CompuCell3D::ContactLocalFlexPlugin Class Reference

#include <ContactLocalFlexPlugin.h>

Inheritance diagram for CompuCell3D::ContactLocalFlexPlugin:

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Collaboration diagram for CompuCell3D::ContactLocalFlexPlugin:

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List of all members.

Public Member Functions

 ContactLocalFlexPlugin ()
virtual ~ContactLocalFlexPlugin ()
BasicClassAccessor
< ContactLocalFlexDataContainer > * 		getContactDataContainerAccessorPtr ()
void initializeContactLocalFlexData ()
virtual void field3DChange (const Point3D &pt, CellG *newCell, CellG *oldCell)
virtual double changeEnergy (const Point3D &pt, const CellG *newCell, const CellG *oldCell)
virtual void init (Simulator *simulator, CC3DXMLElement *_xmlData=0)
virtual void extraInit (Simulator *simulator)
virtual std::string toString ()
virtual void update (CC3DXMLElement *_xmlData, bool _fullInitFlag=false)
virtual std::string steerableName ()
double contactEnergy (const CellG *cell1, const CellG *cell2)
double defaultContactEnergy (const CellG *cell1, const CellG *cell2)
void setContactEnergy (const std::string typeName1, const std::string typeName2, const double energy)

Protected Member Functions

int getIndex (const int type1, const int type2) const

Private Types

typedef std::map< int, double > contactEnergies_t
typedef std::vector
< std::vector< double > > 		contactEnergyArray_t

Private Member Functions

void updateContactEnergyData (CellG *_cell)

Private Attributes

BasicClassAccessor
< ContactLocalFlexDataContainer > 		contactDataContainerAccessor
Potts3D * potts
Simulator * sim
bool initializadContactData
contactEnergies_t contactEnergies
contactEnergyArray_t contactEnergyArray
std::string autoName
double depth
Automaton * automaton
bool weightDistance
unsigned int maxNeighborIndex
BoundaryStrategy * boundaryStrategy
CC3DXMLElement * xmlData

Detailed Description

Definition at line 54 of file ContactLocalFlexPlugin.h.

Member Typedef Documentation

typedef std::map<int, double> CompuCell3D::ContactLocalFlexPlugin::contactEnergies_t [private]

Definition at line 65 of file ContactLocalFlexPlugin.h.

typedef std::vector<std::vector<double> > CompuCell3D::ContactLocalFlexPlugin::contactEnergyArray_t [private]

Definition at line 66 of file ContactLocalFlexPlugin.h.

Constructor & Destructor Documentation

ContactLocalFlexPlugin::ContactLocalFlexPlugin (  ) 

Definition at line 50 of file ContactLocalFlexPlugin.cpp.

References initializadContactData.

ContactLocalFlexPlugin::~ContactLocalFlexPlugin (  )  [virtual]

Definition at line 54 of file ContactLocalFlexPlugin.cpp.

Member Function Documentation

void ContactLocalFlexPlugin::updateContactEnergyData ( CellG *  _cell  )  [private]

Definition at line 230 of file ContactLocalFlexPlugin.cpp.

References CompuCell3D::NeighborTracker::cellNeighbors, contactDataContainerAccessor, defaultContactEnergy(), CompuCell3D::CellG::extraAttribPtr, BasicClassAccessor< T >::get(), CompuCell3D::NeighborTrackerPlugin::getNeighborTrackerAccessorPtr(), CompuCell3D::ContactLocalFlexData::J, CompuCell3D::NeighborSurfaceData::neighborAddress, CompuCell3D::ContactLocalFlexData::neighborAddress, and CompuCell3D::Simulator::pluginManager.

Referenced by field3DChange(), and initializeContactLocalFlexData().

BasicClassAccessor<ContactLocalFlexDataContainer>* CompuCell3D::ContactLocalFlexPlugin::getContactDataContainerAccessorPtr (  )  [inline]

Definition at line 86 of file ContactLocalFlexPlugin.h.

void ContactLocalFlexPlugin::initializeContactLocalFlexData (  ) 

Definition at line 207 of file ContactLocalFlexPlugin.cpp.

References CompuCell3D::CellInventory::cellInventoryBegin(), CompuCell3D::CellInventory::cellInventoryEnd(), contactDataContainerAccessor, contactEnergyArray, CompuCell3D::CellG::extraAttribPtr, CompuCell3D::Potts3D::getCellInventory(), CompuCell3D::ContactLocalFlexDataContainer::localDefaultContactEnergies, potts, and updateContactEnergyData().

Referenced by field3DChange().

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

Definition at line 289 of file ContactLocalFlexPlugin.cpp.

References CompuCell3D::Simulator::getStep(), initializadContactData, initializeContactLocalFlexData(), sim, and updateContactEnergyData().

double ContactLocalFlexPlugin::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 81 of file ContactLocalFlexPlugin.cpp.

References boundaryStrategy, contactEnergy(), CompuCell3D::Neighbor::distance, CompuCell3D::Field3DImpl< T >::get(), CompuCell3D::Potts3D::getCellFieldG(), CompuCell3D::BoundaryStrategy::getNeighborDirect(), maxNeighborIndex, potts, CompuCell3D::Neighbor::pt, and weightDistance.

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

Reimplemented from CompuCell3D::SimObject.

Definition at line 58 of file ContactLocalFlexPlugin.cpp.

References contactDataContainerAccessor, CompuCell3D::Potts3D::getCellFactoryGroupPtr(), CompuCell3D::Simulator::getPotts(), CompuCell3D::SimObject::init(), SimpleVolumeCallFromPython::plugin, CompuCell3D::Simulator::pluginManager, potts, CompuCell3D::Potts3D::registerCellGChangeWatcher(), BasicClassGroupFactory::registerClass(), CompuCell3D::Potts3D::registerEnergyFunction(), CompuCell3D::Simulator::registerSteerableObject(), sim, and xmlData.

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

Reimplemented from CompuCell3D::SimObject.

Definition at line 77 of file ContactLocalFlexPlugin.cpp.

References update(), and xmlData.

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

Reimplemented from CompuCell3D::Plugin.

Definition at line 375 of file ContactLocalFlexPlugin.cpp.

Referenced by steerableName().

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

Reimplemented from CompuCell3D::SteerableObject.

Definition at line 305 of file ContactLocalFlexPlugin.cpp.

References ASSERT_OR_THROW, automaton, boundaryStrategy, contactEnergies, contactEnergyArray, CompuCell3D::Potts3D::getAutomaton(), CC3DXMLElement::getDouble(), CC3DXMLElement::getElements(), CC3DXMLElement::getFirstElement(), getIndex(), CompuCell3D::BoundaryStrategy::getInstance(), CompuCell3D::BoundaryStrategy::getMaxNeighborIndexFromDepth(), CompuCell3D::BoundaryStrategy::getMaxNeighborIndexFromNeighborOrder(), CompuCell3D::Automaton::getTypeId(), CC3DXMLElement::getUInt(), maxNeighborIndex, potts, and setContactEnergy().

Referenced by extraInit().

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

Reimplemented from CompuCell3D::SteerableObject.

Definition at line 380 of file ContactLocalFlexPlugin.cpp.

References toString().

double ContactLocalFlexPlugin::contactEnergy ( const CellG *  cell1,
const CellG *  cell2 
)

Returns:
The contact energy between cell1 and cell2.

Definition at line 168 of file ContactLocalFlexPlugin.cpp.

References contactDataContainerAccessor, defaultContactEnergy(), CompuCell3D::CellG::extraAttribPtr, and CompuCell3D::ContactLocalFlexData::neighborAddress.

Referenced by changeEnergy().

double ContactLocalFlexPlugin::defaultContactEnergy ( const CellG *  cell1,
const CellG *  cell2 
)

Definition at line 198 of file ContactLocalFlexPlugin.cpp.

References contactEnergyArray, and CompuCell3D::CellG::type.

Referenced by contactEnergy(), and updateContactEnergyData().

void CompuCell3D::ContactLocalFlexPlugin::setContactEnergy ( const std::string  typeName1,
const std::string  typeName2,
const double  energy 
)

Sets the contact energy for two cell types. A -1 type is interpreted as the medium.

Referenced by update().

int ContactLocalFlexPlugin::getIndex ( const int  type1,
const int  type2 
) const [protected]

Returns:
The index used for ordering contact energies in the map.

Definition at line 161 of file ContactLocalFlexPlugin.cpp.

Referenced by update().

Member Data Documentation

BasicClassAccessor<ContactLocalFlexDataContainer> CompuCell3D::ContactLocalFlexPlugin::contactDataContainerAccessor [private]

Definition at line 56 of file ContactLocalFlexPlugin.h.

Referenced by contactEnergy(), init(), initializeContactLocalFlexData(), and updateContactEnergyData().

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

Definition at line 57 of file ContactLocalFlexPlugin.h.

Referenced by changeEnergy(), init(), initializeContactLocalFlexData(), and update().

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

Definition at line 58 of file ContactLocalFlexPlugin.h.

Referenced by field3DChange(), and init().

bool CompuCell3D::ContactLocalFlexPlugin::initializadContactData [private]

Definition at line 60 of file ContactLocalFlexPlugin.h.

Referenced by ContactLocalFlexPlugin(), and field3DChange().

contactEnergies_t CompuCell3D::ContactLocalFlexPlugin::contactEnergies [private]

Definition at line 68 of file ContactLocalFlexPlugin.h.

Referenced by update().

contactEnergyArray_t CompuCell3D::ContactLocalFlexPlugin::contactEnergyArray [private]

Definition at line 70 of file ContactLocalFlexPlugin.h.

Referenced by defaultContactEnergy(), initializeContactLocalFlexData(), and update().

std::string CompuCell3D::ContactLocalFlexPlugin::autoName [private]

Definition at line 72 of file ContactLocalFlexPlugin.h.

double CompuCell3D::ContactLocalFlexPlugin::depth [private]

Definition at line 73 of file ContactLocalFlexPlugin.h.

Automaton* CompuCell3D::ContactLocalFlexPlugin::automaton [private]

Definition at line 75 of file ContactLocalFlexPlugin.h.

Referenced by update().

bool CompuCell3D::ContactLocalFlexPlugin::weightDistance [private]

Definition at line 76 of file ContactLocalFlexPlugin.h.

Referenced by changeEnergy().

unsigned int CompuCell3D::ContactLocalFlexPlugin::maxNeighborIndex [private]

Definition at line 78 of file ContactLocalFlexPlugin.h.

Referenced by changeEnergy(), and update().

BoundaryStrategy* CompuCell3D::ContactLocalFlexPlugin::boundaryStrategy [private]

Definition at line 79 of file ContactLocalFlexPlugin.h.

Referenced by changeEnergy(), and update().

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

Definition at line 80 of file ContactLocalFlexPlugin.h.

Referenced by extraInit(), and init().

The documentation for this class was generated from the following files:
Generated on Thu Dec 4 11:42:18 2008 for CompuCell3D by  doxygen 1.5.6