CompuCell3D::ChemotaxisDictyPlugin Class Reference

#include <ChemotaxisDictyPlugin.h>

Inheritance diagram for CompuCell3D::ChemotaxisDictyPlugin:

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Collaboration diagram for CompuCell3D::ChemotaxisDictyPlugin:

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List of all members.

Public Member Functions
	ChemotaxisDictyPlugin ()
virtual	~ChemotaxisDictyPlugin ()
virtual void	init (Simulator *simulator, CC3DXMLElement *_xmlData=0)
virtual void	extraInit (Simulator *_simulator)
	will initialize chemotactic field here - need to deffer this after all steppables which contain field had been pre-initialzied
virtual void	field3DChange (const Point3D &pt, CellG *newCell, CellG *oldCell)
	CellChangeWatcher interface.
virtual void	step ()
virtual double	changeEnergy (const Point3D &pt, const CellG *newCell, const CellG *oldCell)
virtual void	update (CC3DXMLElement *_xmlData, bool _fullInitFlag=false)
virtual std::string	steerableName ()
virtual std::string	toString ()
double	getConcentration (const Point3D &pt)
double	getLambda ()
Field3D< float > *	getField ()
void	initializeField ()
Private Attributes
Simulator *	sim
Field3D< float > *	concentrationField
Field3DImpl< float > *	field
Potts3D *	potts
BasicClassAccessor< SimpleClock > *	simpleClockAccessorPtr
double	lambda
std::string	chemicalFieldSource
std::string	chemicalFieldName
bool	chemotax
bool	gotChemicalField
std::vector< unsigned char >	nonChemotacticTypeVector
CC3DXMLElement *	xmlData

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Detailed Description

Definition at line 56 of file ChemotaxisDictyPlugin.h.

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Constructor & Destructor Documentation

ChemotaxisDictyPlugin::ChemotaxisDictyPlugin

(

)

Definition at line 56 of file ChemotaxisDictyPlugin.cpp.

ChemotaxisDictyPlugin::~ChemotaxisDictyPlugin

(

)

[virtual]

Definition at line 59 of file ChemotaxisDictyPlugin.cpp.

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Member Function Documentation

void ChemotaxisDictyPlugin::init	(	Simulator *	simulator,
		CC3DXMLElement *	_xmlData = 0
	)			[virtual]

Reimplemented from CompuCell3D::SimObject.

Definition at line 64 of file ChemotaxisDictyPlugin.cpp.

References CompuCell3D::Simulator::getPotts(), CompuCell3D::SimpleClockPlugin::getSimpleClockAccessorPtr(), CompuCell3D::SimpleClockPlugin::init(), CompuCell3D::SimObject::init(), SimpleVolumeCallFromPython::plugin, CompuCell3D::Simulator::pluginManager, potts, CompuCell3D::Potts3D::registerEnergyFunctionWithName(), CompuCell3D::Simulator::registerSteerableObject(), sim, simpleClockAccessorPtr, and xmlData.

void ChemotaxisDictyPlugin::extraInit

(

Simulator *

_simulator

)

[virtual]

will initialize chemotactic field here - need to deffer this after all steppables which contain field had been pre-initialzied

Reimplemented from CompuCell3D::SimObject.

Definition at line 94 of file ChemotaxisDictyPlugin.cpp.

References update(), and xmlData.

void ChemotaxisDictyPlugin::field3DChange	(	const Point3D &	pt,
		CellG *	newCell,
		CellG *	oldCell
	)			[virtual]

CellChangeWatcher interface.

in medium we assume concentration 0

Definition at line 103 of file ChemotaxisDictyPlugin.cpp.

References concentrationField, and CompuCell3D::Field3D< T >::set().

virtual void CompuCell3D::ChemotaxisDictyPlugin::step

(

)

[inline, virtual]

Definition at line 92 of file ChemotaxisDictyPlugin.h.

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

Parameters:

	pt	The point of change.
	newCell	The new spin.

Returns:

The energy change of changing point pt to newCell.

Reimplemented from CompuCell3D::EnergyFunction.

Definition at line 127 of file ChemotaxisDictyPlugin.cpp.

References CompuCell3D::CellG::extraAttribPtr, field, CompuCell3D::Field3DImpl< T >::get(), CompuCell3D::Potts3D::getFlipNeighbor(), gotChemicalField, lambda, potts, and simpleClockAccessorPtr.

void ChemotaxisDictyPlugin::update	(	CC3DXMLElement *	_xmlData,
		bool	_fullInitFlag = false
	)			[virtual]

Reimplemented from CompuCell3D::SteerableObject.

Definition at line 113 of file ChemotaxisDictyPlugin.cpp.

References chemicalFieldName, chemicalFieldSource, CC3DXMLElement::findElement(), CC3DXMLElement::getAttribute(), CC3DXMLElement::getByte(), CC3DXMLElement::getDouble(), CC3DXMLElement::getFirstElement(), CC3DXMLElement::getText(), initializeField(), lambda, and nonChemotacticTypeVector.

Referenced by extraInit().

std::string ChemotaxisDictyPlugin::steerableName

(

)

[virtual]

Reimplemented from CompuCell3D::SteerableObject.

Definition at line 261 of file ChemotaxisDictyPlugin.cpp.

References toString().

std::string ChemotaxisDictyPlugin::toString

(

)

[virtual]

Reimplemented from CompuCell3D::Plugin.

Definition at line 255 of file ChemotaxisDictyPlugin.cpp.

Referenced by steerableName().

double ChemotaxisDictyPlugin::getConcentration

(

const Point3D &

pt

)

Definition at line 230 of file ChemotaxisDictyPlugin.cpp.

References ASSERT_OR_THROW, field, and CompuCell3D::Field3DImpl< T >::get().

double CompuCell3D::ChemotaxisDictyPlugin::getLambda

(

)

[inline]

Definition at line 111 of file ChemotaxisDictyPlugin.h.

Field3D<float>* CompuCell3D::ChemotaxisDictyPlugin::getField

(

)

[inline]

Definition at line 114 of file ChemotaxisDictyPlugin.h.

void ChemotaxisDictyPlugin::initializeField

(

)

this is only temporary solution will have to come up with something better

Definition at line 235 of file ChemotaxisDictyPlugin.cpp.

References ASSERT_OR_THROW, chemicalFieldName, chemicalFieldSource, field, CompuCell3D::Simulator::getClassRegistry(), CompuCell3D::ClassRegistry::getStepper(), gotChemicalField, and sim.

Referenced by update().

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Member Data Documentation

Simulator* CompuCell3D::ChemotaxisDictyPlugin::sim [private]

Definition at line 58 of file ChemotaxisDictyPlugin.h.

Referenced by init(), and initializeField().

Field3D<float>* CompuCell3D::ChemotaxisDictyPlugin::concentrationField [private]

Definition at line 59 of file ChemotaxisDictyPlugin.h.

Referenced by field3DChange().

Field3DImpl<float>* CompuCell3D::ChemotaxisDictyPlugin::field [private]

Definition at line 61 of file ChemotaxisDictyPlugin.h.

Referenced by changeEnergy(), getConcentration(), and initializeField().

Potts3D* CompuCell3D::ChemotaxisDictyPlugin::potts [private]

Definition at line 64 of file ChemotaxisDictyPlugin.h.

Referenced by changeEnergy(), and init().

BasicClassAccessor<SimpleClock>* CompuCell3D::ChemotaxisDictyPlugin::simpleClockAccessorPtr [private]

Definition at line 65 of file ChemotaxisDictyPlugin.h.

Referenced by changeEnergy(), and init().

double CompuCell3D::ChemotaxisDictyPlugin::lambda [private]

Definition at line 67 of file ChemotaxisDictyPlugin.h.

Referenced by changeEnergy(), and update().

std::string CompuCell3D::ChemotaxisDictyPlugin::chemicalFieldSource [private]

Definition at line 69 of file ChemotaxisDictyPlugin.h.

Referenced by initializeField(), and update().

std::string CompuCell3D::ChemotaxisDictyPlugin::chemicalFieldName [private]

Definition at line 70 of file ChemotaxisDictyPlugin.h.

Referenced by initializeField(), and update().

bool CompuCell3D::ChemotaxisDictyPlugin::chemotax [private]

Definition at line 71 of file ChemotaxisDictyPlugin.h.

bool CompuCell3D::ChemotaxisDictyPlugin::gotChemicalField [private]

Definition at line 72 of file ChemotaxisDictyPlugin.h.

Referenced by changeEnergy(), and initializeField().

std::vector<unsigned char> CompuCell3D::ChemotaxisDictyPlugin::nonChemotacticTypeVector [private]

Definition at line 74 of file ChemotaxisDictyPlugin.h.

Referenced by update().

CC3DXMLElement* CompuCell3D::ChemotaxisDictyPlugin::xmlData [private]

Definition at line 75 of file ChemotaxisDictyPlugin.h.

Referenced by extraInit(), and init().

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The documentation for this class was generated from the following files:

• CompuCell/DOXYGEN/core/CompuCell3D/plugins/ChemotaxisDicty/ChemotaxisDictyPlugin.h
• CompuCell/DOXYGEN/core/CompuCell3D/plugins/ChemotaxisDicty/ChemotaxisDictyPlugin.cpp