#include <CardiacElectroMechanicsProblem.hpp>

Inheritance diagram for CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >:

Collaboration diagram for CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >:

Public Member Functions
	CardiacElectroMechanicsProblem (CompressibilityType compressibilityType, ElectricsProblemType electricsProblemType, TetrahedralMesh< DIM, DIM > pElectricsMesh, QuadraticMesh< DIM > pMechanicsMesh, AbstractCardiacCellFactory< DIM > pCellFactory, ElectroMechanicsProblemDefinition< DIM > pProblemDefinition, std::string outputDirectory)

virtual	~CardiacElectroMechanicsProblem ()

void	Initialise ()

void	Solve ()

double	Max (std::vector< double > &vec)

void	SetNoElectricsOutput ()

void	SetWatchedPosition (c_vector< double, DIM > watchedLocation)

void	SetOutputDeformationGradientsAndStress (double timestep)

std::vector< c_vector< double, DIM > > &	rGetDeformedPosition ()

c_matrix< double, DIM, DIM > &	rCalculateModifiedConductivityTensor (unsigned elementIndex, const c_matrix< double, DIM, DIM > &rOriginalConductivity, unsigned domainIndex)

virtual void	PrepareForSolve ()

virtual void	OnEndOfTimeStep (unsigned counter)

AbstractNonlinearElasticitySolver< DIM > *	GetMechanicsSolver ()

Public Member Functions inherited from AbstractConductivityModifier< DIM, DIM >
virtual	~AbstractConductivityModifier ()

c_matrix< double, SPACE_DIM, SPACE_DIM > &	rGetModifiedConductivityTensor (unsigned elementIndex, const c_matrix< double, SPACE_DIM, SPACE_DIM > &rOriginalConductivity, unsigned domainIndex)

virtual c_matrix< double, SPACE_DIM, SPACE_DIM > &	rCalculateModifiedConductivityTensor (unsigned elementIndex, const c_matrix< double, SPACE_DIM, SPACE_DIM > &rOriginalConductivity, unsigned domainIndex)=0

Protected Member Functions
void	DetermineWatchedNodes ()

void	WriteWatchedLocationData (double time, Vec voltage)

Protected Attributes
CompressibilityType	mCompressibilityType

AbstractCardiacProblem< DIM, DIM, ELEC_PROB_DIM > *	mpElectricsProblem

AbstractCardiacMechanicsSolverInterface< DIM > *	mpCardiacMechSolver

AbstractNonlinearElasticitySolver< DIM > *	mpMechanicsSolver

unsigned	mNumElecTimestepsPerMechTimestep

std::vector< double >	mInterpolatedCalciumConcs

std::vector< double >	mInterpolatedVoltages

TetrahedralMesh< DIM, DIM > *	mpElectricsMesh

QuadraticMesh< DIM > *	mpMechanicsMesh

ElectroMechanicsProblemDefinition< DIM > *	mpProblemDefinition

bool	mHasBath

FineCoarseMeshPair< DIM > *	mpMeshPair

std::string	mOutputDirectory

std::string	mDeformationOutputDirectory

bool	mWriteOutput

bool	mNoElectricsOutput

bool	mIsWatchedLocation

c_vector< double, DIM >	mWatchedLocation

unsigned	mWatchedElectricsNodeIndex

unsigned	mWatchedMechanicsNodeIndex

out_stream	mpWatchedLocationFile

unsigned	mNumTimestepsToOutputDeformationGradientsAndStress

std::vector< double >	mStretchesForEachMechanicsElement

std::vector< c_matrix< double, DIM, DIM > >	mDeformationGradientsForEachMechanicsElement

c_matrix< double, DIM, DIM >	mModifiedConductivityTensor

Static Protected Attributes
static const int	WRITE_EVERY_NTH_TIME = 1

Friends
class	TestAbstractContractionCellFactory

class	TestCardiacElectroMechanicsProblem

class	TestCardiacElectroMechanicsFurtherFunctionality

class	TestElectroMechanicsExactSolution

Detailed Description

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>
class CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >

CardiacElectroMechanicsProblem

For solving full electro-mechanical problems.

Solves a monodomain problem (diffusion plus cell models) on a (fine) electrics mesh, and a mechanics problem (finite elasticity plus contraction model) on a coarse mesh. An implicit scheme (Jon Whiteley's algorithm) be be used.

For solving problems on regular grids use CardiacElectroMechProbRegularGeom

The implicit algorithm:

Store the position in the electrics mesh of each quad point in the mechanics mesh For every time: Solve the monodomain problem (ie integrate ODEs, solve PDE) Get intracellular [Ca] at each electrics node and interpolate on each mechanics quad point Set [Ca] on each contraction model (one for each point) Solve static finite elasticity problem implicity

guess solution
this gives the fibre stretch and stretch rate to be set on contraction models
integrate contraction models (implicitly if NHS) to get for active tension
use this active tension in computing the stress for that guess of the deformation end

Definition at line 94 of file CardiacElectroMechanicsProblem.hpp.

Constructor & Destructor Documentation

◆ CardiacElectroMechanicsProblem()

template<unsigned DIM, unsigned ELEC_PROB_DIM>

CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::CardiacElectroMechanicsProblem	(	CompressibilityType	compressibilityType,
		ElectricsProblemType	electricsProblemType,
		TetrahedralMesh< DIM, DIM > *	pElectricsMesh,
		QuadraticMesh< DIM > *	pMechanicsMesh,
		AbstractCardiacCellFactory< DIM > *	pCellFactory,
		ElectroMechanicsProblemDefinition< DIM > *	pProblemDefinition,
		std::string	outputDirectory
	)

Constructor.

Parameters

compressibilityType	Should be either INCOMPRESSIBLE or COMPRESSIBLE
electricsProblemType	the type of electrics problem (MONODOMAIN or BIDOMAIN)
pElectricsMesh	Mesh on which to solve electrics (Monodomain)
pMechanicsMesh	Mesh (2nd order) on which to solve mechanics
pCellFactory	factory to use to create cells
pProblemDefinition	electro-mechanics problem definition
outputDirectory	the output directory

Definition at line 256 of file CardiacElectroMechanicsProblem.cpp.

References GenericEventHandler< 7, MechanicsEventHandler >::BeginEvent(), CreateElectricsProblem< DIM, PROBLEM_DIM >::Create(), GenericEventHandler< 16, HeartEventHandler >::Disable(), HeartConfig::Instance(), CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::mDeformationOutputDirectory, CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::mHasBath, CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::mOutputDirectory, CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::mpElectricsProblem, CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::mWriteOutput, GenericEventHandler< 7, MechanicsEventHandler >::Reset(), HeartConfig::SetOutputDirectory(), and HeartConfig::SetOutputFilenamePrefix().

◆ ~CardiacElectroMechanicsProblem()

template<unsigned DIM, unsigned ELEC_PROB_DIM>

CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::~CardiacElectroMechanicsProblem ( )

virtual

Delete allocated memory and close the watched location file

NOTE if SetWatchedLocation but not Initialise has been called, mpWatchedLocationFile will be uninitialised and using it will cause a seg fault. Hence the mpMechanicsMesh!=NULL it is true if Initialise has been called.

Definition at line 327 of file CardiacElectroMechanicsProblem.cpp.

References LogFile::Close().

Member Function Documentation

◆ DetermineWatchedNodes()

template<unsigned DIM, unsigned ELEC_PROB_DIM>

void CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::DetermineWatchedNodes ( )

protected

Determine which node is closest to the watched location

Definition at line 60 of file CardiacElectroMechanicsProblem.cpp.

References NEVER_REACHED, OutputFileHandler::OpenOutputFile(), and UNSIGNED_UNSET.

◆ GetMechanicsSolver()

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>

AbstractNonlinearElasticitySolver< DIM > * CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::GetMechanicsSolver ( )

inline

Get the mechanics solver used in the solve. Only call after a solve.

Returns: The mechanics (nonlinear elasticity) PDE solver.

Definition at line 300 of file CardiacElectroMechanicsProblem.hpp.

References CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::mpMechanicsSolver.

◆ Initialise()

template<unsigned DIM, unsigned ELEC_PROB_DIM>

void CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Initialise ( )

Initialise the class. Initialises the MonodomainProblem and sets up the electrics mesh to mechanics mesh data.

Todo:: This is fragile: check how the TimeStepper does it, and possibly refactor the behaviour there into a static helper method if it isn't already.

Definition at line 345 of file CardiacElectroMechanicsProblem.cpp.

References EXCEPTION, HeartConfig::GetPdeTimeStep(), LogFile::Instance(), HeartConfig::Instance(), NEVER_REACHED, LogFile::Set(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and LogFile::WriteHeader().

◆ Max()

template<unsigned DIM, unsigned ELEC_PROB_DIM>

double CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Max ( std::vector< double > & vec )

Short helper function

Returns: the max of a std::vector

Parameters

vec	a vector of doubles

Definition at line 946 of file CardiacElectroMechanicsProblem.cpp.

◆ OnEndOfTimeStep()

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>

virtual void CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::OnEndOfTimeStep ( unsigned counter )

inlinevirtual

Called in Solve() at the end of every time step

Parameters

counter time step

Definition at line 291 of file CardiacElectroMechanicsProblem.hpp.

◆ PrepareForSolve()

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>

virtual void CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::PrepareForSolve ( )

inlinevirtual

Called in Solve() before the time loop

Definition at line 285 of file CardiacElectroMechanicsProblem.hpp.

◆ rCalculateModifiedConductivityTensor()

template<unsigned DIM, unsigned ELEC_PROB_DIM>

c_matrix< double, DIM, DIM > & CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::rCalculateModifiedConductivityTensor	(	unsigned	elementIndex,
		const c_matrix< double, DIM, DIM > &	rOriginalConductivity,
		unsigned	domainIndex
	)

The implementation of the pure method defined in the base class AbstractConductivityModifier. The tissue class will call this method.

Parameters

elementIndex	Index of current element
rOriginalConductivity	Reference to the original (for example, undeformed) conductivity tensor
domainIndex	Used to tailor modification to the domain. 0 = intracellular, 1 = extracellular, 2 = second intracellular (tridomain)

Returns: Reference to a modified conductivity tensor.

Definition at line 169 of file CardiacElectroMechanicsProblem.cpp.

References Inverse().

◆ rGetDeformedPosition()

template<unsigned DIM, unsigned ELEC_PROB_DIM>

std::vector< c_vector< double, DIM > > & CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::rGetDeformedPosition ( )

Returns: the current deformed position of the nodes

Definition at line 980 of file CardiacElectroMechanicsProblem.cpp.

◆ SetNoElectricsOutput()

template<unsigned DIM, unsigned ELEC_PROB_DIM>

void CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::SetNoElectricsOutput ( )

Call to not write out voltages

Definition at line 957 of file CardiacElectroMechanicsProblem.cpp.

◆ SetOutputDeformationGradientsAndStress()

template<unsigned DIM, unsigned ELEC_PROB_DIM>

void CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::SetOutputDeformationGradientsAndStress ( double timestep )

Call this for a files containing the deformation gradients (F), evaluated at the centroids of element, and the 2nd PK stress for each element (averaged over the values at the quadrature points of that element), to be written,

Parameters

timestep how often to write this. Must be a multiple of the mechanics timestep.

Definition at line 970 of file CardiacElectroMechanicsProblem.cpp.

References EXCEPTION.

◆ SetWatchedPosition()

template<unsigned DIM, unsigned ELEC_PROB_DIM>

void CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::SetWatchedPosition ( c_vector< double, DIM > watchedLocation )

Set a location to be watched - for which lots of output is given. Should correspond to nodes in both meshes.

The watched file will have rows that look like: time x_pos y_pos [z_pos] voltage Ca_i_conc.

NOTE: for the Calcium - assumes LUO_RUDY IS USED

Parameters

watchedLocation location (x,y,z) in space. Watched node is the closest to this point.

Definition at line 963 of file CardiacElectroMechanicsProblem.cpp.

◆ Solve()

template<unsigned DIM, unsigned ELEC_PROB_DIM>

void CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve ( )

Solve the electromechanics problem

Definition at line 488 of file CardiacElectroMechanicsProblem.cpp.

◆ WriteWatchedLocationData()

template<unsigned DIM, unsigned ELEC_PROB_DIM>

void CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::WriteWatchedLocationData	(	double	time,
		Vec	voltage
	)

protected

Write info (x, y, [z], V) for the watched node.

Parameters

time	Time-step now, to write out
voltage	Vm vector (this is Monodomain)

Todo:: Improve efficiency of this method?

Definition at line 144 of file CardiacElectroMechanicsProblem.cpp.

Friends And Related Symbol Documentation

◆ TestAbstractContractionCellFactory

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>

friend class TestAbstractContractionCellFactory

friend

Definition at line 98 of file CardiacElectroMechanicsProblem.hpp.

◆ TestCardiacElectroMechanicsFurtherFunctionality

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>

friend class TestCardiacElectroMechanicsFurtherFunctionality

friend

Definition at line 100 of file CardiacElectroMechanicsProblem.hpp.

◆ TestCardiacElectroMechanicsProblem

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>

friend class TestCardiacElectroMechanicsProblem

friend

Definition at line 99 of file CardiacElectroMechanicsProblem.hpp.

◆ TestElectroMechanicsExactSolution

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>

friend class TestElectroMechanicsExactSolution

friend

Definition at line 101 of file CardiacElectroMechanicsProblem.hpp.

Member Data Documentation

◆ mCompressibilityType

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>

CompressibilityType CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::mCompressibilityType

protected

Either COMPRESSIBLE or INCOMPRESSIBLE

Definition at line 105 of file CardiacElectroMechanicsProblem.hpp.

◆ mDeformationGradientsForEachMechanicsElement

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>

std::vector<c_matrix<double,DIM,DIM> > CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::mDeformationGradientsForEachMechanicsElement

protected

A vector of deformation gradients (each entry a matrix), one for each element in the mechanics mesh

Definition at line 175 of file CardiacElectroMechanicsProblem.hpp.

◆ mDeformationOutputDirectory

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>

std::string CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::mDeformationOutputDirectory

protected

Deformation output-sub-directory

Definition at line 149 of file CardiacElectroMechanicsProblem.hpp.

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::CardiacElectroMechanicsProblem().

◆ mHasBath

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>

bool CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::mHasBath

protected

Whether the mesh has a bath (non-active) region or not. False by default.

Definition at line 141 of file CardiacElectroMechanicsProblem.hpp.

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::CardiacElectroMechanicsProblem().

◆ mInterpolatedCalciumConcs

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>

std::vector<double> CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::mInterpolatedCalciumConcs

protected

A cache for the interpolated calcium concentrations from electrics to mechanics mesh. Memory is allocated within Initialise(). Filled in during Solve() and passed on to the mechanics solver

Definition at line 124 of file CardiacElectroMechanicsProblem.hpp.

◆ mInterpolatedVoltages

template<unsigned DIM, unsigned ELEC_PROB_DIM = 1>

std::vector<double> CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::mInterpolatedVoltages

protected

A cache for the interpolated voltages from electrics to mechanics mesh. Memory is allocated within Initialise(). Filled in during Solve() and passed on to the mechanics solver

Definition at line 130 of file CardiacElectroMechanicsProblem.hpp.