public IEnumerable <TimePoint <ChemicalSystem> > GetPath(IList <Reaction> reactions, ChemicalSystem initialSystem, double endTime, int numPoints)
{
double t = 0;
var evolvingSystem = initialSystem;
int numReactions = reactions.Count;
double reportingInterval = endTime / (double)numPoints;
double nextPoint = reportingInterval;
do
{
var randoms = _random.GetNext();
var propensities = reactions.Select(r => r.Propensity(evolvingSystem));
var totalPropensity = propensities.Sum();
var normalisedPropensities = propensities.Select(p => p / totalPropensity).ToList();
var selectedReaction = Partitioner.ToIntervals(normalisedPropensities)
.Zip(reactions, (interval, reaction) => new Tuple <Tuple <double, double>, Reaction>(interval, reaction))
.Single(pair => randoms.r2 > pair.Item1.Item1 && randoms.r2 < pair.Item1.Item2)
.Item2;
t += Math.Log(1.0 / randoms.r1) / totalPropensity;
evolvingSystem = evolvingSystem.React(selectedReaction);
if (t > nextPoint)
{
yield return(new TimePoint <ChemicalSystem>(t, evolvingSystem));
nextPoint += reportingInterval;
}
} while (t <= endTime);
}
public void should_partition_unit_interval()
{
var sequence = new [] { 0.5, 0.25, 0.125, 0.06025 };
var expected = new [] {
new Tuple <double, double>(0, 0.5),
new Tuple <double, double>(0.5, 0.75),
new Tuple <double, double>(0.75, 0.875),
new Tuple <double, double>(0.875, 1.0)
};
Assert.Equal(expected, Partitioner.ToIntervals(sequence));
}
