CompuCell3D Namespace Reference

Classes
class	Automaton
class	CellType
class	CellTypeDynamicClassNode
class	CellTypeNode
class	Transition
class	Algorithm
class	AlgorithmFactory
class	Boundary
class	BoundaryFactory
class	BoundaryStrategy
class	LatticeMultiplicativeFactors
class	ChengbangAlgorithm
class	DefaultAlgorithm
class	NoFluxBoundary
class	PeriodicBoundary
class	ClassRegistry
class	AdjacentNeighbor
class	Array3D
class	Array3DField3DAdapter
class	Array3DBorders
class	Array3DBordersField3DAdapter
class	Array2DBorders
class	Array2DBordersField3DAdapter
class	Dim3D
class	Field3D
class	Field3DChangeWatcher
class	Field3DImpl
class	Field3DIndex
class	Neighbor
class	NeighborFinder
class	Point3D
class	WatchableField3D
class	ParseData
class	Parser
class	ParserStorage
class	Plugin
class	PluginBase
class	PluginManager
class	BoundaryData
class	NeighborSurfaceData
class	BoundaryTracker
class	CellBoundaryTracker
class	CellBoundaryTrackerPlugin
class	LambdaCellOrientation
class	CellOrientationPlugin
class	CellOrientationVector
class	CellTypeG
class	CellTypePlugin
class	CellInstantVelocityPlugin
class	CellVelocityData
class	CellVelocityPlugin
class	InstantCellVelocityData
class	CenterOfMassPlugin
class	ChemotaxisData
class	ChemotaxisFieldData
class	ChemotaxisPlugin
class	ChemotaxisDictyPlugin
class	ChemotaxisSimpleEnergy
class	ChickGrowthCondensingTransition
class	ChickGrowthNonCondensingTransition
class	ChickGrowthTypePlugin
class	ChickCondensingTransition
class	ChickNonCondensingTransition
class	ChickTypePlugin
class	CompartmentPlugin
class	Concentration
class	ConcentrationPlugin
class	ConnectivityPlugin
class	ConnectivityLocalFlexData
class	ConnectivityLocalFlexPlugin
class	ContactPlugin
class	ContactLocalFlexData
class	ContactLocalFlexDataContainer
class	ContactLocalFlexPlugin
class	ContactLocalProductData
class	ContactLocalProductPlugin
class	ContactMultiCadData
class	CadherinData
class	ContactMultiCadSpecificityCadherin
class	ContactMultiCadPlugin
class	ExternalPotentialParam
class	ExternalPotentialPlugin
class	GlobalBoundaryPixelTrackerPlugin
class	GrowthPlugin
class	LengthEnergyParam
class	LengthConstraintPlugin
class	LengthConstraintLocalFlexData
class	LengthConstraintLocalFlexPlugin
class	MitosisPlugin
class	MitosisSimplePlugin
class	CellMomentOfInertia
class	MomentOfInertiaPlugin
class	NeighborStickPlugin
class	NeighborTracker
class	NeighborTrackerPlugin
class	OrientedContactPlugin
class	SolverData
class	PDESolverCallerPlugin
class	BoundaryPixelTrackerData
class	BoundaryPixelTracker
class	BoundaryPixelTrackerPlugin
class	PixelTrackerData
class	PixelTracker
class	PixelTrackerPlugin
class	PlasticityPlugin
class	PlasticityTrackerData
class	PlasticityTracker
class	PlasticityTrackerPlugin
class	PlayerSettings
class	PlayerSettingsPlugin
class	PolarizationVector
class	PolarizationVectorPlugin
class	RealPlasticityPlugin
class	RealPlasticityTrackerData
class	RealPlasticityTracker
class	RealPlasticityTrackerPlugin
class	RearrangementPlugin
class	SimpleArray
class	SimpleArrayPlugin
class	SimpleClock
class	SimpleClockPlugin
class	StretchnessPlugin
class	SurfaceEnergyParam
class	SurfacePlugin
class	SurfaceTrackerPlugin
class	VelocityData
class	VelocityPlugin
class	ViscosityEnergy
class	ViscosityPlugin
class	VolumeEnergyParam
class	VolumePlugin
class	VolumeTrackerPlugin
class	AcceptanceFunction
class	AttributeAdder
class	CellG
class	Cell
class	CellPtr
class	CellChangeWatcher
class	CellGChangeWatcher
class	CellInventory
class	CellTypeMotilityData
class	DefaultAcceptanceFunction
class	EnergyFunction
class	EnergyFunctionCalculator
class	EnergyFunctionCalculatorStatistics
class	FirstOrderExpansionAcceptanceFunction
class	FixedStepper
class	Potts3D
class	Stepper
class	TypeChangeWatcher
class	TypeTransition
class	EnergyFunctionCalculatorParseData
class	EnergyFunctionCalculatorStatisticsParseData
class	PottsParseData
class	Serializer
class	SimObject
class	Simulator
class	SteerableObject
class	Steppable
class	BlobFieldInitializerData
class	EngulfmentData
class	BlobFieldInitializer
class	BoxWatcher
class	CellDiffusionDataOutput
class	CellVelocity
class	DictyChemotaxisSteppable
class	DictyFieldInitializer
class	FoamDataOutput
class	SecretionDataFlexAD
class	DiffusionSecretionADFieldTupple
class	AdvectionDiffusionSolverFE
class	SecretionOnContactData
class	UptakeData
class	SecretionData
class	CouplingData
class	DiffusionData
class	Diffusable
class	DiffusableGraph
class	DiffusableVector
class	DiffusableVector2D
class	SecretionDataFast
class	DiffusionSecretionFastFieldTupple
class	FastDiffusionSolver2DFE
class	FastDiffusionSolver2DSerializer
class	SecretionDataADE
class	DiffusionSecretionADEFieldTupple
class	FlexibleDiffusionSolverADE
class	FlexibleDiffusionSolverADESerializer
class	SecretionDataFlex
class	DiffusionSecretionFlexFieldTupple
class	FlexibleDiffusionSolverFE
class	FlexibleDiffusionSolverSerializer
class	SecretionDataKernel
class	DiffusionSecretionKernelFieldTupple
class	KernelDiffusionSolver
class	KernelDiffusionSolverSerializer
class	ReactionDiffusionSolverFE_SavHog
class	TestFlexibleDiffusionSolver
class	PIFDumper
class	PIFInitializer
class	UniformFieldInitializerData
class	UniformFieldInitializer
class	TestMainCC3D
class	FancyVolumePlugin
class	SimpleVolumePlugin
class	VolumeMean
class	ChangeWatcherPyWrapper
class	EnergyFunctionPyWrapper
class	NeighborFinderParams
class	PyAttributeAdder
class	PyCompuCellObjAdapter
class	PyPlugin
class	StepperPyWrapper
class	TypeChangeWatcherPyWrapper
Typedefs
typedef std::pair < Coordinates3D< float > , Coordinates3D< float > >	CenterOfMassPair_t
Enumerations
enum	HexOddEvenFlags {   Y_ODD = 1, Z_ODD = 2, X_ODD = 0, Y_EVEN = 0,   Z_EVEN = 0, X_EVEN = 0 }
enum	LatticeType { SQUARE_LATTICE = 1, HEXAGONAL_LATTICE = 2 }
Functions
template<class T>
std::ofstream &	operator<< (std::ofstream &, const Field3D< T > &)
template<class T>
std::ifstream &	operator>> (std::ifstream &, Field3D< T > &)
std::ostream &	operator<< (std::ostream &_scr, const Neighbor &_n)
std::ostream &	operator<< (std::ostream &stream, const Point3D &pt)
Point3D	operator+ (const Point3D pt1, const Point3D pt2)
Point3D	operator- (const Point3D pt1, const Point3D pt2)
std::string	operator+ (const std::string s, const Point3D pt)
std::ostream &	operator<< (std::ostream &out, CompuCell3D::DiffusionData &diffData)
Coordinates3D< double >	precalculateCentroid (const Point3D &pt, const CellG *_cell, int _volumeIncrement, const Point3D &fieldDim, BoundaryStrategy *boundaryStrategy)
double	distInvariantCM (double x0, double y0, double z0, double x1, double y1, double z1, const Point3D &fieldDim, BoundaryStrategy *boundaryStrategy)
Point3D	distanceVectorInvariant (const Point3D &_pt1, const Point3D &_pt0, const Point3D &_fieldDim)
CenterOfMassPair_t	precalculateAfterFlipCM (const Point3D &pt, const CellG *newCell, const CellG *oldCell, const Point3D &fieldDim, const Point3D &boundaryConditionIndicator)

---

Detailed Description

Author:

m This class will cache offsets of a given latice site that will lead to adjacent lattice points you will have to use getByOffset function from Field3D class to access lattice points Notice that offsets may be negative as well. getByIndex from Field3DImpl.h will return default value of the field element if the array index is out range (i.e negative or greater than internal field array len see Field3DImpl.h for the details). Example: let's say a given point has field array index 20. To access its adjacent neighbors you add 20+neighbor_offset and call getByIndex(20+neighbor_offset) adjFace2FaceNeighborOffsets stores offsets of a negihboring cells that touch a given cell face to face and not just by corner or edge

m

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Typedef Documentation

typedef std::pair<Coordinates3D<float>, Coordinates3D<float> > CompuCell3D::CenterOfMassPair_t

Definition at line 30 of file NumericalUtils.h.

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Enumeration Type Documentation

enum CompuCell3D::HexOddEvenFlags

Enumerator:

Y_ODD
Z_ODD
X_ODD
Y_EVEN
Z_EVEN
X_EVEN

Definition at line 58 of file BoundaryStrategy.h.

enum CompuCell3D::LatticeType

Enumerator:

SQUARE_LATTICE
HEXAGONAL_LATTICE

Definition at line 32 of file BoundaryTypeDefinitions.h.

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Function Documentation

Point3D CompuCell3D::distanceVectorInvariant	(	const Point3D &	_pt1,
		const Point3D &	_pt0,
		const Point3D &	_fieldDim
	)

Definition at line 331 of file NumericalUtils.cpp.

References CompuCell3D::Point3D::x, CompuCell3D::Point3D::y, and CompuCell3D::Point3D::z.

Referenced by CompuCell3D::CellOrientationPlugin::changeEnergy().

double CompuCell3D::distInvariantCM	(	double	x0,
		double	y0,
		double	z0,
		double	x1,
		double	y1,
		double	z1,
		const Point3D &	fieldDim,
		BoundaryStrategy *	boundaryStrategy
	)

Definition at line 207 of file NumericalUtils.cpp.

References CompuCell3D::BoundaryStrategy::calculatePointCoordinates(), dist(), Coordinates3D< T >::x, CompuCell3D::Point3D::x, Coordinates3D< T >::y, CompuCell3D::Point3D::y, Coordinates3D< T >::z, and CompuCell3D::Point3D::z.

Referenced by CompuCell3D::RealPlasticityPlugin::changeEnergy(), and CompuCell3D::PlasticityPlugin::changeEnergy().

std::string CompuCell3D::operator+	(	const std::string	s,
		const Point3D	pt
	)			[inline]

Overloads the operator std::string + Point3D.

Definition at line 135 of file Point3D.h.

References CompuCell3D::Point3D::x, CompuCell3D::Point3D::y, and CompuCell3D::Point3D::z.

Point3D CompuCell3D::operator+	(	const Point3D	pt1,
		const Point3D	pt2
	)			[inline]

Overloads the + operator for Point3D.

Definition at line 121 of file Point3D.h.

References CompuCell3D::Point3D::x, CompuCell3D::Point3D::y, and CompuCell3D::Point3D::z.

Point3D CompuCell3D::operator-	(	const Point3D	pt1,
		const Point3D	pt2
	)			[inline]

Overloads the - operator for Point3D.

Definition at line 128 of file Point3D.h.

References CompuCell3D::Point3D::x, CompuCell3D::Point3D::y, and CompuCell3D::Point3D::z.

std::ostream& CompuCell3D::operator<<	(	std::ostream &	out,
		CompuCell3D::DiffusionData &	diffData
	)			[inline]

Definition at line 204 of file DiffSecrData.h.

References CompuCell3D::DiffusionData::decayConst, CompuCell3D::DiffusionData::deltaT, CompuCell3D::DiffusionData::deltaX, CompuCell3D::DiffusionData::diffConst, and CompuCell3D::DiffusionData::fieldName.

std::ostream& CompuCell3D::operator<<	(	std::ostream &	stream,
		const Point3D &	pt
	)			[inline]

Print a Point3D to a std::ostream. The format is (x,y,z).

Definition at line 113 of file Point3D.h.

References CompuCell3D::Point3D::x, CompuCell3D::Point3D::y, and CompuCell3D::Point3D::z.

std::ostream& CompuCell3D::operator<<	(	std::ostream &	_scr,
		const Neighbor &	_n
	)			[inline]

Definition at line 48 of file Neighbor.h.

References CompuCell3D::Neighbor::distance, CompuCell3D::Neighbor::pt, and CompuCell3D::Neighbor::ptTrans.

template<class T>

std::ofstream & CompuCell3D::operator<<	(	std::ofstream &	stream,
		const Field3D< T > &	field
	)			[inline]

Generic operator for writing Field3D data in a platform independent way.

The format is as follows:

Bytes	Type	Description
2	char	Data type string.
1	char	Number of dimensions. Always 3.
4	uint32_t	X dimension.
4	uint32_t	Y dimension.
4	uint32_t	Z dimension.
X*Y*Z*sizeof(data type)	data type according to the type string	The field data

The predefined data type strings are as follows:

" i"	4 byte signed integer
"ui"	4 byte unsigned integer
" d"	8 byte double
" f"	4 byte float
" c"	1 byte signed character
"uc"	1 byte unsigned character
" l"	4 byte signed integer
"ul"	4 byte unsigned integer

If you what to write a field of a data type not listed in this table you must define const char Field3D<T>::typeStr[3] for that type somewhere in your code or you will get link errors.

All data is written in network byte order. (ie. Most significant byte first)

Long data types and pointers are different on 64 bit machines. Such data fields will be incompatable between 64 bit and 32 bit machines.

Parameters:

	stream	The output stream.
	field	The field to write.

Returns:

A reference to the passed stream.

Definition at line 90 of file Field3DIO.h.

References ASSERT_OR_THROW, TypeChangeWatcherExample::dim, CompuCell3D::Point3D::x, CompuCell3D::Point3D::y, and CompuCell3D::Point3D::z.

template<class T>

std::ifstream & CompuCell3D::operator>>	(	std::ifstream &	stream,
		Field3D< T > &	field
	)			[inline]

Generic operator for reading Field3D data in a platform independent way.

See std::ofstream &operator<<(std::ofstream &, Field3D<T> &)

Definition at line 124 of file Field3DIO.h.

References ASSERT_OR_THROW, CompuCell3D::Field3D< T >::getDim(), CompuCell3D::Field3D< T >::set(), CompuCell3D::Field3D< T >::typeStr, CompuCell3D::Point3D::x, CompuCell3D::Point3D::y, and CompuCell3D::Point3D::z.

CenterOfMassPair_t CompuCell3D::precalculateAfterFlipCM	(	const Point3D &	pt,
		const CellG *	newCell,
		const CellG *	oldCell,
		const Point3D &	fieldDim,
		const Point3D &	boundaryConditionIndicator
	)

Definition at line 379 of file NumericalUtils.cpp.

References CompuCell3D::CellG::volume, CompuCell3D::Point3D::x, CompuCell3D::CellG::xCM, Coordinates3D< T >::XRef(), CompuCell3D::Point3D::y, CompuCell3D::CellG::yCM, Coordinates3D< T >::YRef(), CompuCell3D::Point3D::z, CompuCell3D::CellG::zCM, and Coordinates3D< T >::ZRef().

Referenced by CompuCell3D::VelocityPlugin::changeEnergy().

Coordinates3D< double > CompuCell3D::precalculateCentroid	(	const Point3D &	pt,
		const CellG *	_cell,
		int	_volumeIncrement,
		const Point3D &	fieldDim,
		BoundaryStrategy *	boundaryStrategy
	)

Definition at line 45 of file NumericalUtils.cpp.

References CompuCell3D::BoundaryStrategy::calculatePointCoordinates(), CompuCell3D::CellG::volume, Coordinates3D< T >::x, CompuCell3D::Point3D::x, CompuCell3D::CellG::xCM, Coordinates3D< T >::y, CompuCell3D::Point3D::y, CompuCell3D::CellG::yCM, Coordinates3D< T >::z, CompuCell3D::Point3D::z, and CompuCell3D::CellG::zCM.

Referenced by CompuCell3D::RealPlasticityPlugin::changeEnergy(), and CompuCell3D::PlasticityPlugin::changeEnergy().