public void reset() {
super.reset();
system.reset();
if (s != null) {
for (int i = 0; i < numberOfSubstances; i++) {
s[i].storeValue();
s[i].storeRate();
}
timer.storeTimePoint();
}
}
public void update() {
double t = 0.0;
double errRatio;
if (step > samplingStep) step = samplingStep;
int nSteps = 0;
for (; ; ) {
if ((samplingStep - t < step) && (samplingStep - t > 0.0)) step = samplingStep - t;
rkckStep(step);
errRatio = Numerics.max(yerr) / tolerance;
//
// Update the substance levels and go to the next step if
// 1. The target tolerance is reached.
// 2. The maximum # of iteractions is exceeded.
// 3. The minimum time step is reached.
//
if (errRatio <= 1.0) {
t += step;
updateSystem(step);
//
// grow the step a little bit. but not more than a factor of
// five
//
step *= Math.min(SAFETY * Math.pow(errRatio, PGROW), 5.0);
} else if (nSteps > maxIterations) {
System.out.println(" WARNING: # of iterations exceeds " + maxIterations);
t += step;
updateSystem(step);
} else if (step < minStep) {
System.out.println(" WARNING: Minimum integrateion step size (" + minStep + ") reached");
t += step;
updateSystem(step);
} else {
// step size too large.
// Need to reset the values of all the substances
//
for (int i = 0; i < numberOfSubstances; i++) s[i].setValue(y1[i]);
//
// reset the Timer back to where it started.
//
timer.step(0 - step);
//
// shrink the step size
// and recompute. But shrink by a factor smaller than 10.
//
step *= Math.max(SAFETY * Math.pow(errRatio, PSHRINK), 0.1);
}
if (t >= samplingStep) break;
}
//
// Store the data if the sampling step is reached.
//
timer.storeTimePoint();
for (int i = 0; i < numberOfSubstances; i++) {
s[i].storeValue();
s[i].storeRate();
}
}