public class SDRun extends Object implements IOutputSet
Modifier and Type | Field and Description |
---|---|
String |
action |
String |
algorithm |
String |
calculation |
double |
depth2D |
String |
distribution |
double |
leap_min_jump
How many times our calculated allowed leap must be longer than
normal event waiting time, for us to choose leaping.
|
String |
output |
String |
outputQuantity |
OutputScheme |
outputScheme |
long |
simulationSeed |
int |
spineSeed |
Statistics |
statistics |
double |
tolerance
Accepted tolerance for adaptive calculations
(delta f / f for an algorithm dependent function f).
|
Constructor and Description |
---|
SDRun() |
public OutputScheme outputScheme
public String action
public double depth2D
public String output
public int spineSeed
public long simulationSeed
public String outputQuantity
public double tolerance
public double leap_min_jump
public String calculation
public Statistics statistics
public String distribution
public String algorithm
public BaseCalc.algorithm_t getAlgorithm()
public VolumeGrid.geometry_t getGeometry()
public String getRegion()
getRegion
in interface IOutputSet
public String getIdentifier()
getIdentifier
in interface IOutputSet
public double getOutputInterval(double fallback)
getOutputInterval
in interface IOutputSet
public double getOutputInterval()
public void overrideRuntime(double runtime)
public String getStatistics()
public double getStatisticsInterval()
public double getFixedStepDt()
public List<? extends IOutputSet> getOutputSets()
public boolean writeDependencies()
public ReactionTable getReactionTable()
public StimulationTable getStimulationTable()
public Morphology getMorphology()
public String[] getSpecies()
public List<String> getNamesOfOutputSpecies()
getNamesOfOutputSpecies
in interface IOutputSet
public int[] getIndicesOfOutputSpecies(String[] species)
getIndicesOfOutputSpecies
in interface IOutputSet
public Discretization getDiscretization()
public InitialConditions getInitialConditions()
public double getStartTime()
public double getEndTime()
public VolumeGrid getVolumeGrid()
public int[][] getStimulationTargets()
public double[] getRegionConcentration(String region)
public double[][] getRegionConcentrations()
public double[] getRegionSurfaceDensity(String region)
public double[][] getRegionSurfaceDensities()
public String serialize()
public int[][] getPopulation()
public static SDRun loadFromFile(File model_file, File ic_file, int trial, double population_from_time)
public double stepSize()
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