/**
* initialize before simulation begins. Rewind/forward any population model values to the start
* time of the sequencer
*
* @param time
*/
public void initialize(STEMTime time) {
EList<Decorator> redoList = new BasicEList<Decorator>();
boolean redo = false;
for (Decorator d : this.getDecorators()) {
if (d instanceof IntegrationDecorator) {
EList<DynamicLabel> labels = d.getLabelsToUpdate();
for (DynamicLabel l : labels) {
if (l instanceof IntegrationLabel) {
IntegrationLabel il = (IntegrationLabel) l;
il.reset(time);
if (((SimpleDataExchangeLabelValue) il.getDeltaValue()).getArrivals().size() > 0
|| ((SimpleDataExchangeLabelValue) il.getDeltaValue()).getDepartures().size() > 0)
redo = true;
}
}
}
if (!redo) redoList.add(d);
}
// Fix decorators with unapplied deltas
if (redo) {
for (Decorator d : redoList) {
if (d instanceof IntegrationDecorator) {
EList<DynamicLabel> labels = d.getLabelsToUpdate();
for (DynamicLabel l : labels) {
if (l instanceof IntegrationLabel) {
IntegrationLabel il = (IntegrationLabel) l;
il.reset(time);
}
}
}
}
}
this.setInitialized(true);
}
/**
* _step Do the step for a single thread
*
* @param time
* @param timeDelta
* @param cycle
* @param threadnum
*/
protected void _step(STEMTime time, long timeDelta, int cycle, short threadnum) {
// this.setProgress(0.0);
// We only deal with standard disease model decorators
ArrayList<Decorator> iDecorators = new ArrayList<Decorator>();
for (Decorator d : getDecorators()) {
if (d instanceof IntegrationDecorator) iDecorators.add(d);
}
// First we get the step size, either the default step size
// (initially 1.0) or the last step size used.
double h = this.getStepSize();
// x is to keep track of how far we have advanced in the solution. It is essentially
// a double cycle representation
double x = this.getCurrentX();
// Substantial performance can be gained here. Basically if the current cycle
// is greater than the cycle requested by the simulation, we are done. This
// means that the error tolerance between last step and this step is small
// enough so we don't need to update the labels. The error tolerance is
// specified in the disease model
// *** OBSERVE: Since we limit h to max 1 below, this code is never invoked. It's kept
// *** around in case we want to allow time to be calculated far out in the future if
// *** the error is small enough
if (x >= cycle) {
// Just copy the next value the same as the current value for all labels
for (Decorator sdm : iDecorators) {
EList<DynamicLabel> myLabels = sdm.getLabelsToUpdate(threadnum, num_threads);
int numLabels = myLabels.size();
double n = 0.0;
int setProgressEveryNthNode = num_threads * numLabels / (MAX_PROGRESS_REPORTS);
if (setProgressEveryNthNode == 0) setProgressEveryNthNode = 1;
for (final Iterator<DynamicLabel> currentStateLabelIter = myLabels.iterator();
currentStateLabelIter.hasNext(); ) {
final IntegrationLabel diseaseLabel = (IntegrationLabel) currentStateLabelIter.next();
// The estimated disease value contains the value calculated at position x
IntegrationLabelValue nextValueAtX =
(IntegrationLabelValue) EcoreUtil.copy(diseaseLabel.getProbeValue());
IntegrationLabelValue currentValueAtCycle =
(IntegrationLabelValue) diseaseLabel.getCurrentValue();
IntegrationLabelValue nextState = (IntegrationLabelValue) diseaseLabel.getNextValue();
adjustValuesToCycle(currentValueAtCycle, nextValueAtX, x, cycle);
// NextValueAtX has been modified here to the correct value for this cycle.
nextState.set(nextValueAtX);
// The next value is valid now.
diseaseLabel.setNextValueValid(true);
double progress = n / numLabels;
jobs[threadnum].setProgress(progress);
if (n % setProgressEveryNthNode == 0) {
// Get the progress for all threads
for (int i = 0; i < num_threads; ++i)
if (i != threadnum && jobs[i] != null) progress += jobs[i].getProgress();
progress /= num_threads;
sdm.setProgress(progress);
}
n += 1.0;
}
} // For each decorator
// So that validation code above is happy
jobs[threadnum].h = h;
jobs[threadnum].t = x;
return;
}
// When x (or time) is this we're done
double end = Math.floor(this.getCurrentX()) + 1.0;
// Make sure we actually have labels to update
boolean workToDo = false;
for (Decorator sdm : iDecorators)
if (sdm.getLabelsToUpdate(threadnum, num_threads).size() > 0) {
workToDo = true;
break;
}
if (!workToDo) {
// Nothing to do, just advance x and set h
jobs[threadnum].h = h;
jobs[threadnum].t = x;
// Be nice and walk in step with others until done
while (x < end) {
try {
// Set to a large number to make sure it's larger than any step size reported
// by another thread
do {
jobs[threadnum].h = Double.MAX_VALUE;
stepSizeBarrier.await();
} while (this.maximumError > 1.0);
updateDoneBarrier.await();
} catch (InterruptedException ie) {
// Should never happen
Activator.logError(ie.getMessage(), ie);
} catch (BrokenBarrierException bbe) {
// Should never happen
Activator.logError(bbe.getMessage(), bbe);
}
// Set to the smallest value reported by another thread
h = this.smallestH;
x += h;
jobs[threadnum].h = h;
jobs[threadnum].t = x;
}
return;
}
// We use the Runge Kutta Kash Carp method to advance to the next
// step in the simulation. Two estimates of the disease deltas
// are calculated and compared to each other. If they differ
// by more than a maximum error (determined by a parameter for
// the disease model), we reduce the step size until an acceptable
// error is reached.
// These are used during Runge Kutta calculations:
Map<IntegrationLabel, IntegrationLabelValue> k1map =
new HashMap<IntegrationLabel, IntegrationLabelValue>();
Map<IntegrationLabel, IntegrationLabelValue> k2map =
new HashMap<IntegrationLabel, IntegrationLabelValue>();
Map<IntegrationLabel, IntegrationLabelValue> k3map =
new HashMap<IntegrationLabel, IntegrationLabelValue>();
Map<IntegrationLabel, IntegrationLabelValue> k4map =
new HashMap<IntegrationLabel, IntegrationLabelValue>();
Map<IntegrationLabel, IntegrationLabelValue> k5map =
new HashMap<IntegrationLabel, IntegrationLabelValue>();
Map<IntegrationLabel, IntegrationLabelValue> k6map =
new HashMap<IntegrationLabel, IntegrationLabelValue>();
// Used below as temporary place holder, one for each decorator
IntegrationLabelValue _k1[], _k2[], _k3[], _k4[], _k5[], _k6[];
int numDecorators = iDecorators.size();
_k1 = new IntegrationLabelValue[numDecorators];
_k2 = new IntegrationLabelValue[numDecorators];
_k3 = new IntegrationLabelValue[numDecorators];
_k4 = new IntegrationLabelValue[numDecorators];
_k5 = new IntegrationLabelValue[numDecorators];
_k6 = new IntegrationLabelValue[numDecorators];
// The final estimates for label values are stored here
Map<IntegrationLabel, IntegrationLabelValue> finalEstimate =
new HashMap<IntegrationLabel, IntegrationLabelValue>();
// Delta is used to scale the step (h)
double delta = 0.0;
int n = 0;
for (Decorator sdm : iDecorators) {
Iterator<DynamicLabel> iter = sdm.getLabelsToUpdate(threadnum, num_threads).iterator();
IntegrationLabel firstLabel = (IntegrationLabel) iter.next();
// Initialize temporary place holders just by creating dups of the first label available
_k1[n] = (IntegrationLabelValue) EcoreUtil.copy(firstLabel.getCurrentValue());
_k2[n] = (IntegrationLabelValue) EcoreUtil.copy(firstLabel.getCurrentValue());
_k3[n] = (IntegrationLabelValue) EcoreUtil.copy(firstLabel.getCurrentValue());
_k4[n] = (IntegrationLabelValue) EcoreUtil.copy(firstLabel.getCurrentValue());
_k5[n] = (IntegrationLabelValue) EcoreUtil.copy(firstLabel.getCurrentValue());
_k6[n++] = (IntegrationLabelValue) EcoreUtil.copy(firstLabel.getCurrentValue());
}
// Keep track if whether anyone want to stop
// or pause updating labels
boolean interrupt = false, pause = false;
// We keep these around to determine when to call setProgress(...) on the decorators.
// If we call too frequently we can too many callbacks which affects performance.
double nextProgressReportStep = num_threads * (end - x) / MAX_PROGRESS_REPORTS;
double nextProgressReport = x + nextProgressReportStep;
// HashMap<StandardDiseaseModelLabel, StandardDiseaseModelLabelValue> validate = new
// HashMap<StandardDiseaseModelLabel, StandardDiseaseModelLabelValue>();
// This is the main loop we keep iterating over until we are done with the step
while (x < end) {
k1map.clear();
k2map.clear();
k3map.clear();
k4map.clear();
k5map.clear();
k6map.clear();
finalEstimate.clear();
// Validation code kept here if needed in the future
/*
HashMap<StandardDiseaseModelLabel, StandardDiseaseModelLabelValue> validate = new HashMap<StandardDiseaseModelLabel, StandardDiseaseModelLabelValue>();
if(!redo)
for(StandardDiseaseModelImpl sdm:diseaseModelDecorators) {
for (final Iterator<DynamicLabel> currentStateLabelIter = sdm.getLabelsToUpdate(threadnum, num_threads)
.iterator(); currentStateLabelIter.hasNext();) {
final StandardDiseaseModelLabel diseaseLabel = (StandardDiseaseModelLabel) currentStateLabelIter
.next();
final StandardDiseaseModelLabelValue val = (StandardDiseaseModelLabelValue)diseaseLabel.getCurrentDiseaseModelTempLabelValue();
validate.put(diseaseLabel, val);
}
}
else {
for(StandardDiseaseModelImpl sdm:diseaseModelDecorators)
for (final Iterator<DynamicLabel> currentStateLabelIter = sdm.getLabelsToUpdate(threadnum, num_threads)
.iterator(); currentStateLabelIter.hasNext();) {
final StandardDiseaseModelLabel diseaseLabel = (StandardDiseaseModelLabel) currentStateLabelIter
.next();
final SIRLabelValue val = (SIRLabelValue)diseaseLabel.getCurrentDiseaseModelTempLabelValue();
validate.put(diseaseLabel, val);
final SIRLabelValue oldVal = (SIRLabelValue)validate.get(diseaseLabel);
if(val.getI() != oldVal.getI() ||
val.getS() != oldVal.getS() ||
val.getR() != oldVal.getR() ||
//val.getE() != oldVal.getE() ||
val.getBirths() != oldVal.getBirths() ||
val.getDeaths() != oldVal.getDeaths() ||
val.getDiseaseDeaths() != oldVal.getDiseaseDeaths()
)
Activator.logError("Error, old and new value not the same label: "+diseaseLabel, new Exception());
}
}
*/
// ToDo: We should check if a maximum number of iterations have been
// exceeded here and throw an error.
// First, get the delta values at the current state
for (Decorator sdm : iDecorators)
((IntegrationDecorator) sdm)
.calculateDelta(time, timeDelta, sdm.getLabelsToUpdate(threadnum, num_threads));
for (Decorator sdm : iDecorators)
((IntegrationDecorator) sdm)
.applyExternalDeltas(time, timeDelta, sdm.getLabelsToUpdate(threadnum, num_threads));
// Set the scaling factor for disease parameters for each decorator and location
for (Decorator sdm : iDecorators) {
for (final Iterator<DynamicLabel> currentStateLabelIter =
sdm.getLabelsToUpdate(threadnum, num_threads).iterator();
currentStateLabelIter.hasNext(); ) {
final IntegrationLabel diseaseLabel = (IntegrationLabel) currentStateLabelIter.next();
IntegrationLabelValue scale = (IntegrationLabelValue) diseaseLabel.getErrorScale();
scale.set((IntegrationLabelValue) diseaseLabel.getTempValue());
IntegrationLabelValue dt =
(IntegrationLabelValue) EcoreUtil.copy(diseaseLabel.getDeltaValue());
dt.scale(h);
dt.abs();
dt.add(TINY);
scale.abs();
scale.add(dt);
}
}
// Step 1 in Runge Kutta Fehlberg.
// Get the delta values out of each node label and
// build a first estimate of the next value'
for (Decorator sdm : iDecorators) {
for (final Iterator<DynamicLabel> currentStateLabelIter =
sdm.getLabelsToUpdate(threadnum, num_threads).iterator();
currentStateLabelIter.hasNext(); ) {
final IntegrationLabel diseaseLabel = (IntegrationLabel) currentStateLabelIter.next();
IntegrationLabelValue deltaLabel = (IntegrationLabelValue) diseaseLabel.getDeltaValue();
k1map.put(diseaseLabel, (IntegrationLabelValue) EcoreUtil.copy(deltaLabel));
deltaLabel.scale(h);
deltaLabel.scale(b21);
((IntegrationLabelValue) diseaseLabel.getProbeValue())
.set(deltaLabel.add((IntegrationLabelValue) diseaseLabel.getTempValue()));
}
}
// Now get the next delta values
for (Decorator sdm : iDecorators)
((IntegrationDecorator) sdm)
.calculateDelta(time, timeDelta, sdm.getLabelsToUpdate(threadnum, num_threads));
for (Decorator sdm : iDecorators)
((IntegrationDecorator) sdm)
.applyExternalDeltas(time, timeDelta, sdm.getLabelsToUpdate(threadnum, num_threads));
// Step 2 in Runge Kutta Fehlberg.
// Get the delta values out of each node label and
// build a second estimate of the next value
n = 0;
for (Decorator sdm : iDecorators) {
for (final Iterator<DynamicLabel> currentStateLabelIter =
sdm.getLabelsToUpdate(threadnum, num_threads).iterator();
currentStateLabelIter.hasNext(); ) {
final IntegrationLabel diseaseLabel = (IntegrationLabel) currentStateLabelIter.next();
IntegrationLabelValue deltaLabel = (IntegrationLabelValue) diseaseLabel.getDeltaValue();
k2map.put(diseaseLabel, (IntegrationLabelValue) EcoreUtil.copy(deltaLabel));
_k1[n].set(k1map.get(diseaseLabel));
_k2[n].set(deltaLabel);
IntegrationLabelValue estDelta = _k1[n].scale(b31);
_k2[n].scale(b32);
estDelta.add(_k2[n]);
estDelta.scale(h);
((IntegrationLabelValue) diseaseLabel.getProbeValue())
.set(estDelta.add((IntegrationLabelValue) diseaseLabel.getTempValue()));
}
++n;
}
// Now get the next delta values
for (Decorator sdm : iDecorators)
((IntegrationDecorator) sdm)
.calculateDelta(time, timeDelta, sdm.getLabelsToUpdate(threadnum, num_threads));
for (Decorator sdm : iDecorators)
((IntegrationDecorator) sdm)
.applyExternalDeltas(time, timeDelta, sdm.getLabelsToUpdate(threadnum, num_threads));
// Step 3 in Runge Kutta Fehlberg.
// Get the delta values out of each node label and
// build a third estimate of the next value
n = 0;
for (Decorator sdm : iDecorators) {
for (final Iterator<DynamicLabel> currentStateLabelIter =
sdm.getLabelsToUpdate(threadnum, num_threads).iterator();
currentStateLabelIter.hasNext(); ) {
final IntegrationLabel diseaseLabel = (IntegrationLabel) currentStateLabelIter.next();
IntegrationLabelValue deltaLabel = (IntegrationLabelValue) diseaseLabel.getDeltaValue();
k3map.put(diseaseLabel, (IntegrationLabelValue) EcoreUtil.copy(deltaLabel));
_k1[n].set(k1map.get(diseaseLabel));
_k2[n].set(k2map.get(diseaseLabel));
_k3[n].set(deltaLabel);
_k1[n].scale(b41);
_k2[n].scale(b42);
_k3[n].scale(b43);
IntegrationLabelValue estDelta = _k1[n];
estDelta.add(_k2[n]);
estDelta.add(_k3[n]);
estDelta.scale(h);
((IntegrationLabelValue) diseaseLabel.getProbeValue())
.set(estDelta.add((IntegrationLabelValue) diseaseLabel.getTempValue()));
}
++n;
}
// Now get the next delta values
for (Decorator sdm : iDecorators)
((IntegrationDecorator) sdm)
.calculateDelta(time, timeDelta, sdm.getLabelsToUpdate(threadnum, num_threads));
for (Decorator sdm : iDecorators)
((IntegrationDecorator) sdm)
.applyExternalDeltas(time, timeDelta, sdm.getLabelsToUpdate(threadnum, num_threads));
// Step 4 in Runge Kutta Fehlberg.
// Get the delta values out of each node label and
// build a fourth estimate of the next value
n = 0;
for (Decorator sdm : iDecorators) {
for (final Iterator<DynamicLabel> currentStateLabelIter =
sdm.getLabelsToUpdate(threadnum, num_threads).iterator();
currentStateLabelIter.hasNext(); ) {
final IntegrationLabel diseaseLabel = (IntegrationLabel) currentStateLabelIter.next();
IntegrationLabelValue deltaLabel = (IntegrationLabelValue) diseaseLabel.getDeltaValue();
k4map.put(diseaseLabel, (IntegrationLabelValue) EcoreUtil.copy(deltaLabel));
_k1[n].set(k1map.get(diseaseLabel));
_k2[n].set(k2map.get(diseaseLabel));
_k3[n].set(k3map.get(diseaseLabel));
_k4[n].set(deltaLabel);
_k1[n].scale(b51);
_k2[n].scale(b52);
_k3[n].scale(b53);
_k4[n].scale(b54);
IntegrationLabelValue estDelta = _k1[n];
estDelta.add(_k2[n]);
estDelta.add(_k3[n]);
estDelta.add(_k4[n]);
estDelta.scale(h);
((IntegrationLabelValue) diseaseLabel.getProbeValue())
.set(estDelta.add((IntegrationLabelValue) diseaseLabel.getTempValue()));
}
++n;
}
// Now get the next delta values
for (Decorator sdm : iDecorators)
((IntegrationDecorator) sdm)
.calculateDelta(time, timeDelta, sdm.getLabelsToUpdate(threadnum, num_threads));
for (Decorator sdm : iDecorators)
((IntegrationDecorator) sdm)
.applyExternalDeltas(time, timeDelta, sdm.getLabelsToUpdate(threadnum, num_threads));
// Step 5 in Runge Kutta Fehlberg.
// Get the delta values out of each node label and
// build a fifth estimate of the next value
n = 0;
for (Decorator sdm : iDecorators) {
for (final Iterator<DynamicLabel> currentStateLabelIter =
sdm.getLabelsToUpdate(threadnum, num_threads).iterator();
currentStateLabelIter.hasNext(); ) {
final IntegrationLabel diseaseLabel = (IntegrationLabel) currentStateLabelIter.next();
IntegrationLabelValue deltaLabel = (IntegrationLabelValue) diseaseLabel.getDeltaValue();
k5map.put(diseaseLabel, (IntegrationLabelValue) EcoreUtil.copy(deltaLabel));
_k1[n].set(k1map.get(diseaseLabel));
_k2[n].set(k2map.get(diseaseLabel));
_k3[n].set(k3map.get(diseaseLabel));
_k4[n].set(k4map.get(diseaseLabel));
_k5[n].set(deltaLabel);
_k1[n].scale(b61);
_k2[n].scale(b62);
_k3[n].scale(b63);
_k4[n].scale(b64);
_k5[n].scale(b65);
IntegrationLabelValue estDelta = _k1[n];
estDelta.add(_k2[n]);
estDelta.add(_k3[n]);
estDelta.add(_k4[n]);
estDelta.add(_k5[n]);
estDelta.scale(h);
((IntegrationLabelValue) diseaseLabel.getProbeValue())
.set(estDelta.add((IntegrationLabelValue) diseaseLabel.getTempValue()));
}
++n;
}
// Now get the next delta values
for (Decorator sdm : iDecorators)
((IntegrationDecorator) sdm)
.calculateDelta(time, timeDelta, sdm.getLabelsToUpdate(threadnum, num_threads));
for (Decorator sdm : iDecorators)
((IntegrationDecorator) sdm)
.applyExternalDeltas(time, timeDelta, sdm.getLabelsToUpdate(threadnum, num_threads));
// Step 6 in Runge Kutta Fehlberg.
// Calculate k6
n = 0;
for (Decorator sdm : iDecorators) {
for (final Iterator<DynamicLabel> currentStateLabelIter =
sdm.getLabelsToUpdate(threadnum, num_threads).iterator();
currentStateLabelIter.hasNext(); ) {
final IntegrationLabel diseaseLabel = (IntegrationLabel) currentStateLabelIter.next();
IntegrationLabelValue deltaLabel = (IntegrationLabelValue) diseaseLabel.getDeltaValue();
k6map.put(diseaseLabel, (IntegrationLabelValue) EcoreUtil.copy(deltaLabel));
}
++n;
}
// Step 7 in Runge Kutta Fehlberg
// Calculate the two estimates from k1, .. k6 values
// and determine the maximum difference (error) between them.
boolean success = true; // Were we able to update all labels without a large enough error?
double maxerror = 0.0;
n = 0;
for (Decorator sdm : iDecorators) {
for (final Iterator<DynamicLabel> currentStateLabelIter =
sdm.getLabelsToUpdate(threadnum, num_threads).iterator();
currentStateLabelIter.hasNext(); ) {
final IntegrationLabel diseaseLabel = (IntegrationLabel) currentStateLabelIter.next();
IntegrationLabelValue currentValue = (IntegrationLabelValue) diseaseLabel.getTempValue();
_k1[n].set(k1map.get(diseaseLabel));
_k3[n].set(k3map.get(diseaseLabel));
_k4[n].set(k4map.get(diseaseLabel));
_k5[n].set(k5map.get(diseaseLabel));
_k6[n].set(k6map.get(diseaseLabel));
_k1[n].scale(c1);
_k3[n].scale(c3);
_k4[n].scale(c4);
_k6[n].scale(c6);
// New Y
IntegrationLabelValue yout =
(IntegrationLabelValue) EcoreUtil.copy(_k1[n].add(_k3[n]).add(_k4[n]).add(_k6[n]));
yout.scale(h);
yout.add(currentValue);
// Get the error
_k1[n].set(k1map.get(diseaseLabel));
_k3[n].set(k3map.get(diseaseLabel));
_k4[n].set(k4map.get(diseaseLabel));
_k5[n].set(k5map.get(diseaseLabel));
_k6[n].set(k6map.get(diseaseLabel));
_k1[n].scale(dc1);
_k3[n].scale(dc3);
_k4[n].scale(dc4);
_k5[n].scale(dc5);
_k6[n].scale(dc6);
IntegrationLabelValue yerror =
(IntegrationLabelValue)
EcoreUtil.copy(_k1[n].add(_k3[n]).add(_k4[n]).add(_k5[n]).add(_k6[n]));
yerror.scale(h);
yerror.divide((IntegrationLabelValue) diseaseLabel.getErrorScale());
double error = yerror.max();
error /= relativeTolerance;
if (error > maxerror) {
maxerror = error;
}
if (error <= 1.0)
finalEstimate.put(diseaseLabel, (IntegrationLabelValue) EcoreUtil.copy(yout));
}
++n;
}
jobs[threadnum].h = h;
jobs[threadnum].maxerror = maxerror;
try {
stepSizeBarrier.await();
} catch (InterruptedException ie) {
// Should never happen
Activator.logError(ie.getMessage(), ie);
} catch (BrokenBarrierException bbe) {
// Should never happen
Activator.logError(bbe.getMessage(), bbe);
}
// At least one of the threads had to large of an error, fail
if (this.maximumError > 1.0) success = false;
// Are we done?
if (success) {
// Check to make sure
if (this.smallestH > h)
Activator.logError(
"Error, h was less than the smallest, perhaps barrier process failed to execute? h:"
+ h
+ " vs "
+ this.smallestH,
new Exception());
// Yes, hurrah, advance x using the step size h
x += h;
if (this.maximumError > ERRCON) h = SAFETY * h * Math.pow(this.maximumError, PGROW);
else h = 5.0 * h;
// Limit to max 1
if (h > 1.0) h = 1.0;
// Make sure we don't overshoot
if (x < end && x + h > end) h = (end - x);
// Update the current value to the new position
for (Decorator sdm : iDecorators) {
for (final Iterator<DynamicLabel> currentStateLabelIter =
sdm.getLabelsToUpdate(threadnum, num_threads).iterator();
currentStateLabelIter.hasNext(); ) {
final IntegrationLabel diseaseLabel = (IntegrationLabel) currentStateLabelIter.next();
((IntegrationLabelValue) diseaseLabel.getTempValue())
.set(finalEstimate.get(diseaseLabel));
((IntegrationLabelValue) diseaseLabel.getProbeValue())
.set(finalEstimate.get(diseaseLabel));
}
}
// Wait until all other threads have updated the current value
try {
updateDoneBarrier.await();
} catch (InterruptedException ie) {
// Should never happen
Activator.logError(ie.getMessage(), ie);
} catch (BrokenBarrierException bbe) {
// Should never happen
Activator.logError(bbe.getMessage(), bbe);
}
double progress = (end - x < 0.0) ? 1.0 : 1.0 - (end - x);
jobs[threadnum].setProgress(progress);
if (x > nextProgressReport) {
// Get the progress for all threads
for (int i = 0; i < num_threads; ++i)
if (i != threadnum && jobs[i] != null) progress += jobs[i].getProgress();
progress /= num_threads;
for (Decorator sdm : iDecorators) sdm.setProgress(progress);
nextProgressReport += nextProgressReportStep;
}
} else {
// At least one thread failed, change the step size
// Problem, error too big, we need to reduce the step size
delta = SAFETY * h * Math.pow(this.maximumError, PSHRNK);
if (h > 0.0) h = (delta > 0.1 * h) ? delta : 0.1 * h;
else h = (delta > 0.1 * h) ? 0.1 * h : delta;
// We didn't succeed.
// Reset the estimated value back to the original, the step size
// has been reduced so we well try again.
// Set the estimated value back to the current original value
for (Decorator sdm : iDecorators) {
for (final Iterator<DynamicLabel> currentStateLabelIter =
sdm.getLabelsToUpdate(threadnum, num_threads).iterator();
currentStateLabelIter.hasNext(); ) {
final IntegrationLabel diseaseLabel = (IntegrationLabel) currentStateLabelIter.next();
((IntegrationLabelValue) diseaseLabel.getProbeValue())
.set((IntegrationLabelValue) diseaseLabel.getTempValue());
}
}
}
} // While x < end
jobs[threadnum].t = x;
jobs[threadnum].h = h;
// Remember the step size and position in the solver
this.setStepSize(h);
this.setCurrentX(x);
// We're done
for (Decorator sdm : iDecorators) {
for (final Iterator<DynamicLabel> currentStateLabelIter =
sdm.getLabelsToUpdate(threadnum, num_threads).iterator();
currentStateLabelIter.hasNext(); ) {
final IntegrationLabel diseaseLabel = (IntegrationLabel) currentStateLabelIter.next();
// This is the next state for the label
IntegrationLabelValue nextState = (IntegrationLabelValue) diseaseLabel.getNextValue();
// This is the original current state at the previous cycle
IntegrationLabelValue originalState =
(IntegrationLabelValue) diseaseLabel.getCurrentValue();
// This is the final value calculated at position x.
IntegrationLabelValue newValue = finalEstimate.get(diseaseLabel);
// x could be larger than the requested cycle, so we do a linear interpolation
// to fit it exactly to the requested cycle
// *** Not needed since we always end exactly at the requested cycle
// adjustValuesToCycle(originalState, newValue, x, cycle);
// New value has been modified here to fit the requested cycle
nextState.set(newValue);
// Do any model specific work for instance add noise
((IntegrationDecorator) sdm).doModelSpecificAdjustments((LabelValue) nextState);
// The next value is valid now.
diseaseLabel.setNextValueValid(true);
}
}
}
/**
*
* <!-- begin-user-doc -->
* <!-- end-user-doc -->
*
* @generated NOT
*/
@Override
public boolean step(STEMTime time, long timeDelta, int cycle) {
// Validate all decorators that return deltas to make sure
// they are of deterministic nature. The Runge Kutta integratio
// can only handle determininistic variants
for (Decorator decorator : this.getDecorators())
if (decorator instanceof IntegrationDecorator) {
IntegrationDecorator idec = (IntegrationDecorator) decorator;
if (!idec.isDeterministic()) {
Activator.logError(
"Error, decorator: "
+ idec
+ " is not deterministic. The Runge Kutta Integrator can only handle deterministic models.",
new Exception());
return false;
}
}
Activator act = org.eclipse.stem.ui.Activator.getDefault();
if (act != null) {
final Preferences preferences = act.getPluginPreferences();
num_threads =
(short)
preferences.getInt(
org.eclipse.stem.ui.preferences.PreferenceConstants.SIMULATION_THREADS);
} else num_threads = 2; // Just so we can run inside junit test
final int c = cycle;
// Initialize latches
stepSizeBarrier =
new CyclicBarrier(
num_threads,
new Runnable() {
public void run() {
// All threads successfully advanced time by some step h.
// Find the smallest
smallestH = Double.MAX_VALUE;
maximumError = -Double.MAX_VALUE;
for (int i = 0; i < num_threads; ++i) {
if (jobs[i].h <= smallestH) {
if (maximumError < jobs[i].maxerror) maximumError = jobs[i].maxerror;
smallestH = jobs[i].h;
}
}
}
});
updateDoneBarrier = new CyclicBarrier(num_threads);
// Find triggers and make sure they are invoked
for (Decorator decorator : this.getDecorators()) {
if (decorator instanceof Trigger) {
decorator.updateLabels(time, timeDelta, cycle);
}
}
// First initialize the probe and temp label values from the current
// label values.
for (Decorator decorator : this.getDecorators()) {
EList<DynamicLabel> allLabels = decorator.getLabelsToUpdate();
for (final Iterator<DynamicLabel> currentStateLabelIter = allLabels.iterator();
currentStateLabelIter.hasNext(); ) {
if (decorator instanceof IntegrationDecorator) {
// It's a standard disease model with a standard disease model label
final IntegrationLabel iLabel = (IntegrationLabel) currentStateLabelIter.next();
((IntegrationLabelValue) iLabel.getProbeValue())
.set((IntegrationLabelValue) iLabel.getCurrentValue());
((IntegrationLabelValue) iLabel.getTempValue())
.set((IntegrationLabelValue) iLabel.getCurrentValue());
((IntegrationLabelValue) iLabel.getTempValue()).prepareCycle();
((IntegrationLabelValue) iLabel.getProbeValue()).prepareCycle();
} else currentStateLabelIter.next();
}
}
if (jobs == null || jobs.length != num_threads) {
// Initialize the jobs if not done yet or of the number of threads changes
jobs = new RkJob[num_threads];
for (short i = 0; i < num_threads; ++i) {
final short threadnum = i;
jobs[i] = new RkJob("Worker " + i, threadnum, this);
} // For each job
} // If not initialized
// Initialize
int thread = 0;
for (RkJob j : jobs) {
j.cycle = c;
j.time = time;
j.timeDelta = timeDelta;
}
// Schedule. Jobs can be rescheduled after finished
for (RkJob j : jobs) j.schedule();
// Wait until all jobs completed
for (RkJob j : jobs) {
try {
j.join();
} catch (InterruptedException ie) {
Activator.logError(ie.getMessage(), ie);
}
}
// Set the common time and step size here and validate everything is right
double minStep = Double.MAX_VALUE;
double currentT = jobs[0].t;
for (RkJob j : jobs) {
// The jobs have calculated new step sizes after they finished. Pick the
// smallest one for the next cycle
if (j.h < minStep) minStep = j.h;
if (j.t != currentT)
Activator.logError(
"Error, one thread was in misstep with other threads, its time was "
+ j.t
+ " versus "
+ currentT,
new Exception());
}
return true;
}