTS, double* RATES, double* OLDRATES, double* STATES,
             double* OLDSTATES, double* ALGEBRAIC, double* CONDVARS)
{
CONDVAR[0] = VOI - CONSTANTS[7];
CONDVAR[1] =  (int)(VOI - CONSTANTS[7]) % (int)(CONSTANTS[5]) - CONSTANTS[6];
}