CompuCell3D::AdvectionDiffusionSolverFE Class Reference

void CompuCell3D::AdvectionDiffusionSolverFE::scrarch2Concentration	(	std::map< CellG , float >	scratchField,
		std::map< CellG , float >	concentrationField
	)			`[protected]`

Referenced by diffuseSingleField().

void AdvectionDiffusionSolverFE::cellMap2Field	(	std::map< CellG , float >	concentrationMapField,
		ConcentrationField_t *	concentrationField
	)			`[protected]`

Definition at line 236 of file AdevectionDiffusionSolverFE.cpp.

References cellFieldG, CompuCell3D::Array3DBorders< T >::getContainer(), workFieldDim, CompuCell3D::Point3D::x, CompuCell3D::Point3D::y, and CompuCell3D::Point3D::z.

Referenced by diffuseSingleField(), initializeConcentration(), and step().

void AdvectionDiffusionSolverFE::field2CellMap	(	ConcentrationField_t *	concentrationField,
		std::map< CellG , float >	concentrationMapField
	)			`[protected]`

Definition at line 265 of file AdevectionDiffusionSolverFE.cpp.

References cellFieldG, CompuCell3D::Array3DBorders< T >::getContainer(), workFieldDim, CompuCell3D::Point3D::x, CompuCell3D::Point3D::y, and CompuCell3D::Point3D::z.

Referenced by initializeConcentration().

void AdvectionDiffusionSolverFE::readConcentrationField	(	std::string	fileName,
		ConcentrationField_t *	concentrationField
	)			`[protected]`

Definition at line 217 of file AdevectionDiffusionSolverFE.cpp.

References ASSERT_OR_THROW, and CompuCell3D::Array3DBordersField3DAdapter< T >::set().

Referenced by initializeConcentration().

void AdvectionDiffusionSolverFE::initializeConcentration ( ) [protected]

Definition at line 200 of file AdevectionDiffusionSolverFE.cpp.

References cellMap2Field(), CompuCell3D::DiffusableGraph< float >::concentrationFieldMapVector, CompuCell3D::DiffusableVector< float >::concentrationFieldVector, diffDataVec, diffSecrFieldTuppleVec, field2CellMap(), and readConcentrationField().

Referenced by start().

double AdvectionDiffusionSolverFE::computeAverageCellRadius ( ) [protected]

Definition at line 124 of file AdevectionDiffusionSolverFE.cpp.

References CompuCell3D::CellInventory::cellInventoryBegin(), CompuCell3D::CellInventory::cellInventoryEnd(), cellInventoryPtr, and CompuCell3D::CellG::volume.

Referenced by diffuse().

void AdvectionDiffusionSolverFE::update ( ) [protected]

Definition at line 144 of file AdevectionDiffusionSolverFE.cpp.

References diffDataVec, and updateLocalCellInventory().

Referenced by init(), start(), and step().

void AdvectionDiffusionSolverFE::updateLocalCellInventory ( unsigned int idx ) [protected]

Definition at line 153 of file AdevectionDiffusionSolverFE.cpp.

References CompuCell3D::CellInventory::cellInventoryBegin(), CompuCell3D::CellInventory::cellInventoryEnd(), cellInventoryPtr, CompuCell3D::DiffusableGraph< float >::concentrationFieldMapVector, and CompuCell3D::CellInventory::find().

Referenced by update().

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

getting cell inventory

getting field ptr from Potts3D

setting member function pointers

allocate fields including scrartch field

assign vector of field names

assigning member method ptrs to the vector

Reimplemented from CompuCell3D::SimObject.

Definition at line 45 of file AdevectionDiffusionSolverFE.cpp.

References CompuCell3D::DiffusableGraph< float >::allocateDiffusableFieldVector(), automaton, cellFieldG, cellInventoryPtr, CompuCell3D::DiffusableVector< float >::concentrationFieldNameVector, CompuCell3D::DiffusableVector< float >::concentrationFieldVector, diffDataVec, diffSecrFieldTuppleVec, diffuse(), diffusePtr, fieldDim, CompuCell3D::Potts3D::getAutomaton(), CompuCell3D::Potts3D::getCellFieldG(), CompuCell3D::Potts3D::getCellInventory(), CompuCell3D::NeighborTrackerPlugin::getNeighborTrackerAccessorPtr(), CompuCell3D::Simulator::getPotts(), neighborTrackerAccessorPtr, numberOfFields, CompuCell3D::Simulator::pluginManager, potts, CompuCell3D::Simulator::registerConcentrationField(), secrete(), secreteOnContactSingleField(), secretePtr, secreteSingleField(), simPtr, update(), workFieldDim, CompuCell3D::Point3D::x, CompuCell3D::Point3D::y, and CompuCell3D::Point3D::z.

void AdvectionDiffusionSolverFE::extraInit ( Simulator * simulator ) [virtual]

Reimplemented from CompuCell3D::SimObject.

Definition at line 119 of file AdevectionDiffusionSolverFE.cpp.

void AdvectionDiffusionSolverFE::start ( ) [virtual]

Implements CompuCell3D::Steppable.

Definition at line 189 of file AdevectionDiffusionSolverFE.cpp.

References initializeConcentration(), and update().

void AdvectionDiffusionSolverFE::step ( const unsigned int _currentStep ) [virtual]

Implements CompuCell3D::Steppable.

Definition at line 301 of file AdevectionDiffusionSolverFE.cpp.

References cellMap2Field(), CompuCell3D::DiffusableGraph< float >::concentrationFieldMapVector, CompuCell3D::DiffusableVector< float >::concentrationFieldVector, currentStep, diffusePtr, secretePtr, and update().

virtual void CompuCell3D::AdvectionDiffusionSolverFE::finish ( ) [inline, virtual]

Implements CompuCell3D::Steppable.

Definition at line 135 of file AdvectionDiffusionSolverFE.h.

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

Reimplemented from CompuCell3D::SteerableObject.

Definition at line 550 of file AdevectionDiffusionSolverFE.cpp.

References diffSecrFieldTuppleVec, CC3DXMLElement::getElements(), CompuCell3D::SecretionData::update(), and CompuCell3D::DiffusionData::update().

std::string AdvectionDiffusionSolverFE::steerableName ( ) [virtual]

Reimplemented from CompuCell3D::SteerableObject.

Definition at line 585 of file AdevectionDiffusionSolverFE.cpp.

References toString().

std::string AdvectionDiffusionSolverFE::toString ( ) [virtual]

Reimplemented from CompuCell3D::Steppable.

Definition at line 580 of file AdevectionDiffusionSolverFE.cpp.

Referenced by steerableName().

Member Data Documentation

Potts3D* CompuCell3D::AdvectionDiffusionSolverFE::potts [protected]

Definition at line 77 of file AdvectionDiffusionSolverFE.h.

Referenced by init().

Simulator* CompuCell3D::AdvectionDiffusionSolverFE::simPtr [protected]

Definition at line 78 of file AdvectionDiffusionSolverFE.h.

Referenced by init().

unsigned int CompuCell3D::AdvectionDiffusionSolverFE::currentStep [protected]

Definition at line 80 of file AdvectionDiffusionSolverFE.h.

Referenced by step().

unsigned int CompuCell3D::AdvectionDiffusionSolverFE::maxDiffusionZ [protected]

Definition at line 81 of file AdvectionDiffusionSolverFE.h.

float CompuCell3D::AdvectionDiffusionSolverFE::averageRadius [protected]

Definition at line 82 of file AdvectionDiffusionSolverFE.h.

Referenced by diffuse(), and diffuseSingleField().

WatchableField3D<CellG *>* CompuCell3D::AdvectionDiffusionSolverFE::cellFieldG [protected]

Definition at line 84 of file AdvectionDiffusionSolverFE.h.

Referenced by cellMap2Field(), field2CellMap(), and init().

Automaton* CompuCell3D::AdvectionDiffusionSolverFE::automaton [protected]

Definition at line 85 of file AdvectionDiffusionSolverFE.h.

Referenced by init(), and secreteSingleField().

std::vector<DiffusionData> CompuCell3D::AdvectionDiffusionSolverFE::diffDataVec [protected]

Definition at line 87 of file AdvectionDiffusionSolverFE.h.

Referenced by diffuseSingleField(), init(), initializeConcentration(), and update().

std::vector<SecretionDataFlexAD> CompuCell3D::AdvectionDiffusionSolverFE::secrDataVec [protected]

Definition at line 88 of file AdvectionDiffusionSolverFE.h.

CellInventory* CompuCell3D::AdvectionDiffusionSolverFE::cellInventoryPtr [protected]

Definition at line 91 of file AdvectionDiffusionSolverFE.h.

Referenced by computeAverageCellRadius(), init(), secreteOnContactSingleField(), secreteSingleField(), and updateLocalCellInventory().

void(AdvectionDiffusionSolverFE::* CompuCell3D::AdvectionDiffusionSolverFE::diffusePtr)(void) [protected]

Referenced by init(), and step().

void(AdvectionDiffusionSolverFE::* CompuCell3D::AdvectionDiffusionSolverFE::secretePtr)(void) [protected]

ptr to member method - Forward Euler diffusion solver

Referenced by init(), and step().

unsigned int CompuCell3D::AdvectionDiffusionSolverFE::numberOfFields [protected]

Definition at line 108 of file AdvectionDiffusionSolverFE.h.

Referenced by init().

Dim3D CompuCell3D::AdvectionDiffusionSolverFE::fieldDim [protected]

Definition at line 109 of file AdvectionDiffusionSolverFE.h.

Referenced by init().

Dim3D CompuCell3D::AdvectionDiffusionSolverFE::workFieldDim [protected]

Definition at line 110 of file AdvectionDiffusionSolverFE.h.

Referenced by cellMap2Field(), field2CellMap(), and init().

std::vector<DiffusionSecretionADFieldTupple> CompuCell3D::AdvectionDiffusionSolverFE::diffSecrFieldTuppleVec [protected]

Definition at line 112 of file AdvectionDiffusionSolverFE.h.

Referenced by diffuse(), diffuseSingleField(), init(), initializeConcentration(), secrete(), secreteOnContactSingleField(), secreteSingleField(), and update().

BasicClassAccessor<NeighborTracker>* CompuCell3D::AdvectionDiffusionSolverFE::neighborTrackerAccessorPtr [protected]

Definition at line 121 of file AdvectionDiffusionSolverFE.h.

Referenced by diffuseSingleField(), init(), and secreteOnContactSingleField().

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

CompuCell/DOXYGEN/core/CompuCell3D/steppables/PDESolvers/AdvectionDiffusionSolverFE.h
CompuCell/DOXYGEN/core/CompuCell3D/steppables/PDESolvers/AdevectionDiffusionSolverFE.cpp


Public Types
typedef void(AdvectionDiffusionSolverFE::*	diffSecrFcnPtr_t )(void)
typedef void(AdvectionDiffusionSolverFE::*	secrSingleFieldFcnPtr_t )(unsigned int)
typedef float	precision_t
typedef Array3DBorders < precision_t >::ContainerType	Array3D_t
typedef Array3DBordersField3DAdapter < precision_t >	ConcentrationField_t
Public Member Functions
	AdvectionDiffusionSolverFE ()
virtual	~AdvectionDiffusionSolverFE ()
virtual void	init (Simulator simulator, CC3DXMLElement _xmlData=0)
virtual void	extraInit (Simulator *simulator)
virtual void	start ()
virtual void	step (const unsigned int _currentStep)
virtual void	finish ()
virtual void	update (CC3DXMLElement *_xmlData, bool _fullInitFlag=false)
virtual std::string	steerableName ()
virtual std::string	toString ()
Protected Member Functions
void	diffuse ()
	ptr to member method - Forward Euler diffusion solver
void	diffuseSingleField (unsigned int idx)
void	secrete ()
void	secreteSingleField (unsigned int idx)
void	secreteOnContactSingleField (unsigned int idx)
void	scrarch2Concentration (std::map< CellG , float > scratchField, std::map< CellG , float > concentrationField)
void	cellMap2Field (std::map< CellG , float > concentrationMapField, ConcentrationField_t *concentrationField)
void	field2CellMap (ConcentrationField_t concentrationField, std::map< CellG , float > *concentrationMapField)
void	readConcentrationField (std::string fileName, ConcentrationField_t *concentrationField)
void	initializeConcentration ()
double	computeAverageCellRadius ()
void	update ()
void	updateLocalCellInventory (unsigned int idx)
Protected Attributes
Potts3D *	potts
Simulator *	simPtr
unsigned int	currentStep
unsigned int	maxDiffusionZ
float	averageRadius
WatchableField3D< CellG * > *	cellFieldG
Automaton *	automaton
std::vector< DiffusionData >	diffDataVec
std::vector< SecretionDataFlexAD >	secrDataVec
CellInventory *	cellInventoryPtr
void(AdvectionDiffusionSolverFE::*	diffusePtr )(void)
void(AdvectionDiffusionSolverFE::*	secretePtr )(void)
	ptr to member method - Forward Euler diffusion solver
unsigned int	numberOfFields
Dim3D	fieldDim
Dim3D	workFieldDim
std::vector < DiffusionSecretionADFieldTupple >	diffSecrFieldTuppleVec
BasicClassAccessor < NeighborTracker > *	neighborTrackerAccessorPtr