CompuCell3D::Potts3D Class Reference

#include <Potts3D.h>

Inheritance diagram for CompuCell3D::Potts3D:

[legend]

Collaboration diagram for CompuCell3D::Potts3D:

[legend]

List of all members.

Public Types
typedef unsigned int(Potts3D::*	metropolisFcnPtr_t )(const unsigned int, const double)
Public Member Functions
	Potts3D ()
	Potts3D (const Dim3D dim)
virtual	~Potts3D ()
void	createCellField (const Dim3D dim)
unsigned int	getCurrentAttempt ()
unsigned int	getNumberOfAttempts ()
unsigned int	getNumberOfAttemptedEnergyCalculations ()
unsigned int	getNumberOfAcceptedSpinFlips ()
std::set< Point3D > *	getBoundaryPixelSetPtr ()
LatticeType	getLatticeType ()
double	getDepth ()
void	setDepth (double _depth)
void	setNeighborOrder (unsigned int _neighborOrder)
void	initializeCellTypeMotility (std::vector< CellTypeMotilityData > &_cellTypeMotilityVector)
void	setCellTypeMotilityVec (std::vector< float > &_cellTypeMotilityVec)
const std::vector< float > &	getCellTypeMotilityVec ()
void	setDebugOutputFrequency (unsigned int _freq)
void	setSimulator (Simulator *_sim)
void	setFrozenTypeVector (std::vector< unsigned char > &_frozenTypeVec)
const std::vector< unsigned char > &	getFrozenTypeVector ()
Point3D	getFlipNeighbor ()
void	setBoundaryXName (std::string const &_xName)
void	setBoundaryYName (std::string const &_yName)
void	setBoundaryZName (std::string const &_zName)
std::string const &	getBoundaryXName () const
std::string const &	getBoundaryYName () const
std::string const &	getBoundaryZName () const
void	setMinCoordinates (Point3D _minCoord)
void	setMaxCoordinates (Point3D _maxCoord)
Point3D	getMinCoordinates () const
Point3D	getMaxCoordinates () const
TypeTransition *	getTypeTransition ()
virtual void	createEnergyFunction (std::string _energyFunctionType)
EnergyFunctionCalculator *	getEnergyFunctionCalculator ()
CellInventory &	getCellInventory ()
virtual void	registerAttributeAdder (AttributeAdder *_attrAdder)
virtual void	registerEnergyFunction (EnergyFunction *function)
	Add an energy function to the list.
virtual void	registerEnergyFunctionWithName (EnergyFunction *_function, std::string _functionName)
virtual void	unregisterEnergyFunction (std::string _functionName)
double	getNewNumber ()
virtual void	registerAutomaton (Automaton *autom)
	Add the automaton.
virtual Automaton *	getAutomaton ()
	Return the automaton for this simulation.
virtual void	registerAcceptanceFunction (AcceptanceFunction *function)
virtual void	setAcceptanceFunctionByName (std::string _acceptanceFunctionName)
virtual AcceptanceFunction *	getAcceptanceFunction ()
virtual void	registerCellGChangeWatcher (CellGChangeWatcher *_watcher)
	Add a cell field update watcher.
virtual void	registerClassAccessor (BasicClassAccessorBase *_accessor)
	Register accessor to a class with a cellGroupFactory. Accessor will access a class which is a mamber of a BasicClassGroup.
virtual void	registerStepper (Stepper *stepper)
	Add a potts stepper to be called after each potts step.
virtual void	registerFixedStepper (FixedStepper *fixedStepper)
double	getEnergy ()
virtual CellG *	createCellG (const Point3D pt)
virtual void	destroyCellG (CellG *cell, bool _removeFromInventory=true)
BasicClassGroupFactory *	getCellFactoryGroupPtr ()
virtual unsigned int	getNumCells ()
	dealocate a BasicClassGroup
virtual double	totalEnergy ()
virtual double	changeEnergy (Point3D pt, const CellG *newCell, const CellG *oldCell)
virtual unsigned int	metropolis (const unsigned int steps, const double temp)
unsigned int	metropolisList (const unsigned int steps, const double temp)
unsigned int	metropolisFast (const unsigned int steps, const double temp)
unsigned int	metropolisBoundaryWalker (const unsigned int steps, const double temp)
void	setMetropolisAlgorithm (std::string _algName)
virtual Field3D< CellG * > *	getCellFieldG ()
virtual Field3DImpl< CellG * > *	getCellFieldGImpl ()
virtual void	update (CC3DXMLElement *_xmlData, bool _fullInitFlag=false)
virtual std::string	steerableName ()
Public Attributes
metropolisFcnPtr_t	metropolisFcnPtr
Private Member Functions
bool	checkIfFrozen (unsigned char _type)
Private Attributes
WatchableField3D< CellG * > *	cellFieldG
	The potts field of cell spins.
AttributeAdder *	attrAdder
EnergyFunctionCalculator *	energyCalculator
BasicClassGroupFactory	cellFactoryGroup
	Cell class aggregator and allocator.
std::vector< EnergyFunction * >	energyFunctions
	An array of energy functions to be evaluated to determine energy costs.
std::map< std::string, EnergyFunction * >	nameToEnergyFuctionMap
std::set< Point3D >	boundaryPixelSet
TypeTransition *	typeTransition
std::vector< Stepper * >	steppers
	An array of potts steppers. These are called after each potts step.
std::vector< FixedStepper * >	fixedSteppers
Automaton *	automaton
	The automaton to use. Assuming one automaton per simulation.
DefaultAcceptanceFunction	defaultAcceptanceFunction
FirstOrderExpansionAcceptanceFunction	firstOrderExpansionAcceptanceFunction
AcceptanceFunction *	acceptanceFunction
	Used to determine the probablity that a pixel flip should be taken.
double	energy
	The current total energy of the system.
std::string	boundary_x
std::string	boundary_y
std::string	boundary_z
CellInventory	cellInventory
Point3D	flipNeighbor
double	depth
std::vector< Point3D >	neighbors
std::vector< unsigned char >	frozenTypeVec
unsigned int	sizeFrozenTypeVec
	lists types which will remain frozen throughout the simulation
long	recentlyCreatedCellId
unsigned int	currentAttempt
unsigned int	numberOfAttempts
unsigned int	maxNeighborIndex
unsigned int	debugOutputFrequency
Simulator *	sim
Point3D	minCoordinates
Point3D	maxCoordinates
unsigned int	attemptedEC
unsigned int	flips
std::vector< float >	cellTypeMotilityVec

---

Detailed Description

A generic implementation of the potts model in 3D.

See http://scienceworld.wolfram.com/physics/PottsModel.html for more information about the potts model.

Definition at line 87 of file Potts3D.h.

---

Member Typedef Documentation

typedef unsigned int(Potts3D::* CompuCell3D::Potts3D::metropolisFcnPtr_t)(const unsigned int, const double)

---

Constructor & Destructor Documentation

Potts3D::Potts3D

(

)

Definition at line 58 of file Potts3D.cpp.

References cellInventory, energyCalculator, frozenTypeVec, metropolisFast(), metropolisFcnPtr, neighbors, CompuCell3D::EnergyFunctionCalculator::setPotts(), CompuCell3D::CellInventory::setPotts3DPtr(), and typeTransition.

Potts3D::Potts3D

(

const Dim3D

dim

)

Definition at line 78 of file Potts3D.cpp.

References cellInventory, createCellField(), energyCalculator, frozenTypeVec, metropolisFast(), metropolisFcnPtr, neighbors, CompuCell3D::EnergyFunctionCalculator::setPotts(), CompuCell3D::CellInventory::setPotts3DPtr(), and typeTransition.

Potts3D::~Potts3D

(

)

[virtual]

Definition at line 102 of file Potts3D.cpp.

References cellFieldG, energyCalculator, and typeTransition.

---

Member Function Documentation

bool Potts3D::checkIfFrozen

(

unsigned char

_type

)

[private]

Definition at line 832 of file Potts3D.cpp.

References frozenTypeVec.

Referenced by metropolisBoundaryWalker(), metropolisFast(), and metropolisList().

void Potts3D::createCellField

(

const Dim3D

dim

)

Create the cell field.

Parameters:

dim

The field dimensions.

Definition at line 191 of file Potts3D.cpp.

References ASSERT_OR_THROW, and cellFieldG.

Referenced by CompuCell3D::Simulator::initializePottsCC3D(), and Potts3D().

unsigned int CompuCell3D::Potts3D::getCurrentAttempt

(

)

[inline]

Definition at line 165 of file Potts3D.h.

Referenced by CompuCell3D::PDESolverCallerPlugin::step().

unsigned int CompuCell3D::Potts3D::getNumberOfAttempts

(

)

[inline]

Definition at line 166 of file Potts3D.h.

Referenced by CompuCell3D::PDESolverCallerPlugin::step().

unsigned int CompuCell3D::Potts3D::getNumberOfAttemptedEnergyCalculations

(

)

[inline]

Definition at line 167 of file Potts3D.h.

unsigned int CompuCell3D::Potts3D::getNumberOfAcceptedSpinFlips

(

)

[inline]

Definition at line 168 of file Potts3D.h.

std::set<Point3D>* CompuCell3D::Potts3D::getBoundaryPixelSetPtr

(

)

[inline]

Definition at line 169 of file Potts3D.h.

Referenced by CompuCell3D::GlobalBoundaryPixelTrackerPlugin::update().

LatticeType Potts3D::getLatticeType

(

)

Definition at line 123 of file Potts3D.cpp.

References CompuCell3D::BoundaryStrategy::getInstance(), and CompuCell3D::BoundaryStrategy::getLatticeType().

Referenced by CompuCell3D::Simulator::initializePottsCC3D(), and CC3DTransaction::preStartInit().

double CompuCell3D::Potts3D::getDepth

(

)

[inline]

Definition at line 173 of file Potts3D.h.

void Potts3D::setDepth

(

double

_depth

)

Definition at line 127 of file Potts3D.cpp.

References cellFieldG, depth, TypeChangeWatcherExample::dim, CompuCell3D::BoundaryStrategy::getInstance(), CompuCell3D::BoundaryStrategy::getMaxDistance(), CompuCell3D::BoundaryStrategy::getMaxNeighborIndexFromDepth(), maxCoordinates, maxNeighborIndex, minCoordinates, neighbors, CompuCell3D::BoundaryStrategy::prepareNeighborLists(), CompuCell3D::Point3D::x, CompuCell3D::Point3D::y, and CompuCell3D::Point3D::z.

Referenced by CompuCell3D::Simulator::initializePottsCC3D(), and update().

void Potts3D::setNeighborOrder

(

unsigned int

_neighborOrder

)

Definition at line 177 of file Potts3D.cpp.

References cellFieldG, TypeChangeWatcherExample::dim, CompuCell3D::BoundaryStrategy::getInstance(), CompuCell3D::BoundaryStrategy::getMaxNeighborIndexFromNeighborOrder(), maxCoordinates, maxNeighborIndex, minCoordinates, neighbors, CompuCell3D::BoundaryStrategy::prepareNeighborListsBasedOnNeighborOrder(), CompuCell3D::Point3D::x, CompuCell3D::Point3D::y, and CompuCell3D::Point3D::z.

Referenced by CompuCell3D::Simulator::initializePottsCC3D(), and update().

void Potts3D::initializeCellTypeMotility

(

std::vector< CellTypeMotilityData > &

_cellTypeMotilityVector

)

Definition at line 803 of file Potts3D.cpp.

References ASSERT_OR_THROW, automaton, cellTypeMotilityVec, and CompuCell3D::Automaton::getTypeId().

Referenced by CompuCell3D::Simulator::initializeCC3D().

void Potts3D::setCellTypeMotilityVec

(

std::vector< float > &

_cellTypeMotilityVec

)

Definition at line 799 of file Potts3D.cpp.

References cellTypeMotilityVec.

const std::vector<float>& CompuCell3D::Potts3D::getCellTypeMotilityVec

(

)

[inline]

Definition at line 179 of file Potts3D.h.

void CompuCell3D::Potts3D::setDebugOutputFrequency

(

unsigned int

_freq

)

[inline]

Definition at line 181 of file Potts3D.h.

Referenced by CompuCell3D::Simulator::initializePottsCC3D(), and update().

void CompuCell3D::Potts3D::setSimulator

(

Simulator *

_sim

)

[inline]

Definition at line 182 of file Potts3D.h.

Referenced by CompuCell3D::Simulator::Simulator().

void Potts3D::setFrozenTypeVector

(

std::vector< unsigned char > &

_frozenTypeVec

)

Definition at line 844 of file Potts3D.cpp.

References frozenTypeVec, and sizeFrozenTypeVec.

Referenced by CompuCell3D::CellTypePlugin::update().

const std::vector<unsigned char>& CompuCell3D::Potts3D::getFrozenTypeVector

(

)

[inline]

Definition at line 185 of file Potts3D.h.

Referenced by CompuCell3D::BoxWatcher::extraInit().

Point3D CompuCell3D::Potts3D::getFlipNeighbor

(

)

[inline]

Definition at line 187 of file Potts3D.h.

Referenced by CompuCell3D::EnergyFunctionPyWrapper::changeEnergy(), CompuCell3D::ChemotaxisDictyPlugin::changeEnergy(), CompuCell3D::CellOrientationPlugin::changeEnergy(), CompuCell3D::ExternalPotentialPlugin::changeEnergyByCellId(), CompuCell3D::ExternalPotentialPlugin::changeEnergyByCellType(), CompuCell3D::ExternalPotentialPlugin::changeEnergyGlobal(), CompuCell3D::ChemotaxisPlugin::merksChemotaxis(), and CompuCell3D::ChemotaxisPlugin::regularChemotaxis().

void CompuCell3D::Potts3D::setBoundaryXName

(

std::string const &

_xName

)

[inline]

Definition at line 189 of file Potts3D.h.

Referenced by CompuCell3D::Simulator::initializePottsCC3D().

void CompuCell3D::Potts3D::setBoundaryYName

(

std::string const &

_yName

)

[inline]

Definition at line 190 of file Potts3D.h.

Referenced by CompuCell3D::Simulator::initializePottsCC3D().

void CompuCell3D::Potts3D::setBoundaryZName

(

std::string const &

_zName

)

[inline]

Definition at line 191 of file Potts3D.h.

Referenced by CompuCell3D::Simulator::initializePottsCC3D().

std::string const& CompuCell3D::Potts3D::getBoundaryXName

(

)

const [inline]

Definition at line 192 of file Potts3D.h.

Referenced by CompuCell3D::CellVelocity::extraInit(), CompuCell3D::FlexibleDiffusionSolverFE::init(), CompuCell3D::FlexibleDiffusionSolverADE::init(), CompuCell3D::FastDiffusionSolver2DFE::init(), CompuCell3D::VelocityPlugin::init(), CompuCell3D::NeighborTrackerPlugin::init(), CompuCell3D::MomentOfInertiaPlugin::init(), CompuCell3D::ExternalPotentialPlugin::init(), CompuCell3D::CenterOfMassPlugin::init(), CompuCell3D::CellInstantVelocityPlugin::init(), CompuCell3D::CellBoundaryTrackerPlugin::init(), and CompuCell3D::ViscosityEnergy::initializeViscosityEnergy().

std::string const& CompuCell3D::Potts3D::getBoundaryYName

(

)

const [inline]

Definition at line 193 of file Potts3D.h.

Referenced by CompuCell3D::CellVelocity::extraInit(), CompuCell3D::FlexibleDiffusionSolverFE::init(), CompuCell3D::FlexibleDiffusionSolverADE::init(), CompuCell3D::FastDiffusionSolver2DFE::init(), CompuCell3D::VelocityPlugin::init(), CompuCell3D::NeighborTrackerPlugin::init(), CompuCell3D::MomentOfInertiaPlugin::init(), CompuCell3D::ExternalPotentialPlugin::init(), CompuCell3D::CenterOfMassPlugin::init(), CompuCell3D::CellInstantVelocityPlugin::init(), CompuCell3D::CellBoundaryTrackerPlugin::init(), and CompuCell3D::ViscosityEnergy::initializeViscosityEnergy().

std::string const& CompuCell3D::Potts3D::getBoundaryZName

(

)

const [inline]

Definition at line 194 of file Potts3D.h.

Referenced by CompuCell3D::CellVelocity::extraInit(), CompuCell3D::FlexibleDiffusionSolverFE::init(), CompuCell3D::FlexibleDiffusionSolverADE::init(), CompuCell3D::FastDiffusionSolver2DFE::init(), CompuCell3D::VelocityPlugin::init(), CompuCell3D::NeighborTrackerPlugin::init(), CompuCell3D::MomentOfInertiaPlugin::init(), CompuCell3D::ExternalPotentialPlugin::init(), CompuCell3D::CenterOfMassPlugin::init(), CompuCell3D::CellInstantVelocityPlugin::init(), CompuCell3D::CellBoundaryTrackerPlugin::init(), and CompuCell3D::ViscosityEnergy::initializeViscosityEnergy().

void CompuCell3D::Potts3D::setMinCoordinates

(

Point3D

_minCoord

)

[inline]

Definition at line 196 of file Potts3D.h.

Referenced by CompuCell3D::BoxWatcher::adjustBox().

void CompuCell3D::Potts3D::setMaxCoordinates

(

Point3D

_maxCoord

)

[inline]

Definition at line 197 of file Potts3D.h.

Referenced by CompuCell3D::BoxWatcher::adjustBox().

Point3D CompuCell3D::Potts3D::getMinCoordinates

(

)

const [inline]

Definition at line 198 of file Potts3D.h.

Point3D CompuCell3D::Potts3D::getMaxCoordinates

(

)

const [inline]

Definition at line 199 of file Potts3D.h.

TypeTransition* CompuCell3D::Potts3D::getTypeTransition

(

)

[inline]

Definition at line 200 of file Potts3D.h.

Referenced by CompuCell3D::PIFInitializer::start().

void Potts3D::createEnergyFunction

(

std::string

_energyFunctionType

)

[virtual]

Definition at line 109 of file Potts3D.cpp.

References energyCalculator, and CompuCell3D::EnergyFunctionCalculator::setPotts().

Referenced by CompuCell3D::Simulator::initializePottsCC3D().

EnergyFunctionCalculator* CompuCell3D::Potts3D::getEnergyFunctionCalculator

(

)

[inline]

Definition at line 203 of file Potts3D.h.

Referenced by CompuCell3D::Simulator::initializePottsCC3D().

CellInventory& CompuCell3D::Potts3D::getCellInventory

(

)

[inline]

Definition at line 205 of file Potts3D.h.

Referenced by CompuCell3D::ReactionDiffusionSolverFE_SavHog::init(), CompuCell3D::KernelDiffusionSolver::init(), CompuCell3D::FlexibleDiffusionSolverFE::init(), CompuCell3D::FlexibleDiffusionSolverADE::init(), CompuCell3D::FastDiffusionSolver2DFE::init(), CompuCell3D::AdvectionDiffusionSolverFE::init(), CompuCell3D::FoamDataOutput::init(), CompuCell3D::DictyChemotaxisSteppable::init(), CompuCell3D::CellVelocity::init(), CompuCell3D::CellDiffusionDataOutput::init(), CompuCell3D::SimpleArrayPlugin::init(), CompuCell3D::RealPlasticityTrackerPlugin::init(), CompuCell3D::PlasticityTrackerPlugin::init(), CompuCell3D::NeighborTrackerPlugin::init(), CompuCell3D::UniformFieldInitializer::initializeCellTypes(), CompuCell3D::DictyFieldInitializer::initializeCellTypes(), CompuCell3D::BlobFieldInitializer::initializeCellTypesCellSort(), CompuCell3D::ContactLocalFlexPlugin::initializeContactLocalFlexData(), CompuCell3D::BlobFieldInitializer::initializeEngulfment(), CompuCell3D::VolumeMean::step(), and CompuCell3D::Simulator::step().

void Potts3D::registerAttributeAdder

(

AttributeAdder *

_attrAdder

)

[virtual]

Definition at line 199 of file Potts3D.cpp.

References attrAdder.

void Potts3D::registerEnergyFunction

(

EnergyFunction *

function

)

[virtual]

Add an energy function to the list.

Definition at line 210 of file Potts3D.cpp.

References energyCalculator, CompuCell3D::EnergyFunctionCalculator::registerEnergyFunctionWithName(), and CompuCell3D::EnergyFunction::toString().

Referenced by CompuCell3D::ViscosityPlugin::init(), CompuCell3D::ContactLocalFlexPlugin::init(), and CompuCell3D::ConnectivityPlugin::init().

void Potts3D::registerEnergyFunctionWithName	(	EnergyFunction *	_function,
		std::string	_functionName
	)			[virtual]

Definition at line 217 of file Potts3D.cpp.

References energyCalculator, and CompuCell3D::EnergyFunctionCalculator::registerEnergyFunctionWithName().

Referenced by CompuCell3D::VelocityPlugin::extraInit(), CompuCell3D::SimpleVolumePlugin::init(), CompuCell3D::FancyVolumePlugin::init(), CompuCell3D::VolumePlugin::init(), CompuCell3D::SurfacePlugin::init(), CompuCell3D::StretchnessPlugin::init(), CompuCell3D::RearrangementPlugin::init(), CompuCell3D::RealPlasticityPlugin::init(), CompuCell3D::PlasticityPlugin::init(), CompuCell3D::OrientedContactPlugin::init(), CompuCell3D::NeighborStickPlugin::init(), CompuCell3D::LengthConstraintLocalFlexPlugin::init(), CompuCell3D::LengthConstraintPlugin::init(), CompuCell3D::ExternalPotentialPlugin::init(), CompuCell3D::ContactMultiCadPlugin::init(), CompuCell3D::ContactLocalProductPlugin::init(), CompuCell3D::ContactPlugin::init(), CompuCell3D::ConnectivityLocalFlexPlugin::init(), CompuCell3D::CompartmentPlugin::init(), CompuCell3D::ChemotaxisDictyPlugin::init(), CompuCell3D::ChemotaxisPlugin::init(), and CompuCell3D::CellOrientationPlugin::init().

void Potts3D::unregisterEnergyFunction

(

std::string

_functionName

)

[virtual]

Definition at line 225 of file Potts3D.cpp.

References energyCalculator, and CompuCell3D::EnergyFunctionCalculator::unregisterEnergyFunction().

double CompuCell3D::Potts3D::getNewNumber

(

)

[inline]

Definition at line 214 of file Potts3D.h.

void Potts3D::registerAutomaton

(

Automaton *

autom

)

[virtual]

Add the automaton.

Definition at line 207 of file Potts3D.cpp.

References automaton.

Referenced by CompuCell3D::ChickTypePlugin::init(), CompuCell3D::ChickGrowthTypePlugin::init(), and CompuCell3D::CellTypePlugin::init().

Automaton * Potts3D::getAutomaton

(

)

[virtual]

Return the automaton for this simulation.

Definition at line 208 of file Potts3D.cpp.

References automaton.

Referenced by CompuCell3D::RealPlasticityTrackerPlugin::extraInit(), CompuCell3D::PlasticityTrackerPlugin::extraInit(), CompuCell3D::ReactionDiffusionSolverFE_SavHog::init(), CompuCell3D::KernelDiffusionSolver::init(), CompuCell3D::FlexibleDiffusionSolverFE::init(), CompuCell3D::FlexibleDiffusionSolverADE::init(), CompuCell3D::FastDiffusionSolver2DFE::init(), CompuCell3D::AdvectionDiffusionSolverFE::init(), CompuCell3D::DictyFieldInitializer::init(), CompuCell3D::UniformFieldInitializer::initCellType(), CompuCell3D::BlobFieldInitializer::initCellType(), CompuCell3D::LengthConstraintPlugin::initTypeId(), CompuCell3D::ViscosityEnergy::readXML(), CompuCell3D::PIFInitializer::start(), CompuCell3D::VolumePlugin::update(), CompuCell3D::SurfacePlugin::update(), CompuCell3D::OrientedContactPlugin::update(), CompuCell3D::NeighborStickPlugin::update(), CompuCell3D::ExternalPotentialPlugin::update(), CompuCell3D::ContactMultiCadPlugin::update(), CompuCell3D::ContactLocalProductPlugin::update(), CompuCell3D::ContactLocalFlexPlugin::update(), CompuCell3D::ContactPlugin::update(), CompuCell3D::CompartmentPlugin::update(), and CompuCell3D::ChemotaxisPlugin::update().

void Potts3D::registerAcceptanceFunction

(

AcceptanceFunction *

function

)

[virtual]

Set the acceptance function. This is DefaultAcceptanceFunction by default.

Definition at line 245 of file Potts3D.cpp.

References acceptanceFunction, and ASSERT_OR_THROW.

void Potts3D::setAcceptanceFunctionByName

(

std::string

_acceptanceFunctionName

)

[virtual]

Definition at line 235 of file Potts3D.cpp.

References acceptanceFunction, defaultAcceptanceFunction, and firstOrderExpansionAcceptanceFunction.

Referenced by CompuCell3D::Simulator::initializePottsCC3D().

virtual AcceptanceFunction* CompuCell3D::Potts3D::getAcceptanceFunction

(

)

[inline, virtual]

Definition at line 229 of file Potts3D.h.

Referenced by CompuCell3D::Simulator::initializePottsCC3D(), and update().

void Potts3D::registerCellGChangeWatcher

(

CellGChangeWatcher *

_watcher

)

[virtual]

Add a cell field update watcher.

BasicClassChange watcher reistration.

registration of the BCG watcher

Definition at line 254 of file Potts3D.cpp.

References ASSERT_OR_THROW, and cellFieldG.

Referenced by CompuCell3D::VelocityPlugin::extraInit(), CompuCell3D::CellInstantVelocityPlugin::extraInit(), CompuCell3D::VolumeTrackerPlugin::init(), CompuCell3D::SurfaceTrackerPlugin::init(), CompuCell3D::RealPlasticityTrackerPlugin::init(), CompuCell3D::PlasticityTrackerPlugin::init(), CompuCell3D::PixelTrackerPlugin::init(), CompuCell3D::BoundaryPixelTrackerPlugin::init(), CompuCell3D::NeighborTrackerPlugin::init(), CompuCell3D::MomentOfInertiaPlugin::init(), CompuCell3D::MitosisPlugin::init(), CompuCell3D::LengthConstraintLocalFlexPlugin::init(), CompuCell3D::LengthConstraintPlugin::init(), CompuCell3D::GrowthPlugin::init(), CompuCell3D::GlobalBoundaryPixelTrackerPlugin::init(), CompuCell3D::ContactLocalFlexPlugin::init(), CompuCell3D::ConcentrationPlugin::init(), CompuCell3D::ChickTypePlugin::init(), CompuCell3D::ChickGrowthTypePlugin::init(), CompuCell3D::CenterOfMassPlugin::init(), CompuCell3D::CellTypePlugin::init(), and CompuCell3D::CellBoundaryTrackerPlugin::init().

void Potts3D::registerClassAccessor

(

BasicClassAccessorBase *

_accessor

)

[virtual]

Register accessor to a class with a cellGroupFactory. Accessor will access a class which is a mamber of a BasicClassGroup.

Definition at line 262 of file Potts3D.cpp.

References ASSERT_OR_THROW, cellFactoryGroup, and BasicClassGroupFactory::registerClass().

void Potts3D::registerStepper

(

Stepper *

stepper

)

[virtual]

Add a potts stepper to be called after each potts step.

Definition at line 269 of file Potts3D.cpp.

References ASSERT_OR_THROW, and steppers.

Referenced by CompuCell3D::VolumeTrackerPlugin::init(), CompuCell3D::MitosisPlugin::init(), CompuCell3D::GrowthPlugin::init(), and CompuCell3D::ConcentrationPlugin::init().

void Potts3D::registerFixedStepper

(

FixedStepper *

fixedStepper

)

[virtual]

Definition at line 275 of file Potts3D.cpp.

References ASSERT_OR_THROW, and fixedSteppers.

Referenced by CompuCell3D::PDESolverCallerPlugin::init().

double Potts3D::getEnergy

(

)

Returns:

Current energy.

Definition at line 233 of file Potts3D.cpp.

References energy.

Referenced by CompuCell3D::Simulator::start(), and CompuCell3D::Simulator::step().

CellG * Potts3D::createCellG

(

const Point3D

pt

)

[virtual]

Allocate a cell.

Parameters:

pt

The point in the cell field to put the new cell.

Returns:

The newly created cell.

Definition at line 283 of file Potts3D.cpp.

References CompuCell3D::AttributeAdder::addAttribute(), CompuCell3D::CellInventory::addToInventory(), ASSERT_OR_THROW, attrAdder, cellFactoryGroup, cellFieldG, cellInventory, BasicClassGroupFactory::create(), and recentlyCreatedCellId.

Referenced by CompuCell3D::MitosisPlugin::doMitosis(), CompuCell3D::UniformFieldInitializer::layOutCells(), CompuCell3D::BlobFieldInitializer::layOutCells(), CompuCell3D::PIFInitializer::start(), and CompuCell3D::DictyFieldInitializer::start().

void Potts3D::destroyCellG	(	CellG *	cell,
		bool	_removeFromInventory = true
	)			[virtual]

Definition at line 299 of file Potts3D.cpp.

References attrAdder, cellFactoryGroup, cellInventory, BasicClassGroupFactory::destroy(), CompuCell3D::AttributeAdder::destroyAttribute(), CompuCell3D::CellG::extraAttribPtr, CompuCell3D::CellG::pyAttrib, and CompuCell3D::CellInventory::removeFromInventory().

Referenced by CompuCell3D::VolumeTrackerPlugin::step(), and CompuCell3D::CellInventory::~CellInventory().

BasicClassGroupFactory* CompuCell3D::Potts3D::getCellFactoryGroupPtr

(

)

[inline]

Definition at line 265 of file Potts3D.h.

Referenced by CompuCell3D::VelocityPlugin::extraInit(), CompuCell3D::CellVelocityPlugin::extraInit(), CompuCell3D::SimpleClockPlugin::init(), CompuCell3D::SimpleArrayPlugin::init(), CompuCell3D::RealPlasticityTrackerPlugin::init(), CompuCell3D::PolarizationVectorPlugin::init(), CompuCell3D::PlasticityTrackerPlugin::init(), CompuCell3D::PixelTrackerPlugin::init(), CompuCell3D::BoundaryPixelTrackerPlugin::init(), CompuCell3D::NeighborTrackerPlugin::init(), CompuCell3D::LengthConstraintLocalFlexPlugin::init(), CompuCell3D::ContactMultiCadPlugin::init(), CompuCell3D::ContactLocalProductPlugin::init(), CompuCell3D::ContactLocalFlexPlugin::init(), CompuCell3D::ConnectivityLocalFlexPlugin::init(), CompuCell3D::ConcentrationPlugin::init(), CompuCell3D::CellOrientationPlugin::init(), and CompuCell3D::CellBoundaryTrackerPlugin::init().

virtual unsigned int CompuCell3D::Potts3D::getNumCells

(

)

[inline, virtual]

dealocate a BasicClassGroup

Deallocate a cell.

Parameters:

cell

The cell to destroy.

Returns:

The current number of cells in the field.

Definition at line 279 of file Potts3D.h.

Referenced by CompuCell3D::Simulator::start(), and CompuCell3D::Simulator::step().

double Potts3D::totalEnergy

(

)

[virtual]

Returns:

The current size in bytes of a cell. Calculate the current total energy of the system.

The freshly calculated energy.

Definition at line 321 of file Potts3D.cpp.

References cellFieldG, TypeChangeWatcherExample::dim, energy, energyFunctions, CompuCell3D::Point3D::x, CompuCell3D::Point3D::y, and CompuCell3D::Point3D::z.

double Potts3D::changeEnergy	(	Point3D	pt,
		const CellG *	newCell,
		const CellG *	oldCell
	)			[virtual]

Calculate the energy change of a proposed flip.

Parameters:

	pt	The point to flip.
	newCell	The new spin.
	oldCell	The old spin.

Returns:

The energy change.

Definition at line 337 of file Potts3D.cpp.

References energyFunctions.

unsigned int Potts3D::metropolis	(	const unsigned int	steps,
		const double	temp
	)			[virtual]

Run the potts metropolis algorithm.

Parameters:

	steps	The numer of flip attempts to make.
	temp	The current temperature.

Returns:

The total number of accepted flips.

Definition at line 347 of file Potts3D.cpp.

References metropolisFcnPtr.

Referenced by CompuCell3D::Simulator::step().

unsigned int Potts3D::metropolisList	(	const unsigned int	steps,
		const double	temp
	)

Dim3D dim = cellField->getDim();

Cell *cell = cellField->get(pt);

must also make sure that cell ptr is different 0; Will never freeze medium

must also make sure that cell ptr is different 0; Will never freeze medium

change takes place at change pixel and pt is a neighbor of changePixel

cout<<"This is change: "<<change<<endl;

Definition at line 351 of file Potts3D.cpp.

References CompuCell3D::AcceptanceFunction::accept(), acceptanceFunction, ASSERT_OR_THROW, attemptedEC, cellFieldG, cellTypeMotilityVec, CompuCell3D::EnergyFunctionCalculator::changeEnergy(), checkIfFrozen(),