#include <ExtendedBidomainProblem.hpp>

Inheritance diagram for ExtendedBidomainProblem< DIM >:

Collaboration diagram for ExtendedBidomainProblem< DIM >:

Public Member Functions
	ExtendedBidomainProblem (AbstractCardiacCellFactory< DIM > pCellFactory, AbstractCardiacCellFactory< DIM > pSecondCellFactory, bool hasBath=false)

	ExtendedBidomainProblem ()

virtual	~ExtendedBidomainProblem ()

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

void	SetIntracellularConductivitiesForSecondCell (c_vector< double, DIM > conductivities)

void	SetExtendedBidomainParameters (double Am1, double Am2, double AmGap, double Cm1, double Cm2, double Ggap)

void	SetGgapHeterogeneities (std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &rGgapHeterogeneityRegions, std::vector< double > &rGgapValues)

void	SetExtracellularStimulusFactory (AbstractStimulusFactory< DIM > *pFactory)

void	SetNodeForAverageOfPhiZeroed (unsigned node)

ExtendedBidomainTissue< DIM > *	GetExtendedBidomainTissue ()

void	WriteInfo (double time)

virtual void	DefineWriterColumns (bool extending)

virtual void	WriteOneStep (double time, Vec voltageVec)

void	PreSolveChecks ()

bool	GetHasBath ()

void	SetHasBath (bool hasBath)

Public Member Functions inherited from AbstractCardiacProblem< DIM, DIM, 3 >
	AbstractCardiacProblem (AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM > *pCellFactory)

	AbstractCardiacProblem ()

virtual	~AbstractCardiacProblem ()

void	Initialise ()

void	SetNodesPerProcessorFilename (const std::string &rFilename)

void	SetBoundaryConditionsContainer (BccType pBcc)

void	SetMesh (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

void	PrintOutput (bool rPrintOutput)

void	SetWriteInfo (bool writeInfo=true)

Vec	GetSolution ()

DistributedVector	GetSolutionDistributedVector ()

double	GetCurrentTime ()

AbstractTetrahedralMesh < ELEMENT_DIM, SPACE_DIM > &	rGetMesh ()

AbstractCardiacTissue < ELEMENT_DIM, SPACE_DIM > *	GetTissue ()

void	Solve ()

void	CloseFilesAndPostProcess ()

void	DefineExtraVariablesWriterColumns (bool extending)

void	WriteExtraVariablesOneStep ()

bool	InitialiseWriter ()

void	SetUseHdf5DataWriterCache (bool useCache=true)

void	SetHdf5DataWriterTargetChunkSizeAndAlignment (hsize_t size)

void	SetOutputNodes (std::vector< unsigned > &rNodesToOutput)

Hdf5DataReader	GetDataReader ()

virtual void	AtBeginningOfTimestep (double time)

virtual void	OnEndOfTimestep (double time)

virtual void	SetUpAdditionalStoppingTimes (std::vector< double > &rAdditionalStoppingTimes)

void	SetUseTimeAdaptivityController (bool useAdaptivity, AbstractTimeAdaptivityController *pController=NULL)

void	LoadExtraArchive (Archive &archive, unsigned version)

virtual void	SetElectrodes ()

void	AddOutputModifier (boost::shared_ptr< AbstractOutputModifier > pOutputModifier)

Public Member Functions inherited from AbstractUntemplatedCardiacProblem
virtual	~AbstractUntemplatedCardiacProblem ()

Protected Member Functions
Vec	CreateInitialCondition ()

void	AnalyseMeshForBath ()

void	ProcessExtracellularStimulus ()

virtual AbstractCardiacTissue < DIM > *	CreateCardiacTissue ()

virtual AbstractDynamicLinearPdeSolver < DIM, DIM, 3 > *	CreateSolver ()

Protected Member Functions inherited from AbstractCardiacProblem< DIM, DIM, 3 >
virtual void	CreateMeshFromHeartConfig ()

Protected Attributes
AbstractCardiacCellFactory < DIM, DIM > *	mpSecondCellFactory

ExtendedBidomainTissue< DIM > *	mpExtendedBidomainTissue

std::vector< unsigned >	mFixedExtracellularPotentialNodes

c_vector< double, DIM >	mIntracellularConductivitiesSecondCell

unsigned	mVoltageColumnId_Vm1

unsigned	mVoltageColumnId_Vm2

unsigned	mVoltageColumnId_Phie

std::vector< signed int >	mVariablesIDs

bool	mUserSpecifiedSecondCellConductivities

bool	mUserHasSetBidomainValuesExplicitly

double	mAmFirstCell

double	mAmSecondCell

double	mAmGap

double	mCmFirstCell

double	mCmSecondCell

double	mGGap

std::vector< boost::shared_ptr < AbstractChasteRegion< DIM > > >	mGgapHeterogeneityRegions

std::vector< double >	mGgapHeterogenousValues

AbstractStimulusFactory< DIM > *	mpExtracellularStimulusFactory

int	mRowForAverageOfPhiZeroed

unsigned	mApplyAveragePhieZeroConstraintAfterSolving

bool	mUserSuppliedExtracellularStimulus

bool	mHasBath

AbstractExtendedBidomainSolver < DIM, DIM > *	mpSolver

Protected Attributes inherited from AbstractCardiacProblem< DIM, DIM, 3 >
std::string	mMeshFilename

bool	mAllocatedMemoryForMesh

bool	mWriteInfo

bool	mPrintOutput

std::vector< unsigned >	mNodesToOutput

unsigned	mVoltageColumnId

std::vector< unsigned >	mExtraVariablesId

unsigned	mTimeColumnId

unsigned	mNodeColumnId

AbstractCardiacTissue < ELEMENT_DIM, SPACE_DIM > *	mpCardiacTissue

BccType	mpBoundaryConditionsContainer

BccType	mpDefaultBoundaryConditionsContainer

AbstractDynamicLinearPdeSolver < ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *	mpSolver

AbstractCardiacCellFactory < ELEMENT_DIM, SPACE_DIM > *	mpCellFactory

AbstractTetrahedralMesh < ELEMENT_DIM, SPACE_DIM > *	mpMesh

Vec	mSolution

double	mCurrentTime

AbstractTimeAdaptivityController *	mpTimeAdaptivityController

Hdf5DataWriter *	mpWriter

bool	mUseHdf5DataWriterCache

hsize_t	mHdf5DataWriterChunkSizeAndAlignment

std::vector< boost::shared_ptr < AbstractOutputModifier > >	mOutputModifiers

Private Member Functions
template<class Archive >
void	save (Archive &archive, const unsigned int version) const

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

Friends
class	boost::serialization::access

class	TestArchivingExtendedBidomain

Detailed Description

template<unsigned DIM>
class ExtendedBidomainProblem< DIM >

Class which specifies and solves an extended bidomain problem.

See Buist ML, Poh YC. An Extended Bidomain Framework Incorporating Multiple Cell Types. Biophysical Journal, Volume 99, Issue 1, 13-18, 7 July 2010.

Briefly, the problems consits of 3 equations, 2 parabolic and one elliptic. The space is divided in 3 compartments:

First cell
Second cell
Extracellular space.

The three unkowns are the the intracellular potential of the two cells and the extracellular potential. This class allows the user to specify the parameters specific for the these simulations and also different intracellular conductivities for the two cells.

The solution vector used for calculations is arranged as a striped vector with this order:

Transmembrane potential of the first cell
Transmembrane potential of the second cell
Extracellular potential

Unlike a bidomain problem, a node-wise extracellular stimulus can be set up in extended bidomain problems in absence of a bath. This is done by setting a stimulus factory via the method SetExtracellularStimulusFactory. See documentation of AbstractStimulusFactory and ElectrodesStimulusFactory for more details. Note that compatibility conditions will be taken care of by this class by calling specific methods within the stimulus factory class.

Definition at line 85 of file ExtendedBidomainProblem.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

ExtendedBidomainProblem< DIM >::ExtendedBidomainProblem	(	AbstractCardiacCellFactory< DIM > *	pCellFactory,
		AbstractCardiacCellFactory< DIM > *	pSecondCellFactory,
		bool	hasBath = `false`
	)

Constructor

Parameters

pCellFactory	User defined cell factory which shows how the pde should create cells.
pSecondCellFactory	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 46 of file ExtendedBidomainProblem.cpp.

References ExtendedBidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

template<unsigned DIM>

ExtendedBidomainProblem< DIM >::ExtendedBidomainProblem ( )

Archiving constructor

Definition at line 63 of file ExtendedBidomainProblem.cpp.

References ExtendedBidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

template<unsigned DIM>

ExtendedBidomainProblem< DIM >::~ExtendedBidomainProblem ( )

virtual

Destructor

Definition at line 260 of file ExtendedBidomainProblem.cpp.

Member Function Documentation

template<unsigned DIM>

void ExtendedBidomainProblem< DIM >::AnalyseMeshForBath ( )

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.

template<unsigned DIM>

AbstractCardiacTissue< DIM > * ExtendedBidomainProblem< DIM >::CreateCardiacTissue ( )

protectedvirtual

Returns: a newly created bidomain PDE object

Implements AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 141 of file ExtendedBidomainProblem.cpp.

References HeartConfig::GetIntracellularConductivities(), HeartConfig::Instance(), and ExtendedBidomainTissue< SPACE_DIM >::SetUserSuppliedExtracellularStimulus().

template<unsigned DIM>

Vec ExtendedBidomainProblem< DIM >::CreateInitialCondition ( )

protectedvirtual

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

Returns: the newly created intial conditions vector

Reimplemented from AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 78 of file ExtendedBidomainProblem.cpp.

References DistributedVector::Begin(), DistributedVectorFactory::CreateDistributedVector(), DistributedVectorFactory::CreateVec(), DistributedVector::End(), and DistributedVector::Restore().

template<unsigned DIM>

AbstractDynamicLinearPdeSolver< DIM, DIM, 3 > * ExtendedBidomainProblem< DIM >::CreateSolver ( )

protectedvirtual

Returns: a newly created suitable bidomain solver

Implements AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 228 of file ExtendedBidomainProblem.cpp.

References AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes().

template<unsigned DIM>

void ExtendedBidomainProblem< DIM >::DefineWriterColumns ( bool extending )

virtual

Define what variables are written to the primary results file. Hardcoded variable names are "V", "V_2" and "Phi_e" for the three variables. If you request any extra variable (via HeartConfig), this method will also define the extra variables by calling a method in the parent class.

Parameters

extending whether we are extending an existing results file

Reimplemented from AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 341 of file ExtendedBidomainProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineExtraVariablesWriterColumns(), TimeStepper::EstimateTimeSteps(), and HeartConfig::Instance().

template<unsigned DIM>

ExtendedBidomainTissue< DIM > * ExtendedBidomainProblem< DIM >::GetExtendedBidomainTissue ( )

Returns: the tissue object. Can only be called after Initialise()

Definition at line 306 of file ExtendedBidomainProblem.cpp.

template<unsigned DIM>

bool ExtendedBidomainProblem< DIM >::GetHasBath ( )

virtual

Returns: whether this is a problem with bath or not

Reimplemented from AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 438 of file ExtendedBidomainProblem.cpp.

template<unsigned DIM>

template<class Archive >

void ExtendedBidomainProblem< DIM >::load	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Load the member variables from an archive.

Parameters

archive
version

Definition at line 160 of file ExtendedBidomainProblem.hpp.

template<unsigned DIM>

void ExtendedBidomainProblem< DIM >::PreSolveChecks ( )

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, 3 >.

Definition at line 418 of file ExtendedBidomainProblem.cpp.

References EXCEPTION, HeartConfig::GetUseRelativeTolerance(), HeartConfig::Instance(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks().

template<unsigned DIM>

void ExtendedBidomainProblem< DIM >::ProcessExtracellularStimulus ( )

protected

Small helper tidy-up method that incorporates everything related to the initialisation of the extracellular stimulus.

It checks whether there is any extracellular stimulus, If not, it creates a one (with default implementation to zero stimulus). In any case, it passes the mesh into the stimulus, calls the SetCompatibleExtracellularStimulus method and also checks if there are any grounded nodes. If so, it calls SetFixedExtracellularPotentialNodes.

Definition at line 105 of file ExtendedBidomainProblem.cpp.

References PetscTools::Barrier().

template<unsigned DIM>

template<class Archive >

void ExtendedBidomainProblem< DIM >::save	(	Archive &	archive,
		const unsigned int	version
	)		const

inlineprivate

Save the member variables to an archive.

Parameters

archive
version

Definition at line 99 of file ExtendedBidomainProblem.hpp.

template<unsigned DIM>

void ExtendedBidomainProblem< DIM >::SetExtendedBidomainParameters	(	double	Am1,
		double	Am2,
		double	AmGap,
		double	Cm1,
		double	Cm2,
		double	Ggap
	)

Allow the user to specify different values for the bidomain parameters in the extened bidomain framework. This method switches the mUserHasSetBidomainValuesExplicitly to true and tells the problem to overwrite the corresponding parameters in HeartConfig. It needs to be called before Initialise() to have any effect.

Parameters

Am1	value of the surface-to-volume ratio for the first cell
Am2	value of the surface-to-volume ratio for the second cell
AmGap	value of the surface-to-volume ratio for the gap junction
Cm1	value of the capacitance for the first cell
Cm2	value of the capacitance for the second cell
Ggap	value, in mS of the gap junction conductance

Definition at line 197 of file ExtendedBidomainProblem.cpp.

template<unsigned DIM>

void ExtendedBidomainProblem< DIM >::SetExtracellularStimulusFactory ( AbstractStimulusFactory< DIM > * pFactory )

Sets a stimulus factory as the extracellular one.

Parameters

pFactory the factory to be set.

Definition at line 221 of file ExtendedBidomainProblem.cpp.

template<unsigned DIM>

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

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.

Todo:: turn this into an exception if the user calls this twice...

Definition at line 279 of file ExtendedBidomainProblem.cpp.

template<unsigned DIM>

void ExtendedBidomainProblem< DIM >::SetGgapHeterogeneities	(	std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &	rGgapHeterogeneityRegions,
		std::vector< double > &	rGgapValues
	)

Set the values of mCellHeterogeneityRegions and mGgapValues for the heterogeneities of Ggap. It just sets the member variables here that will later be passed on to the tissue object. It also checks that the two have the same size. Throws otherwise.

Parameters

rGgapHeterogeneityRegions	a vector of heterogeneity regions for gap junctions
rGgapValues	a vector (of the same size as rGgapHeterogeneityRegions) with the respective values of Ggap for every region.

Definition at line 210 of file ExtendedBidomainProblem.cpp.

References EXCEPTION.

template<unsigned DIM>

void ExtendedBidomainProblem< DIM >::SetHasBath ( bool hasBath )

Set whether there is a bath or not. Useful for covering exceptions only (for example if bath problems are not supported and there is no method to analyse the mesh for a bath).

Parameters

hasBath whether we want the problem to have bath or not.

Definition at line 444 of file ExtendedBidomainProblem.cpp.

template<unsigned DIM>

void ExtendedBidomainProblem< DIM >::SetIntracellularConductivitiesForSecondCell ( c_vector< double, DIM > conductivities )

Allow the user to specify different values for the conductivities of the second cell type

Parameters

conductivities : the intracellular conductivities of the second cell that you wish to set

Definition at line 269 of file ExtendedBidomainProblem.cpp.

template<unsigned DIM>

void ExtendedBidomainProblem< DIM >::SetNodeForAverageOfPhiZeroed ( unsigned node )

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 292 of file ExtendedBidomainProblem.cpp.

template<unsigned DIM>

void ExtendedBidomainProblem< DIM >::WriteInfo ( double time )

virtual

Print out time and max/min of the intracellular potential of the two cells and phi_e values at current time.

Parameters

time	current time.

Implements AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 313 of file ExtendedBidomainProblem.cpp.

References PetscTools::AmMaster().

template<unsigned DIM>

void ExtendedBidomainProblem< DIM >::WriteOneStep	(	double	time,
		Vec	voltageVec
	)

virtual

Write one timestep of output data to the primary results file. The solution of the problem is in terms of V_1, V_2 and Phi_e (i.e., transmembrane potentials of the two cells plus extracellular potential). It then writes to file V_1, V_2 and Phi_e.

It also writes any extra variable (defined by HeartConfig). Note that it does the job by calling the method in the parent class. This implies that the extra variable must be in the first cell (not the second) because the generic method to write extra variables only looks into the first cell factory.

Todo:: write a specific method for extended problems that looks in both cell factories

Parameters

time	the current time
voltageVec	the solution vector to write

Todo:: write a specific method for this class

Implements AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 381 of file ExtendedBidomainProblem.cpp.

References DistributedVector::Begin(), PetscTools::Destroy(), DistributedVector::End(), DistributedVector::Restore(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 88 of file ExtendedBidomainProblem.hpp.

Member Data Documentation

template<unsigned DIM>

double ExtendedBidomainProblem< DIM >::mAmFirstCell

protected

Am for the first cell, set by the user and, if so, set into the PDE

Definition at line 268 of file ExtendedBidomainProblem.hpp.

Referenced by ExtendedBidomainProblem< DIM >::load(), and ExtendedBidomainProblem< DIM >::save().

template<unsigned DIM>

double ExtendedBidomainProblem< DIM >::mAmGap

protected

Am for the gap junctions, set by the user and, if so, set into the PDE

Definition at line 272 of file ExtendedBidomainProblem.hpp.

Referenced by ExtendedBidomainProblem< DIM >::load(), and ExtendedBidomainProblem< DIM >::save().

template<unsigned DIM>

double ExtendedBidomainProblem< DIM >::mAmSecondCell

protected

Am for the second cell, set by the user and, if so, set into the PDE

Definition at line 270 of file ExtendedBidomainProblem.hpp.

Referenced by ExtendedBidomainProblem< DIM >::load(), and ExtendedBidomainProblem< DIM >::save().

template<unsigned DIM>

unsigned ExtendedBidomainProblem< DIM >::mApplyAveragePhieZeroConstraintAfterSolving

protected

An alternative method for constraining the solution and resolving singularity. Singular system is solved and THEN the constraint is applied on the phi_e (after calculating.

This variable is checked within the specialization of "OnEndOfTimestep" method. False by default as initialised in the constructor.

Definition at line 308 of file ExtendedBidomainProblem.hpp.

Referenced by ExtendedBidomainProblem< DIM >::load(), and ExtendedBidomainProblem< DIM >::save().

template<unsigned DIM>

double ExtendedBidomainProblem< DIM >::mCmFirstCell

protected

Cm for the first cell, set by the user and, if so, set into the PDE

Definition at line 274 of file ExtendedBidomainProblem.hpp.

Referenced by ExtendedBidomainProblem< DIM >::load(), and ExtendedBidomainProblem< DIM >::save().

template<unsigned DIM>

double ExtendedBidomainProblem< DIM >::mCmSecondCell

protected

Cm for the second cell, set by the user and, if so, set into the PDE

Definition at line 276 of file ExtendedBidomainProblem.hpp.

Referenced by ExtendedBidomainProblem< DIM >::load(), and ExtendedBidomainProblem< DIM >::save().

template<unsigned DIM>

std::vector<unsigned> ExtendedBidomainProblem< DIM >::mFixedExtracellularPotentialNodes

protected

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

Definition at line 246 of file ExtendedBidomainProblem.hpp.

Referenced by ExtendedBidomainProblem< DIM >::ExtendedBidomainProblem(), ExtendedBidomainProblem< DIM >::load(), and ExtendedBidomainProblem< DIM >::save().

template<unsigned DIM>

double ExtendedBidomainProblem< DIM >::mGGap

protected

Conductance, in mS of the gap junction conductance, set by the user and, if so, set into the PDE (otherwise its default value is 0

Definition at line 279 of file ExtendedBidomainProblem.hpp.

Referenced by ExtendedBidomainProblem< DIM >::load(), and ExtendedBidomainProblem< DIM >::save().

template<unsigned DIM>

std::vector<boost::shared_ptr<AbstractChasteRegion<DIM> > > ExtendedBidomainProblem< DIM >::mGgapHeterogeneityRegions

protected

Vector of Ggap heterogeneity regions. Set by the user, it is passed on to the tissue object. If empty (i.e., the user did not specify any heterogeneities) then the empty vector will still be passed to the tissue object, which, seeing the empty vector, will apply mGgap everywhere

Definition at line 286 of file ExtendedBidomainProblem.hpp.

Referenced by ExtendedBidomainProblem< DIM >::load(), and ExtendedBidomainProblem< DIM >::save().

template<unsigned DIM>

std::vector<double> ExtendedBidomainProblem< DIM >::mGgapHeterogenousValues

protected

Corresponding vector of values of Ggap for every heterogeneous region in mGgapHeterogeneityRegions

Definition at line 289 of file ExtendedBidomainProblem.hpp.

Referenced by ExtendedBidomainProblem< DIM >::load(), and ExtendedBidomainProblem< DIM >::save().

template<unsigned DIM>

bool ExtendedBidomainProblem< DIM >::mHasBath

protected

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