public void should_calculate_propensity_for_multiple_species()
{
var reaction = new Reaction(
new Dictionary <Species, int>()
{
{ "A", 2 }, { "B", 2 }
},
new Dictionary <Species, int>(),
0.5);
var system = new ChemicalSystem(new Dictionary <Species, int> {
{ "A", 2 },
{ "B", 3 }
});
Assert.Equal(6.0, reaction.Propensity(system));
}
public void should_return_()
{
var random = Substitute.For <IRandom>();
random.GetNext().Returns(new RandomPair(0.1, 0.8));
var gillespieAlgorithm = new GillespieDirect(random);
var r1 = new Reaction(
new Dictionary <Species, int>()
{
{ "A", 2 }, { "B", 2 }
},
new Dictionary <Species, int>()
{
{ "C", 1 }
},
0.5);
var r2 = new Reaction(
new Dictionary <Species, int>()
{
{ "A", 1 }, { "B", 1 }
},
new Dictionary <Species, int>(),
0.25);
var r3 = new Reaction(
new Dictionary <Species, int>(),
new Dictionary <Species, int>()
{
{ "A", 1 }
},
0.2);
var system = new ChemicalSystem(new Dictionary <Species, int> {
{ "A", 2 },
{ "B", 3 }
});
var evolvedSystem = gillespieAlgorithm.GetPath(new [] { r1, r2, r3 }, system, 0.0, 1).Single().Value;
Assert.Equal(1, evolvedSystem.Count("A"));
Assert.Equal(2, evolvedSystem.Count("B"));
}
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);
}
