BidomainProblem< DIM > Class Template Reference

#include <BidomainProblem.hpp>

Inheritance diagram for BidomainProblem< DIM >:

Collaboration diagram for BidomainProblem< DIM >:

List of all members.

Public Member Functions

BidomainProblem (AbstractCardiacCellFactory< DIM > *pCellFactory, bool hasBath=false)

void SetFixedExtracellularPotentialNodes (std::vector< unsigned > nodes)

void SetNodeForAverageOfPhiZeroed (unsigned node)

BidomainPde< DIM > * GetBidomainPde ()

void WriteInfo (double time)

virtual void DefineWriterColumns ()

virtual void WriteOneStep (double time, Vec voltageVec)

void PreSolveChecks ()

void SetElectrodes (Electrodes< DIM > &rElectrodes)

void OnEndOfTimestep (double time)

Protected Member Functions

Vec CreateInitialCondition ()

void AnalyseMeshForBath ()

virtual AbstractCardiacPde< DIM > * CreateCardiacPde ()

virtual
AbstractDynamicAssemblerMixin
< DIM, DIM, 2 > * CreateAssembler ()

Protected Attributes

BidomainPde< DIM > * mpBidomainPde

std::vector< unsigned > mFixedExtracellularPotentialNodes

unsigned mExtracelluarColumnId

unsigned mRowForAverageOfPhiZeroed

bool mHasBath

Electrodes< DIM > * mpElectrodes

BidomainDg0Assembler< DIM, DIM > * mpAssembler

Friends

class TestBidomainWithBathAssembler

Detailed Description

template<unsigned DIM>
class BidomainProblem< DIM >

Class which specifies and solves a bidomain problem.

The solution vector is of the form: (V_1, phi_1, V_2, phi_2, ......, V_N, phi_N), where V_j is the voltage at node j and phi_j is the extracellular potential at node j.

Definition at line 53 of file BidomainProblem.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

BidomainProblem< DIM >::BidomainProblem	(	AbstractCardiacCellFactory< DIM > *	pCellFactory,
		bool	hasBath = `false`
	)			`[inline]`

Constructor

Parameters:

	pCellFactory	User defined cell factory which shows how the pde should create cells.
	hasBath	Whether the simulation has a bath (if this is true, all elements with attribute = 1 will be set to be bath elements (the rest should have attribute = 0)).

Definition at line 177 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

Member Function Documentation

template<unsigned DIM>

Vec BidomainProblem< DIM >::CreateInitialCondition ( ) [inline, protected, virtual]

Create normal initial condition but overwrite V to zero for bath nodes, if there are any.

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 87 of file BidomainProblem.cpp.

References HeartRegionCode::BATH, DistributedVector::Begin(), DistributedVectorFactory::CreateDistributedVector(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), DistributedVector::End(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), BidomainProblem< DIM >::mHasBath, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, and DistributedVector::Restore().

template<unsigned DIM>

void BidomainProblem< DIM >::AnalyseMeshForBath ( ) [inline, protected]

Annotate bath nodes with the correct region code, if a bath is present. Will throw if mHasBath is set but no bath is present in the mesh.

Definition at line 41 of file BidomainProblem.cpp.

References HeartRegionCode::BATH, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetRegion(), BidomainProblem< DIM >::mHasBath, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, and HeartRegionCode::TISSUE.

Referenced by BidomainProblem< DIM >::CreateCardiacPde().

template<unsigned DIM>

AbstractCardiacPde< DIM > * BidomainProblem< DIM >::CreateCardiacPde ( ) [inline, protected, virtual]

Create our bidomain PDE object

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 112 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::AnalyseMeshForBath(), BidomainProblem< DIM >::mpBidomainPde, and AbstractCardiacProblem< DIM, DIM, 2 >::mpCellFactory.

template<unsigned DIM>

AbstractDynamicAssemblerMixin< DIM, DIM, 2 > * BidomainProblem< DIM >::CreateAssembler ( ) [inline, protected, virtual]

Create a suitable bidomain assembler

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 120 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes, BidomainProblem< DIM >::mHasBath, BidomainProblem< DIM >::mpAssembler, BidomainProblem< DIM >::mpBidomainPde, AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, BidomainProblem< DIM >::mRowForAverageOfPhiZeroed, AbstractCardiacProblem< DIM, DIM, 2 >::mUseMatrixBasedRhsAssembly, BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::SetRowForAverageOfPhiZeroed().

template<unsigned DIM>

void BidomainProblem< DIM >::SetFixedExtracellularPotentialNodes ( std::vector< unsigned > nodes ) [inline]

Set the nodes at which phi_e (the extracellular potential) is fixed to zero. This does not necessarily have to be called. If it is not, phi_e is only defined up to a constant.

Parameters:

nodes

the nodes to be fixed.

Note:: currently, the value of phi_e at the fixed nodes cannot be set to be anything other than zero.

Definition at line 189 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

template<unsigned DIM>

void BidomainProblem< DIM >::SetNodeForAverageOfPhiZeroed ( unsigned node ) [inline]

Set which row of the linear system should be used to enforce the condition that the average of phi_e is zero. If not called, this condition will not be used.

Parameters:

node

the mesh node index giving the row at which to impose the constraint

Definition at line 201 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mRowForAverageOfPhiZeroed.

template<unsigned DIM>

BidomainPde< DIM > * BidomainProblem< DIM >::GetBidomainPde ( ) [inline]

Get the pde. Can only be called after Initialise()

Definition at line 207 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mpBidomainPde.

template<unsigned DIM>

void BidomainProblem< DIM >::WriteInfo ( double time ) [inline, virtual]

Print out time and max/min voltage/phi_e values at current time.

Parameters:

time

current time.

Implements AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 214 of file BidomainProblem.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, AbstractCardiacProblem< DIM, DIM, 2 >::mSolution, and ReplicatableVector::ReplicatePetscVector().

template<unsigned DIM>

void BidomainProblem< DIM >::DefineWriterColumns ( ) [inline, virtual]

Define what variables are written to the primary results file. Adds the extracellular potential.

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 255 of file BidomainProblem.cpp.

References Hdf5DataWriter::DefineVariable(), AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::DefineWriterColumns(), BidomainProblem< DIM >::mExtracelluarColumnId, and AbstractCardiacProblem< DIM, DIM, 2 >::mpWriter.

template<unsigned DIM>

void BidomainProblem< DIM >::WriteOneStep	(	double	time,
		Vec	voltageVec
	)			`[inline, virtual]`

Write one timestep of output data to the primary results file. Adds the extracellular potential to the results.

Parameters:

	time	the current time
	voltageVec	the solution vector to write

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 262 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mExtracelluarColumnId, AbstractCardiacProblem< DIM, DIM, 2 >::mpWriter, AbstractCardiacProblem< DIM, DIM, 2 >::mVoltageColumnId, Hdf5DataWriter::PutStripedVector(), and Hdf5DataWriter::PutUnlimitedVariable().

template<unsigned DIM>

void BidomainProblem< DIM >::PreSolveChecks ( ) [inline, virtual]

Performs a series of checks before solving. Checks that a suitable method of resolving the singularity is being used.

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 269 of file BidomainProblem.cpp.

References HeartConfig::GetUseRelativeTolerance(), HeartConfig::Instance(), BidomainProblem< DIM >::mFixedExtracellularPotentialNodes, BidomainProblem< DIM >::mRowForAverageOfPhiZeroed, and AbstractCardiacProblem< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks().

template<unsigned DIM>

void BidomainProblem< DIM >::SetElectrodes ( Electrodes< DIM > & rElectrodes ) [inline]

Set an electrode object (which provides boundary conditions). Only valid if there is a bath.

Parameters:

rElectrodes

Definition at line 289 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mHasBath, BidomainProblem< DIM >::mpElectrodes, and AbstractCardiacProblem< DIM, DIM, 2 >::SetBoundaryConditionsContainer().

template<unsigned DIM>

void BidomainProblem< DIM >::OnEndOfTimestep ( double time ) [inline, virtual]

Called at end of each time step in the main time-loop in AbstractCardiacProblem::Solve(). Overloaded here to switch off the electrodes (if there are any).

Parameters:

time

the current time

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 303 of file BidomainProblem.cpp.

References BidomainProblem< DIM >::mpAssembler, AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, DIM, 2 >::mpDefaultBoundaryConditionsContainer, BidomainProblem< DIM >::mpElectrodes, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, and AbstractAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetBoundaryConditionsContainer().

Member Data Documentation

template<unsigned DIM>

BidomainPde<DIM>* BidomainProblem< DIM >::mpBidomainPde [protected]

The bidomain PDE

Definition at line 60 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::CreateAssembler(), BidomainProblem< DIM >::CreateCardiacPde(), and BidomainProblem< DIM >::GetBidomainPde().

template<unsigned DIM>

std::vector<unsigned> BidomainProblem< DIM >::mFixedExtracellularPotentialNodes [protected]

Nodes at which the extracellular voltage is fixed to zero (replicated)

Definition at line 63 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::BidomainProblem(), BidomainProblem< DIM >::CreateAssembler(), BidomainProblem< DIM >::PreSolveChecks(), and BidomainProblem< DIM >::SetFixedExtracellularPotentialNodes().

template<unsigned DIM>

unsigned BidomainProblem< DIM >::mExtracelluarColumnId [protected]

Used by the writer

Definition at line 65 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::DefineWriterColumns(), and BidomainProblem< DIM >::WriteOneStep().

template<unsigned DIM>

unsigned BidomainProblem< DIM >::mRowForAverageOfPhiZeroed [protected]

Another method of resolving the singularity in the bidomain equations. Specifies a row of the matrix at which to impose an extra condition.

Definition at line 70 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::CreateAssembler(), BidomainProblem< DIM >::PreSolveChecks(), and BidomainProblem< DIM >::SetNodeForAverageOfPhiZeroed().

template<unsigned DIM>

bool BidomainProblem< DIM >::mHasBath [protected]

Whether the mesh has a bath, ie whether this is a bath simulation

Definition at line 73 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::AnalyseMeshForBath(), BidomainProblem< DIM >::CreateAssembler(), BidomainProblem< DIM >::CreateInitialCondition(), and BidomainProblem< DIM >::SetElectrodes().

template<unsigned DIM>

Electrodes<DIM>* BidomainProblem< DIM >::mpElectrodes [protected]

Electrodes used to provide a shock

Definition at line 76 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::OnEndOfTimestep(), and BidomainProblem< DIM >::SetElectrodes().

template<unsigned DIM>

BidomainDg0Assembler<DIM,DIM>* BidomainProblem< DIM >::mpAssembler [protected]

We need to save the assembler that is being used to switch off the electrodes (by adding default boundary conditions to the assembler)

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 94 of file BidomainProblem.hpp.

Referenced by BidomainProblem< DIM >::CreateAssembler(), and BidomainProblem< DIM >::OnEndOfTimestep().

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

/tmp/release_1.1/heart/src/problem/BidomainProblem.hpp
/tmp/release_1.1/heart/src/problem/BidomainProblem.cpp


Public Member Functions
	BidomainProblem (AbstractCardiacCellFactory< DIM > *pCellFactory, bool hasBath=false)
void	SetFixedExtracellularPotentialNodes (std::vector< unsigned > nodes)
void	SetNodeForAverageOfPhiZeroed (unsigned node)
BidomainPde< DIM > *	GetBidomainPde ()
void	WriteInfo (double time)
virtual void	DefineWriterColumns ()
virtual void	WriteOneStep (double time, Vec voltageVec)
void	PreSolveChecks ()
void	SetElectrodes (Electrodes< DIM > &rElectrodes)
void	OnEndOfTimestep (double time)
Protected Member Functions
Vec	CreateInitialCondition ()
void	AnalyseMeshForBath ()
virtual AbstractCardiacPde< DIM > *	CreateCardiacPde ()
virtual AbstractDynamicAssemblerMixin < DIM, DIM, 2 > *	CreateAssembler ()
Protected Attributes
BidomainPde< DIM > *	mpBidomainPde
std::vector< unsigned >	mFixedExtracellularPotentialNodes
unsigned	mExtracelluarColumnId
unsigned	mRowForAverageOfPhiZeroed
bool	mHasBath
Electrodes< DIM > *	mpElectrodes
BidomainDg0Assembler< DIM, DIM > *	mpAssembler
Friends
class	TestBidomainWithBathAssembler

BidomainProblem< DIM > Class Template Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

template<unsigned DIM> class BidomainProblem< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class BidomainProblem< DIM >