de.bioforscher.singa.simulation.modules.model

Class Simulation

java.lang.Object

de.bioforscher.singa.simulation.modules.model.Simulation

All Implemented Interfaces:

UpdateEventEmitter<NodeUpdatedEvent>

public class Simulation
extends Object
implements UpdateEventEmitter<NodeUpdatedEvent>

The simulation calss encapsulates everything that is needed to perform a Simulation based on cellular graph automata. Each simulation requires a AutomatonGraph, a set of Modules and a set of ChemicalEntitys. Additionally AssignmentRules can be used to assign concentrations to chemical entities based on rules (functions).

The Class SimulationExamples provides a set of examples where Simulations are being set up. Principally the following steps should be taken:

     // initialize simulation
     Simulation simulation = new Simulation();
     // initialize a graph
     AutomatonGraph graph = AutomatonGraphs.useStructureFrom(Graphs.buildGridGraph(10, 10, defaultBoundingBox));
     // add to simulation
     simulation.setGraph(graph);
     // initialize chemical entities
     ChemicalEntity fructosePhosphate = ChEBIParserService.parse("CHEBI:18105");
     // initialize their concentrations in the graph
     graph.initializeSpeciesWithConcentration(fructosePhosphate, 0.1);
     // add to simulation
     simulation.getChemicalEntities().add(fructosePhosphate);
     // set environmental simulation parameters (e.g. system diameter, temperature, viscosity)
     EnvironmentalParameters.getInstance().setNodeSpacingToDiameter(Quantities.getQuantity(2500.0, NANO(METRE)), 10);
     // add diffusion module (free diffusion will be simulated)
     simulation.getModules().add(new FreeDiffusion(simulation));
 

Afterwards the simulation can be performed stepwise by calling the nextEpoch() method. For each epoch the size of the time step will be adjusted with the TimeStepHarmonizer, to ensure numerical stability up to a given epsilon. The method (TimeStepHarmonizer.setEpsilon(double)) sets the epsilon and the error between two time steps will be kept below that threshold. Epsilons approaching 0 naturally result in very small time steps and therefore long simulation times, at default epsilon is at 0.01. The time step will be optimized for each epoch, resulting in many epochs for critical simulation regimes and large ones for stable regimes.

Changes in simulations can be observed by tagging AutomatonNodes of the AutomatonGraph. By setting AutomatonNode.setObserved(boolean) to true the simulation emits NodeUpdatedEvent for every observed node and every time step to every registered UpdateEventListener (to register a listener use UpdateEventEmitter.addEventListener(UpdateEventListener) method). As a standard implementation there is the EpochUpdateWriter that can be added to the Simulation that will write log files to the specified file locations.

Author:

cl

Constructor Summary

Constructors

Constructor and Description
Simulation() Creates a new plain simulation.

Method Summary

Modifier and Type	Method and Description
void	applyAssignmentRules() Apply all referenced assignment rules.
void	emitNextEpochEvent(AutomatonNode node) Emits the NodeUpdatedEvent to all listeners.
List<AssignmentRule>	getAssignmentRules() Returns the assignment rules.
Set<ChemicalEntity<?>>	getChemicalEntities() Returns the chemical entities.
javax.measure.Quantity<javax.measure.quantity.Time>	getElapsedTime() Returns the elapsed time after the deltas of the current epoch are applied.
long	getEpoch() Returns the current epoch number.
AutomatonGraph	getGraph() Returns the simulation graph.
CopyOnWriteArrayList<UpdateEventListener<NodeUpdatedEvent>>	getListeners()
Set<Module>	getModules() Returns the modules.
void	nextEpoch() Calculates the next epoch.
void	setAssignmentRules(List<AssignmentRule> assignmentRules) Adds a list of assignment rules, sorting them by their dependencies.
void	setChemicalEntities(Set<ChemicalEntity<?>> chemicalEntities) Sets all chemical entities at once.
void	setGraph(AutomatonGraph graph) Sets the simulation graph and adds all entities referenced in the graph to the chemical entities of the simulation.

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.bioforscher.singa.core.events.UpdateEventEmitter

addEventListener, emitEvent, removeEventListener

Constructor Detail

Simulation

public Simulation()

Creates a new plain simulation.

Method Detail

nextEpoch

public void nextEpoch()

Calculates the next epoch.

applyAssignmentRules

public void applyAssignmentRules()

Apply all referenced assignment rules.

getGraph

public AutomatonGraph getGraph()

Returns the simulation graph.

Returns:

The simulation graph.

setGraph

public void setGraph(AutomatonGraph graph)

Sets the simulation graph and adds all entities referenced in the graph to the chemical entities of the simulation.

Parameters:

graph - The simulation graph.

getModules

public Set<Module> getModules()

Returns the modules.

Returns:

The modules.

getAssignmentRules

public List<AssignmentRule> getAssignmentRules()

Returns the assignment rules.

Returns:

The assignment rules.

setAssignmentRules

public void setAssignmentRules(List<AssignmentRule> assignmentRules)

Adds a list of assignment rules, sorting them by their dependencies.

Parameters:

assignmentRules - The assignment rules.

See Also:

AssignmentRules.sortAssignmentRulesByPriority(List)

getChemicalEntities

public Set<ChemicalEntity<?>> getChemicalEntities()

Returns the chemical entities.

Returns:

The chemical entities.

setChemicalEntities

public void setChemicalEntities(Set<ChemicalEntity<?>> chemicalEntities)

Sets all chemical entities at once.

Parameters:

chemicalEntities - The chemical entities.

getEpoch

public long getEpoch()

Returns the current epoch number.

Returns:

The current epoch number

getElapsedTime

public javax.measure.Quantity<javax.measure.quantity.Time> getElapsedTime()

Returns the elapsed time after the deltas of the current epoch are applied.

Returns:

The elapsed time after the deltas of the current epoch are applied.

emitNextEpochEvent

public void emitNextEpochEvent(AutomatonNode node)

Emits the NodeUpdatedEvent to all listeners.

Parameters:

node - The observed node.

getListeners

public CopyOnWriteArrayList<UpdateEventListener<NodeUpdatedEvent>> getListeners()

Specified by:

getListeners in interface UpdateEventEmitter<NodeUpdatedEvent>