Chaste  Build::
Owen11CaUpdateRule< DIM > Class Template Reference

#include <Owen11CaUpdateRule.hpp>

+ Inheritance diagram for Owen11CaUpdateRule< DIM >:
+ Collaboration diagram for Owen11CaUpdateRule< DIM >:

Public Member Functions

 Owen11CaUpdateRule ()
 
 ~Owen11CaUpdateRule ()
 
double EvaluateProbability (unsigned currentNodeIndex, unsigned targetNodeIndex, CaBasedCellPopulation< DIM > &rCellPopulation, double dt, double deltaX, CellPtr cell)
 
units::quantity< unit::diffusivity > GetDiffusionParameter ()
 
void SetVesselNetwork (boost::shared_ptr< VesselNetwork< DIM > > pVesselNetwork)
 
void SetRegularGrid (boost::shared_ptr< RegularGrid< DIM > > pRegularGrid)
 
void SetReferenceLengthScale (units::quantity< unit::length > referenceLengthScale)
 
void SetDiffusionParameter (units::quantity< unit::diffusivity > diffusionParameter)
 
void OutputUpdateRuleParameters (out_stream &rParamsFile)
 
template<>
double EvaluateProbability (unsigned currentNodeIndex, unsigned targetNodeIndex, CaBasedCellPopulation< 1 > &rCellPopulation, double dt, double deltaX, CellPtr pCell)
 

Private Member Functions

template<class Archive >
void serialize (Archive &archive, const unsigned int version)
 

Private Attributes

units::quantity< unit::diffusivity > mDiffusionParameter
 
boost::shared_ptr< VesselNetwork< DIM > > mpVesselNetwork
 
boost::shared_ptr< RegularGrid< DIM > > mpRegularGrid
 
units::quantity< unit::length > mReferenceLengthScale
 
unsigned mCancerCellCarryingCapacity
 

Friends

class TestCaUpdateRules
 
class boost::serialization::access
 

Detailed Description

template<unsigned DIM>
class Owen11CaUpdateRule< DIM >

A diffusion update rule based loosely on Owen et al. 2001. Vessels are treated differently to the paper, as they have their own sprouting and migration rules. However they can occupy space.

The probability of moving to an adjacent lattice site is

D*delta_t*((Nm-N)Nm)/(2*delta_xy)

Where D is the mDiffusionParameter. delta_t is the timestep. delta_xy is the separation of the two lattice sites. Nm is the carrying capacity for the cell type N is the number of cells at the lattice site

In this manifestation only cancer cells diffuse.

Definition at line 65 of file Owen11CaUpdateRule.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
Owen11CaUpdateRule< DIM >::Owen11CaUpdateRule ( )

Constructor.

Definition at line 43 of file Owen11CaUpdateRule.cpp.

Referenced by Owen11CaUpdateRule< DIM >::serialize().

template<unsigned DIM>
Owen11CaUpdateRule< DIM >::~Owen11CaUpdateRule ( )

Destructor.

Definition at line 55 of file Owen11CaUpdateRule.cpp.

Referenced by Owen11CaUpdateRule< DIM >::serialize().

Member Function Documentation

template<>
double Owen11CaUpdateRule< 1 >::EvaluateProbability ( unsigned  currentNodeIndex,
unsigned  targetNodeIndex,
CaBasedCellPopulation< 1 > &  rCellPopulation,
double  dt,
double  deltaX,
CellPtr  pCell 
)

Specialization to allow used with 1D classes

Parameters
currentNodeIndexthe current index
targetNodeIndexthe target index
rCellPopulationthe cell population
dtthe time increment
deltaXthe grid spacing
pCellthe cell
Returns
the movement probability

Definition at line 113 of file Owen11CaUpdateRule.cpp.

template<unsigned DIM>
double Owen11CaUpdateRule< DIM >::EvaluateProbability ( unsigned  currentNodeIndex,
unsigned  targetNodeIndex,
CaBasedCellPopulation< DIM > &  rCellPopulation,
double  dt,
double  deltaX,
CellPtr  cell 
)

Calculate the probability of a given move.

Uses random diffusion to each neighbouring node, scaled according to distance.

Parameters
currentNodeIndexThe index of the current node/lattice site
targetNodeIndexThe index of the target node/lattice site
rCellPopulationThe cell population
dtis the time interval
deltaXdefines the size of the lattice site
cella pointer to the cell (needed if more than one cell per lattice site
Returns
The probability of the cell moving from the current node to the target node

Definition at line 60 of file Owen11CaUpdateRule.cpp.

References BaseUnits::GetReferenceTimeScale(), BaseUnits::Instance(), Owen11CaUpdateRule< DIM >::mCancerCellCarryingCapacity, Owen11CaUpdateRule< DIM >::mDiffusionParameter, Owen11CaUpdateRule< DIM >::mpRegularGrid, Owen11CaUpdateRule< DIM >::mpVesselNetwork, and Owen11CaUpdateRule< DIM >::mReferenceLengthScale.

Referenced by Owen11CaUpdateRule< DIM >::serialize().

template<unsigned DIM>
units::quantity< unit::diffusivity > Owen11CaUpdateRule< DIM >::GetDiffusionParameter ( )
Returns
mDiffusionParameter

Definition at line 142 of file Owen11CaUpdateRule.cpp.

References Owen11CaUpdateRule< DIM >::mDiffusionParameter.

Referenced by Owen11CaUpdateRule< DIM >::serialize().

template<unsigned DIM>
void Owen11CaUpdateRule< DIM >::OutputUpdateRuleParameters ( out_stream &  rParamsFile)

Overridden OutputUpdateRuleParameters() method.

Parameters
rParamsFilethe file stream to which the parameters are output

Definition at line 154 of file Owen11CaUpdateRule.cpp.

References Owen11CaUpdateRule< DIM >::mDiffusionParameter.

Referenced by Owen11CaUpdateRule< DIM >::serialize().

template<unsigned DIM>
void Owen11CaUpdateRule< DIM >::SetDiffusionParameter ( units::quantity< unit::diffusivity >  diffusionParameter)

Set mDiffusionParameter.

Parameters
diffusionParameterthe new value of mDiffusionParameter

Definition at line 148 of file Owen11CaUpdateRule.cpp.

References Owen11CaUpdateRule< DIM >::mDiffusionParameter.

Referenced by Owen11CaUpdateRule< DIM >::serialize().

template<unsigned DIM>
void Owen11CaUpdateRule< DIM >::SetReferenceLengthScale ( units::quantity< unit::length >  referenceLengthScale)

Set the reference length scale

Parameters
referenceLengthScalethe reference length scale

Definition at line 130 of file Owen11CaUpdateRule.cpp.

References Owen11CaUpdateRule< DIM >::mReferenceLengthScale.

Referenced by Owen11CaUpdateRule< DIM >::serialize().

template<unsigned DIM>
void Owen11CaUpdateRule< DIM >::SetRegularGrid ( boost::shared_ptr< RegularGrid< DIM > >  pRegularGrid)

Set the regular grid

Parameters
pRegularGridThe regular grid

Definition at line 136 of file Owen11CaUpdateRule.cpp.

References Owen11CaUpdateRule< DIM >::mpRegularGrid.

Referenced by Owen11CaUpdateRule< DIM >::serialize().

template<unsigned DIM>
void Owen11CaUpdateRule< DIM >::SetVesselNetwork ( boost::shared_ptr< VesselNetwork< DIM > >  pVesselNetwork)

Set the vessel network

Parameters
pVesselNetworkThe vessel network

Definition at line 124 of file Owen11CaUpdateRule.cpp.

References Owen11CaUpdateRule< DIM >::mpVesselNetwork.

Referenced by Owen11CaUpdateRule< DIM >::serialize().

Member Data Documentation

template<unsigned DIM>
unsigned Owen11CaUpdateRule< DIM >::mCancerCellCarryingCapacity
private

Cancer cell carrying capacity

Definition at line 94 of file Owen11CaUpdateRule.hpp.

Referenced by Owen11CaUpdateRule< DIM >::EvaluateProbability(), and Owen11CaUpdateRule< DIM >::serialize().

template<unsigned DIM>
units::quantity<unit::diffusivity> Owen11CaUpdateRule< DIM >::mDiffusionParameter
private
template<unsigned DIM>
boost::shared_ptr<RegularGrid<DIM> > Owen11CaUpdateRule< DIM >::mpRegularGrid
private
template<unsigned DIM>
boost::shared_ptr<VesselNetwork<DIM> > Owen11CaUpdateRule< DIM >::mpVesselNetwork
private
template<unsigned DIM>
units::quantity<unit::length> Owen11CaUpdateRule< DIM >::mReferenceLengthScale
private

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