fern.benchmark
Class SimulatorCorrectness

java.lang.Object
  fern.benchmark.Benchmark
      fern.benchmark.SimulatorPerformance
          fern.benchmark.SimulatorCorrectness

public class SimulatorCorrectness
extends SimulatorPerformance

Benchmark the correctness of the built-in simulators for a given net. For this net and a specified moment in time, the average histogram distance is calculated for given species of the network. Additionally the histograms are plotted. The benchmark method can be invoked repeatedly to calculate the average over many simulations.

For references, see Yang Cao, Linda Petzold, Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems, Journal of Computational Physics 212 (2006) 6�24.

Author:

Florian Erhard

Constructor Summary

SimulatorCorrectness(Network net, double moment, String... speciesNames)
Creates the benchmark instance with given network, moment in time and species.

Method Summary

static void	main(String[] args)
void	present() Gets called after some iterations of the method benchmark in the base class.

Methods inherited from class fern.benchmark.SimulatorPerformance

benchmark, getShowSteps, getSimulators, setShowSteps

Methods inherited from class fern.benchmark.Benchmark

addData, clearData, createRandomDoubleArray, end, getNumBins, setNumBins, start, toGnuplot, toGnuplot, toGnuPlotAsHistogram, toGnuPlotAsHistogram

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimulatorCorrectness

public SimulatorCorrectness(Network net,
                            double moment,
                            String... speciesNames)

Creates the benchmark instance with given network, moment in time and species.

Parameters:

net - the network to benchmark

moment - the moment in time at which the amounts are to be measured

speciesNames - the names of the species of which the amounts are to be measured

Method Detail

present

public void present()

Gets called after some iterations of the method benchmark in the base class. A gnuplot is created containing histograms for each species and simulator and the histogram distances for the simulators is printed to stdout

See Also:

SimulatorPerformance.setShowSteps(int)

main

public static void main(String[] args)
                 throws IOException,
                        org.jdom.JDOMException

Throws:

IOException

org.jdom.JDOMException