Program: 57501
Project: 57501
Buggy source:
/** 
 * {@inheritDoc} 
 */
public double integrate(final FirstOrderDifferentialEquations equations,final double t0,final double[] y0,final double t,final double[] y) throws DerivativeException, IntegratorException {
  sanityChecks(equations,t0,y0,t,y);
  final boolean forward=(t > t0);
  final int stages=c.length + 1;
  if (y != y0) {
    System.arraycopy(y0,0,y,0,y0.length);
  }
  final double[][] yDotK=new double[stages][];
  for (int i=0; i < stages; ++i) {
    yDotK[i]=new double[y0.length];
  }
  final double[] yTmp=new double[y0.length];
  AbstractStepInterpolator interpolator;
  if (requiresDenseOutput() || (!eventsHandlersManager.isEmpty())) {
    final RungeKuttaStepInterpolator rki=(RungeKuttaStepInterpolator)prototype.copy();
    rki.reinitialize(equations,yTmp,yDotK,forward);
    interpolator=rki;
  }
 else {
    interpolator=new DummyStepInterpolator(yTmp,forward);
  }
  interpolator.storeTime(t0);
  stepStart=t0;
  stepSize=step;
  for (  StepHandler handler : stepHandlers) {
    handler.reset();
  }
  CombinedEventsManager manager=addEndTimeChecker(t,eventsHandlersManager);
  boolean lastStep=false;
  while (!lastStep) {
    interpolator.shift();
    for (boolean loop=true; loop; ) {
      equations.computeDerivatives(stepStart,y,yDotK[0]);
      for (int k=1; k < stages; ++k) {
        for (int j=0; j < y0.length; ++j) {
          double sum=a[k - 1][0] * yDotK[0][j];
          for (int l=1; l < k; ++l) {
            sum+=a[k - 1][l] * yDotK[l][j];
          }
          yTmp[j]=y[j] + stepSize * sum;
        }
        equations.computeDerivatives(stepStart + c[k - 1] * stepSize,yTmp,yDotK[k]);
      }
      for (int j=0; j < y0.length; ++j) {
        double sum=b[0] * yDotK[0][j];
        for (int l=1; l < stages; ++l) {
          sum+=b[l] * yDotK[l][j];
        }
        yTmp[j]=y[j] + stepSize * sum;
      }
      interpolator.storeTime(stepStart + stepSize);
      if (manager.evaluateStep(interpolator)) {
        stepSize=manager.getEventTime() - stepStart;
      }
 else {
        loop=false;
      }
    }
    final double nextStep=stepStart + stepSize;
    System.arraycopy(yTmp,0,y,0,y0.length);
    manager.stepAccepted(nextStep,y);
    lastStep=manager.stop();
    interpolator.storeTime(nextStep);
    for (    StepHandler handler : stepHandlers) {
      handler.handleStep(interpolator,lastStep);
    }
    stepStart=nextStep;
    if (manager.reset(stepStart,y) && !lastStep) {
      equations.computeDerivatives(stepStart,y,yDotK[0]);
    }
    stepSize=step;
  }
  final double stopTime=stepStart;
  stepStart=Double.NaN;
  stepSize=Double.NaN;
  return stopTime;
}

Fixed version (ground truth):
/** 
 * {@inheritDoc} 
 */
public double integrate(final FirstOrderDifferentialEquations equations,final double t0,final double[] y0,final double t,final double[] y) throws DerivativeException, IntegratorException {
  sanityChecks(equations,t0,y0,t,y);
  final boolean forward=(t > t0);
  final int stages=c.length + 1;
  if (y != y0) {
    System.arraycopy(y0,0,y,0,y0.length);
  }
  final double[][] yDotK=new double[stages][];
  for (int i=0; i < stages; ++i) {
    yDotK[i]=new double[y0.length];
  }
  final double[] yTmp=new double[y0.length];
  AbstractStepInterpolator interpolator;
  if (requiresDenseOutput() || (!eventsHandlersManager.isEmpty())) {
    final RungeKuttaStepInterpolator rki=(RungeKuttaStepInterpolator)prototype.copy();
    rki.reinitialize(equations,yTmp,yDotK,forward);
    interpolator=rki;
  }
 else {
    interpolator=new DummyStepInterpolator(yTmp,forward);
  }
  interpolator.storeTime(t0);
  stepStart=t0;
  stepSize=step;
  for (  StepHandler handler : stepHandlers) {
    handler.reset();
  }
  CombinedEventsManager manager=addEndTimeChecker(t0,t,eventsHandlersManager);
  boolean lastStep=false;
  while (!lastStep) {
    interpolator.shift();
    for (boolean loop=true; loop; ) {
      equations.computeDerivatives(stepStart,y,yDotK[0]);
      for (int k=1; k < stages; ++k) {
        for (int j=0; j < y0.length; ++j) {
          double sum=a[k - 1][0] * yDotK[0][j];
          for (int l=1; l < k; ++l) {
            sum+=a[k - 1][l] * yDotK[l][j];
          }
          yTmp[j]=y[j] + stepSize * sum;
        }
        equations.computeDerivatives(stepStart + c[k - 1] * stepSize,yTmp,yDotK[k]);
      }
      for (int j=0; j < y0.length; ++j) {
        double sum=b[0] * yDotK[0][j];
        for (int l=1; l < stages; ++l) {
          sum+=b[l] * yDotK[l][j];
        }
        yTmp[j]=y[j] + stepSize * sum;
      }
      interpolator.storeTime(stepStart + stepSize);
      if (manager.evaluateStep(interpolator)) {
        stepSize=manager.getEventTime() - stepStart;
      }
 else {
        loop=false;
      }
    }
    final double nextStep=stepStart + stepSize;
    System.arraycopy(yTmp,0,y,0,y0.length);
    manager.stepAccepted(nextStep,y);
    lastStep=manager.stop();
    interpolator.storeTime(nextStep);
    for (    StepHandler handler : stepHandlers) {
      handler.handleStep(interpolator,lastStep);
    }
    stepStart=nextStep;
    if (manager.reset(stepStart,y) && !lastStep) {
      equations.computeDerivatives(stepStart,y,yDotK[0]);
    }
    stepSize=step;
  }
  final double stopTime=stepStart;
  stepStart=Double.NaN;
  stepSize=Double.NaN;
  return stopTime;
}