bio.singa.simulation.model.modules.concentration

Class ConcentrationBasedModule<DeltaFunctionType extends AbstractDeltaFunction>

java.lang.Object

bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule<DeltaFunctionType>

All Implemented Interfaces:

UpdateModule

Direct Known Subclasses:

ComplexBuildingReaction, Diffusion, DynamicReaction, MembraneDiffusion, Reaction, SingleFileChannelMembraneTransport

public abstract class ConcentrationBasedModule<DeltaFunctionType extends AbstractDeltaFunction>
extends Object
implements UpdateModule

Concentration based modules handle updates that are applied to the concentrations in Updatables during a simulation. Each module has a UpdateScope that regulates the dependence of this module to other parts of the simulation. Further, the UpdateSpecificity defines how fine-grained the updates are calculated. New modules should be created with the ModuleFactory.

Author:

cl

Field Summary

Fields

Modifier and Type	Field and Description
protected FieldSupplier	supplier Frequently required fields.

Constructor Summary

Constructors

Constructor and Description
ConcentrationBasedModule() Creates a new concentration based module.

Method Summary

Modifier and Type	Method and Description
protected void	addDeltaFunction(DeltaFunctionType deltaFunction) Adds a delta function to the module.
protected void	addModuleToSimulation() References the module and referenced entities to the referenced simulation.
protected void	addReferencedEntities(Collection<? extends ChemicalEntity> chemicalEntities) Adds multiple referenced chemical entities.
protected void	addReferencedEntity(ChemicalEntity chemicalEntity) Adds a referenced chemical entity.
void	calculateUpdates()
void	checkFeatures()
boolean	deltaIsValid(ConcentrationDelta delta) Returns true if the delta is valid, i.e.
LocalError	determineLargestLocalError() The local error is calculated and the largest local error of the current epoch resulting from the executing module is returned.
Predicate<Updatable>	getApplicationCondition() Returns the application condition for this module.The module is only evaluated if the updatable fulfills the given predicate.
double	getDeltaCutoff() Returns the cutoff where deltas are validated to be effectively zero.
double	getErrorCutoff() Returns the cutoff where numerical errors to be considered irretrievably unstable.
<FeatureType extends Feature> FeatureType	getFeature(Class<FeatureType> featureTypeClass) Returns the requested feature.
Collection<Feature<?>>	getFeatures() Returns all features of this module (not its entities).
String	getIdentifier() Returns the identifier of this module.
Set<ChemicalEntity>	getReferencedEntities() Returns all chemical entities that might be accessed by this module.
Set<Class<? extends Feature>>	getRequiredFeatures()
protected <FeatureContentType extends javax.measure.Quantity<FeatureContentType>> javax.measure.Quantity<FeatureContentType>	getScaledFeature(ChemicalEntity entity, Class<? extends ScalableFeature<FeatureContentType>> featureClass) Returns the requested feature of the given chemical entities, scaled according to the current time step and spatial scaling.
<FeatureContentType extends javax.measure.Quantity<FeatureContentType>> javax.measure.Quantity<FeatureContentType>	getScaledFeature(Class<? extends ScalableFeature<FeatureContentType>> featureClass)
UpdateScope	getScope() Returns the scope of this module.
Simulation	getSimulation() Returns the referenced simulation.
UpdateSpecificity	getSpecificity() Returns the specificity of this module.
ModuleState	getState()
FieldSupplier	getSupplier() Returns the field supplier.
void	handleDelta(ConcentrationDeltaIdentifier deltaIdentifier, ConcentrationDelta delta) Handles a delta based on the current state of the calculation.
void	onCompletion()
void	onReset()
void	optimizeTimeStep()
void	resetState()
void	scaleScalableFeatures()
protected void	setApplicationCondition(Predicate<Updatable> applicationCondition) Sets the application condition for this module.
void	setDeltaCutoff(double deltaCutoff) Sets the cutoff where deltas are validated to be effectively zero.
void	setErrorCutoff(double errorCutoff) Sets the cutoff where numerical errors to be considered irretrievably unstable.
void	setFeature(Feature<?> feature) Sets a feature.
void	setIdentifier(String identifier) Sets the identifier of this module.
void	setSimulation(Simulation simulation) References the simulation to this module.
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

supplier

protected FieldSupplier supplier

Frequently required fields.

Constructor Detail

ConcentrationBasedModule

public ConcentrationBasedModule()

Creates a new concentration based module.

Method Detail

addDeltaFunction

protected void addDeltaFunction(DeltaFunctionType deltaFunction)

Adds a delta function to the module. Delta functions are applied according to UpdateScope and UpdateSpecificity.

Parameters:

deltaFunction - The delta function.

setApplicationCondition

protected void setApplicationCondition(Predicate<Updatable> applicationCondition)

Sets the application condition for this module. The module is only evaluated if the updatable fulfills the given predicate.

Parameters:

applicationCondition - The application condition.

getApplicationCondition

public Predicate<Updatable> getApplicationCondition()

Returns the application condition for this module.The module is only evaluated if the updatable fulfills the given predicate.

Returns:

The application condition.

getReferencedEntities

public Set<ChemicalEntity> getReferencedEntities()

Returns all chemical entities that might be accessed by this module.

Specified by:

getReferencedEntities in interface UpdateModule

Returns:

All chemical entities that might be accessed by this module.

addReferencedEntity

protected void addReferencedEntity(ChemicalEntity chemicalEntity)

Adds a referenced chemical entity.

Parameters:

chemicalEntity - The chemical entity.

addReferencedEntities

protected void addReferencedEntities(Collection<? extends ChemicalEntity> chemicalEntities)

Adds multiple referenced chemical entities.

Parameters:

chemicalEntities - The chemical entities.

getDeltaCutoff

public double getDeltaCutoff()

Returns the cutoff where deltas are validated to be effectively zero.

Returns:

The delta cutoff.

setDeltaCutoff

public void setDeltaCutoff(double deltaCutoff)

Sets the cutoff where deltas are validated to be effectively zero.

Parameters:

deltaCutoff - The delta cutoff.

getErrorCutoff

public double getErrorCutoff()

Returns the cutoff where numerical errors to be considered irretrievably unstable.

Returns:

The error cutoff.

setErrorCutoff

public void setErrorCutoff(double errorCutoff)

Sets the cutoff where numerical errors to be considered irretrievably unstable.

Parameters:

errorCutoff - The error cutoff.

getSimulation

public Simulation getSimulation()

Returns the referenced simulation.

Returns:

The referenced simulation.

setSimulation

public void setSimulation(Simulation simulation)

References the simulation to this module.

Parameters:

simulation - The simulation.

getIdentifier

public String getIdentifier()

Returns the identifier of this module.

Specified by:

getIdentifier in interface UpdateModule

Returns:

The identifier.

setIdentifier

public void setIdentifier(String identifier)

Sets the identifier of this module.

Parameters:

identifier - The identifier.

getSupplier

public FieldSupplier getSupplier()

Returns the field supplier.

Returns:

The field supplier.

getScope

public UpdateScope getScope()

Returns the scope of this module.

Returns:

The scope of this module.

getSpecificity

public UpdateSpecificity getSpecificity()

Returns the specificity of this module.

Returns:

The specificity of this module.

getState

public ModuleState getState()

Specified by:

getState in interface UpdateModule

handleDelta

public void handleDelta(ConcentrationDeltaIdentifier deltaIdentifier,
                        ConcentrationDelta delta)

Handles a delta based on the current state of the calculation.

Parameters:

deltaIdentifier - The unique identifier of the delta.

delta - The delta itself.

deltaIsValid

public boolean deltaIsValid(ConcentrationDelta delta)

Returns true if the delta is valid, i.e. it is not zero and nor below the numerical threshold.

Parameters:

delta - The delta to be evaluated.

Returns:

true if the delta is valid, i.e. it is not zero and nor below the numerical threshold.

determineLargestLocalError

public LocalError determineLargestLocalError()

The local error is calculated and the largest local error of the current epoch resulting from the executing module is returned. The local error is calculated according to the midpoint method E = abs(1 - (fullDelta / 2.0 * halfDelta)). Intuitively, applying the the delta for the current time step once results in the same result as if the delta for half the time step would be applied twice. This method calculates the difference between the full delta and twice the half delta. If the difference is large the error is large and vice versa.

Returns:

The calculated local error.

Throws:

NumericalInstabilityException - if any of the encountered errors is the result of an numerical instability.

calculateUpdates

public void calculateUpdates()

Specified by:

calculateUpdates in interface UpdateModule

optimizeTimeStep

public void optimizeTimeStep()

Specified by:

optimizeTimeStep in interface UpdateModule

resetState

public void resetState()

Specified by:

resetState in interface UpdateModule

addModuleToSimulation

protected void addModuleToSimulation()

References the module and referenced entities to the referenced simulation.

scaleScalableFeatures

public void scaleScalableFeatures()

Specified by:

scaleScalableFeatures in interface UpdateModule

getRequiredFeatures

public Set<Class<? extends Feature>> getRequiredFeatures()

Specified by:

getRequiredFeatures in interface UpdateModule

getScaledFeature

public <FeatureContentType extends javax.measure.Quantity<FeatureContentType>> javax.measure.Quantity<FeatureContentType> getScaledFeature(Class<? extends ScalableFeature<FeatureContentType>> featureClass)

Specified by:

getScaledFeature in interface UpdateModule

getScaledFeature

protected <FeatureContentType extends javax.measure.Quantity<FeatureContentType>> javax.measure.Quantity<FeatureContentType> getScaledFeature(ChemicalEntity entity,
                                                                                                                                              Class<? extends ScalableFeature<FeatureContentType>> featureClass)

Returns the requested feature of the given chemical entities, scaled according to the current time step and spatial scaling.

Type Parameters:

FeatureContentType - The resulting content type.

Parameters:

entity - The chemical entity.

featureClass - The requested feature.

Returns:

The scaled feature.

getFeature

public <FeatureType extends Feature> FeatureType getFeature(Class<FeatureType> featureTypeClass)

Returns the requested feature.

Type Parameters:

FeatureType - The resulting content type.

Parameters:

featureTypeClass - The requested feature.

Returns:

The requested feature.

setFeature

public void setFeature(Feature<?> feature)

Sets a feature.

Specified by:

setFeature in interface UpdateModule

Parameters:

feature - The feature.

getFeatures

public Collection<Feature<?>> getFeatures()

Returns all features of this module (not its entities).

Specified by:

getFeatures in interface UpdateModule

Returns:

all features of this module.

onReset

public void onReset()

Specified by:

onReset in interface UpdateModule

onCompletion

public void onCompletion()

Specified by:

onCompletion in interface UpdateModule

checkFeatures

public void checkFeatures()

Specified by:

checkFeatures in interface UpdateModule

toString

public String toString()

Overrides:

toString in class Object