#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 ()
	~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)
Protected Member Functions
Vec	CreateInitialCondition ()
void	AnalyseMeshForBath ()
void	ProcessExtracellularStimulus ()
virtual AbstractCardiacTissue < DIM > *	CreateCardiacTissue ()
virtual AbstractDynamicLinearPdeSolver < DIM, DIM, 3 > *	CreateSolver ()
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
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:

Intracellular potential of the first cell
Intracellular potential of the second cell
Extracellular potential

However, the OUTPUT is rearranged as follows. The rearrangament occurs AFTER the solution is calculated:

Transmembrane potential of the first cell (Intracellular potential of the first cell - Extracellular potential)
Transmembrane potential of the second cell (Intracellular potential of the second cell - Extracellular potential)
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 91 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 48 of file ExtendedBidomainProblem.cpp.

References ExtendedBidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

template<unsigned DIM>

ExtendedBidomainProblem< DIM >::ExtendedBidomainProblem ( )

Archiving constructor

Definition at line 65 of file ExtendedBidomainProblem.cpp.

References ExtendedBidomainProblem< DIM >::mFixedExtracellularPotentialNodes.

template<unsigned DIM>

ExtendedBidomainProblem< DIM >::~ExtendedBidomainProblem ( )

Destructor

Definition at line 266 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 ( ) [protected, virtual]

Create our bidomain PDE object

Implements AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 144 of file ExtendedBidomainProblem.cpp.

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

template<unsigned DIM>

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

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

Reimplemented from AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 81 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 ( ) [protected, virtual]

Create a suitable bidomain solver

Implements AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 231 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 349 of file ExtendedBidomainProblem.cpp.

References AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineExtraVariablesWriterColumns().

template<unsigned DIM>

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

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

Definition at line 312 of file ExtendedBidomainProblem.cpp.

template<unsigned DIM>

bool ExtendedBidomainProblem< DIM >::GetHasBath ( ) [virtual]

Return whether this is a problem with bath or not

Reimplemented from AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 440 of file ExtendedBidomainProblem.cpp.

template<unsigned DIM>

template<class Archive >

void ExtendedBidomainProblem< DIM >::load	(	Archive &	archive,
		const unsigned int	version
	)		`[inline, private]`

Load the member variables from an archive.

Parameters:

archive
version

Reimplemented from AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 198 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 420 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 108 of file ExtendedBidomainProblem.cpp.

References PetscTools::Barrier().

template<unsigned DIM>

template<class Archive >

void ExtendedBidomainProblem< DIM >::save	(	Archive &	archive,
		const unsigned int	version
	)		const `[inline, private]`

Save the member variables to an archive.

Parameters:

archive
version

Todo:: #1369

Reimplemented from AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 105 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 200 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 224 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.

Definition at line 285 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 213 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 447 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 275 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 298 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 319 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 term of Phi_i_1, Phi_i_2 and Phi_e (i.e., intracellular potential of the two cells plus extracellular potential). This method works out the transmembrane potential of the two cells (V and V_2) calculated as V = Phi_i_1 - Phi_e and V_2 = Phi_i_2-Phi_e. It then writes to file V, 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

Implements AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 384 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.

Reimplemented from AbstractCardiacProblem< DIM, DIM, 3 >.

Definition at line 94 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 307 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 311 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 309 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 346 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 313 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 315 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 286 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 317 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 324 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 327 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

Definition at line 352 of file ExtendedBidomainProblem.hpp.

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