#include <MichaelisMentenSteadyStateDiffusionReactionPde.hpp>

Inheritance diagram for MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	MichaelisMentenSteadyStateDiffusionReactionPde ()

virtual	~MichaelisMentenSteadyStateDiffusionReactionPde ()

double	ComputeConstantInUSourceTerm (const ChastePoint< SPACE_DIM > &rX, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

units::quantity< unit::concentration_flow_rate >	ComputeConstantInUSourceTerm (unsigned gridIndex=0)

c_matrix< double, SPACE_DIM, SPACE_DIM >	ComputeDiffusionTerm (const ChastePoint< SPACE_DIM > &rX, double u)

c_matrix< double, SPACE_DIM, SPACE_DIM >	ComputeDiffusionTermPrime (const ChastePoint< SPACE_DIM > &rX, double u)

double	ComputeLinearSourceTerm (const ChastePoint< SPACE_DIM > &rX)

double	ComputeLinearInUCoeffInSourceTerm (const ChastePoint< SPACE_DIM > &rX, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

virtual units::quantity< unit::rate >	ComputeLinearInUCoeffInSourceTerm (unsigned gridIndex=0)

double	ComputeNonlinearSourceTerm (const ChastePoint< SPACE_DIM > &rX, double u)

units::quantity< unit::concentration_flow_rate >	ComputeNonlinearSourceTerm (unsigned gridIndex, units::quantity< unit::concentration > u)

double	ComputeNonlinearSourceTermPrime (const ChastePoint< SPACE_DIM > &rX, double u)

units::quantity< unit::rate >	ComputeNonlinearSourceTermPrime (unsigned gridIndex, units::quantity< unit::concentration > u)

units::quantity< unit::concentration >	GetMichaelisMentenThreshold ()

void	SetMichaelisMentenThreshold (units::quantity< unit::concentration > threshold)

Public Member Functions inherited from AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >
	AbstractDiscreteContinuumNonLinearEllipticPde ()

virtual	~AbstractDiscreteContinuumNonLinearEllipticPde ()

void	AddDiscreteSource (boost::shared_ptr< DiscreteSource< ELEMENT_DIM > > pDiscreteSource)

units::quantity< unit::diffusivity >	ComputeIsotropicDiffusionTerm ()

std::vector< boost::shared_ptr< DiscreteSource< ELEMENT_DIM > > >	GetDiscreteSources ()

void	SetContinuumConstantInUTerm (units::quantity< unit::concentration_flow_rate > constantInUTerm)

void	SetIsotropicDiffusionConstant (units::quantity< unit::diffusivity > diffusivity)

void	SetContinuumLinearInUTerm (units::quantity< unit::rate > linearInUTerm)

void	SetRegularGrid (boost::shared_ptr< RegularGrid< ELEMENT_DIM > > pRegularGrid)

void	SetMesh (boost::shared_ptr< TetrahedralMesh< ELEMENT_DIM, ELEMENT_DIM > > pMesh)

void	SetUseRegularGrid (bool useRegularGrid)

virtual void	UpdateDiscreteSourceStrengths ()

Static Public Member Functions
static boost::shared_ptr< MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM > >	Create ()

Private Attributes
units::quantity< unit::concentration >	mMichaelisMentenThreshold

Additional Inherited Members
Protected Attributes inherited from AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >
c_matrix< double, ELEMENT_DIM, ELEMENT_DIM >	mDiffusionTensor

units::quantity< unit::diffusivity >	mDiffusivity

units::quantity< unit::concentration_flow_rate >	mConstantInUTerm

units::quantity< unit::rate >	mLinearInUTerm

std::vector< boost::shared_ptr< DiscreteSource< ELEMENT_DIM > > >	mDiscreteSources

boost::shared_ptr< RegularGrid< ELEMENT_DIM > >	mpRegularGrid

boost::shared_ptr< TetrahedralMesh< ELEMENT_DIM, ELEMENT_DIM > >	mpMesh

bool	mUseRegularGrid

std::vector< units::quantity< unit::concentration_flow_rate > >	mDiscreteConstantSourceStrengths

std::vector< units::quantity< unit::rate > >	mDiscreteLinearSourceStrengths

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >

A steady state concentration based reaction-diffusion pde with michaelis menten type consumption terms.

Definition at line 49 of file MichaelisMentenSteadyStateDiffusionReactionPde.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::MichaelisMentenSteadyStateDiffusionReactionPde ( )

Constructor

Definition at line 40 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::~MichaelisMentenSteadyStateDiffusionReactionPde ( )

virtual

Destructor

Definition at line 55 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::ComputeConstantInUSourceTerm	(	const ChastePoint< SPACE_DIM > &	rX,
		Element< ELEMENT_DIM, SPACE_DIM > *	pElement
	)

Over-ridden method to return the constant in U contribution to the Chaste FE solver

Parameters

rX	grid location
pElement	pointer to containing element

Returns: source strength

Definition at line 61 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

References AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mConstantInUTerm.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

units::quantity< unit::concentration_flow_rate > MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::ComputeConstantInUSourceTerm ( unsigned gridIndex = 0 )

virtual

Over-ridden method to return the constant in U contribution to the regular grid solvers

Parameters

gridIndex grid index

Returns: source strength

Reimplemented from AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >.

Definition at line 67 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

References AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mConstantInUTerm, AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mDiscreteConstantSourceStrengths, and AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mDiscreteLinearSourceStrengths.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_matrix< double, SPACE_DIM, SPACE_DIM > MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::ComputeDiffusionTerm	(	const ChastePoint< SPACE_DIM > &	rX,
		double	u
	)

Over-ridden method to return the diffusion term to the Chaste FE solver

Parameters

rX	the grid location
u	the solution value

Returns: the diffusion matrix

Definition at line 77 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

References AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mDiffusionTensor.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_matrix< double, SPACE_DIM, SPACE_DIM > MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::ComputeDiffusionTermPrime	(	const ChastePoint< SPACE_DIM > &	rX,
		double	u
	)

Return the derivative of the diffusion term

Parameters

rX	the grid location
u	the solution value

Returns: the derivative of the diffusion term

Definition at line 83 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::ComputeLinearInUCoeffInSourceTerm	(	const ChastePoint< SPACE_DIM > &	rX,
		Element< ELEMENT_DIM, SPACE_DIM > *	pElement
	)

Over-ridden method to return the linear in U contribution to the Chaste FE solver

Parameters

rX	grid location
pElement	pointer to containing element

Returns: source strength

Definition at line 89 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

References AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mLinearInUTerm.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

units::quantity< unit::rate > MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::ComputeLinearInUCoeffInSourceTerm ( unsigned gridIndex = 0 )

virtual

Over-ridden method to return the linear in U contribution to the regular grid solvers

Parameters

gridIndex grid index

Returns: source strength

Reimplemented from AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >.

Definition at line 95 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

References AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mDiscreteLinearSourceStrengths, and AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mLinearInUTerm.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::ComputeLinearSourceTerm ( const ChastePoint< SPACE_DIM > & rX )

Over-ridden method to return the linear in U contribution to the Chaste FE solver

Parameters

rX	grid location

Returns: source strength

Definition at line 105 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::ComputeNonlinearSourceTerm	(	const ChastePoint< SPACE_DIM > &	rX,
		double	u
	)

Over-ridden method to return the nonlinear in U contribution to the Chaste FE solver

Parameters

rX	grid location
u	the solution value

Returns: source strength

Definition at line 111 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

References AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mConstantInUTerm, and MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::mMichaelisMentenThreshold.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

units::quantity< unit::concentration_flow_rate > MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::ComputeNonlinearSourceTerm	(	unsigned	gridIndex,
		units::quantity< unit::concentration >	u
	)

virtual

Over-ridden method to return the nonlinear in U contribution to the regular grid solvers

Parameters

gridIndex	grid index
u	the solution value

Returns: source strength

Implements AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >.

Definition at line 138 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

References AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mConstantInUTerm, AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mDiscreteConstantSourceStrengths, AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mDiscreteLinearSourceStrengths, and MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::mMichaelisMentenThreshold.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::ComputeNonlinearSourceTermPrime	(	const ChastePoint< SPACE_DIM > &	rX,
		double	u
	)

Over-ridden method to return the nonlinear in U contribution prime to the Chaste FE solver

Parameters

rX	grid location
u	the solution value

Returns: source strength

Definition at line 124 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

References AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mConstantInUTerm, and MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::mMichaelisMentenThreshold.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

units::quantity< unit::rate > MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::ComputeNonlinearSourceTermPrime	(	unsigned	gridIndex,
		units::quantity< unit::concentration >	u
	)

virtual

Over-ridden method to return the nonlinear in U contribution prime to the regular grid solvers

Parameters

gridIndex	grid index
u	the solution value

Returns: source strength

Implements AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >.

Definition at line 152 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

References AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mConstantInUTerm, AbstractDiscreteContinuumNonLinearEllipticPde< SPACE_DIM >::mDiscreteLinearSourceStrengths, and MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::mMichaelisMentenThreshold.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

boost::shared_ptr< MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM > > MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::Create ( )

static

Factory Constructor

Returns: a pointer to an instance of the pde

Definition at line 48 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

units::quantity< unit::concentration > MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::GetMichaelisMentenThreshold ( )

Get the concentration at half max consumption in the michaelis menten model

Returns: threshold the concentration at half max consumption in the michaelis menten model

Definition at line 167 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

References MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::mMichaelisMentenThreshold.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::SetMichaelisMentenThreshold ( units::quantity< unit::concentration > threshold )

Set the concentration at half max consumption in the michaelis menten model

Parameters

threshold the concentration at half max consumption in the michaelis menten model

Definition at line 173 of file MichaelisMentenSteadyStateDiffusionReactionPde.cpp.

References MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::mMichaelisMentenThreshold.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

units::quantity<unit::concentration> MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::mMichaelisMentenThreshold

private

The concentration value a half maximum reaction rate in the michaelis menten model.

Definition at line 54 of file MichaelisMentenSteadyStateDiffusionReactionPde.hpp.

Referenced by MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::ComputeNonlinearSourceTerm(), MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::ComputeNonlinearSourceTermPrime(), MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::GetMichaelisMentenThreshold(), and MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >::SetMichaelisMentenThreshold().

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

projects/MicrovesselChaste/src/pde/problem/MichaelisMentenSteadyStateDiffusionReactionPde.hpp
projects/MicrovesselChaste/src/pde/problem/MichaelisMentenSteadyStateDiffusionReactionPde.cpp

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM> class MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class MichaelisMentenSteadyStateDiffusionReactionPde< ELEMENT_DIM, SPACE_DIM >