CardiacElectroMechanicsProblem< DIM > Class Template Reference

#include <CardiacElectroMechanicsProblem.hpp>

Inherits AbstractConductivityModifier< DIM, DIM >.

Inherited by CardiacElectroMechProbRegularGeom< DIM >.

Collaboration diagram for CardiacElectroMechanicsProblem< DIM >:

Public Member Functions
	CardiacElectroMechanicsProblem (CompressibilityType compressibilityType, 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)
std::vector< c_vector< double, DIM > > &	rGetDeformedPosition ()
c_matrix< double, DIM, DIM > &	rGetModifiedConductivityTensor (unsigned elementIndex, const c_matrix< double, DIM, DIM > &rOriginalConductivity)
virtual void	PrepareForSolve ()
virtual void	OnEndOfTimeStep (unsigned counter)
Protected Member Functions
void	DetermineWatchedNodes ()
void	WriteWatchedLocationData (double time, Vec voltage)
Protected Attributes
CompressibilityType	mCompressibilityType
MonodomainProblem< DIM > *	mpMonodomainProblem
AbstractCardiacMechanicsSolverInterface < DIM > *	mpCardiacMechSolver
AbstractNonlinearElasticitySolver < DIM > *	mpMechanicsSolver
unsigned	mNumElecTimestepsPerMechTimestep
TetrahedralMesh< DIM, DIM > *	mpElectricsMesh
QuadraticMesh< DIM > *	mpMechanicsMesh
ElectroMechanicsProblemDefinition < DIM > *	mpProblemDefinition
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
std::vector< double >	mStretchesForEachMechanicsElement
std::vector< c_matrix< double, DIM, DIM > >	mDeformationGradientsForEachMechanicsElement
std::pair< unsigned, c_matrix < double, DIM, DIM > >	mLastModifiedConductivity
Static Protected Attributes
static const int	WRITE_EVERY_NTH_TIME = 1
Friends
class	TestCardiacElectroMechanicsProblem
class	TestCardiacElectroMechanicsFurtherFunctionality

Detailed Description

template<unsigned DIM>
class CardiacElectroMechanicsProblem< 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 74 of file CardiacElectroMechanicsProblem.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

CardiacElectroMechanicsProblem< DIM >::CardiacElectroMechanicsProblem	(	CompressibilityType	compressibilityType,
		TetrahedralMesh< DIM, DIM > *	pElectricsMesh,
		QuadraticMesh< DIM > *	pMechanicsMesh,
		AbstractCardiacCellFactory< DIM > *	pCellFactory,
		ElectroMechanicsProblemDefinition< DIM > *	pProblemDefinition,
		std::string	outputDirectory = `""`
	)			`[inline]`

Constructor.

Parameters:

	compressibilityType	Should be either INCOMPRESSIBLE or COMPRESSIBLE
	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 224 of file CardiacElectroMechanicsProblem.cpp.

References GenericEventHandler< 7, MechanicsEventHandler >::BeginEvent(), GenericEventHandler< 16, HeartEventHandler >::Disable(), HeartConfig::Instance(), CardiacElectroMechanicsProblem< DIM >::mDeformationOutputDirectory, CardiacElectroMechanicsProblem< DIM >::mLastModifiedConductivity, CardiacElectroMechanicsProblem< DIM >::mOutputDirectory, CardiacElectroMechanicsProblem< DIM >::mpMonodomainProblem, CardiacElectroMechanicsProblem< DIM >::mWriteOutput, GenericEventHandler< 7, MechanicsEventHandler >::Reset(), HeartConfig::SetOutputDirectory(), HeartConfig::SetOutputFilenamePrefix(), and UNSIGNED_UNSET.

template<unsigned DIM>

CardiacElectroMechanicsProblem< DIM >::~CardiacElectroMechanicsProblem ( ) [inline, 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 290 of file CardiacElectroMechanicsProblem.cpp.

References LogFile::Close(), CardiacElectroMechanicsProblem< DIM >::mIsWatchedLocation, CardiacElectroMechanicsProblem< DIM >::mpCardiacMechSolver, CardiacElectroMechanicsProblem< DIM >::mpMechanicsMesh, CardiacElectroMechanicsProblem< DIM >::mpMeshPair, CardiacElectroMechanicsProblem< DIM >::mpMonodomainProblem, and CardiacElectroMechanicsProblem< DIM >::mpWatchedLocationFile.

Member Function Documentation

template<unsigned DIM>

void CardiacElectroMechanicsProblem< DIM >::DetermineWatchedNodes ( ) [inline, protected]

Determine which node is closest to the watched location

Definition at line 53 of file CardiacElectroMechanicsProblem.cpp.

Referenced by CardiacElectroMechanicsProblem< DIM >::Initialise().

template<unsigned DIM>

void CardiacElectroMechanicsProblem< DIM >::Initialise ( ) [inline]

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

Definition at line 308 of file CardiacElectroMechanicsProblem.cpp.

Referenced by CardiacElectroMechanicsProblem< DIM >::Solve().

template<unsigned DIM>

double CardiacElectroMechanicsProblem< DIM >::Max ( std::vector< double > & vec ) [inline]

Short helper function - the max of a std::vector

Parameters:

vec

a vector of doubles

Definition at line 779 of file CardiacElectroMechanicsProblem.cpp.

Referenced by CardiacElectroMechanicsProblem< DIM >::Solve().

template<unsigned DIM>

virtual void CardiacElectroMechanicsProblem< DIM >::OnEndOfTimeStep ( unsigned counter ) [inline, virtual]

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

Parameters:

counter

time step

Definition at line 251 of file CardiacElectroMechanicsProblem.hpp.

Referenced by CardiacElectroMechanicsProblem< DIM >::Solve().

template<unsigned DIM>

virtual void CardiacElectroMechanicsProblem< DIM >::PrepareForSolve ( ) [inline, virtual]

Called in Solve() before the time loop

Definition at line 245 of file CardiacElectroMechanicsProblem.hpp.

Referenced by CardiacElectroMechanicsProblem< DIM >::Solve().

template<unsigned DIM>

std::vector< c_vector< double, DIM > > & CardiacElectroMechanicsProblem< DIM >::rGetDeformedPosition ( ) [inline]

Returns:: the current deformed position of the nodes

Definition at line 804 of file CardiacElectroMechanicsProblem.cpp.

References CardiacElectroMechanicsProblem< DIM >::mpMechanicsSolver.

Referenced by CardiacElectroMechanicsProblem< DIM >::Solve().

template<unsigned DIM>

c_matrix< double, DIM, DIM > & CardiacElectroMechanicsProblem< DIM >::rGetModifiedConductivityTensor	(	unsigned	elementIndex,
		const c_matrix< double, DIM, DIM > &	rOriginalConductivity
	)			`[inline]`

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

Returns:: Reference to a modified conductivity tensor.

Definition at line 162 of file CardiacElectroMechanicsProblem.cpp.

References Inverse(), CardiacElectroMechanicsProblem< DIM >::mDeformationGradientsForEachMechanicsElement, CardiacElectroMechanicsProblem< DIM >::mLastModifiedConductivity, and CardiacElectroMechanicsProblem< DIM >::mpMeshPair.

template<unsigned DIM>

void CardiacElectroMechanicsProblem< DIM >::SetNoElectricsOutput ( ) [inline]

Call to not write out voltages

Definition at line 790 of file CardiacElectroMechanicsProblem.cpp.

References CardiacElectroMechanicsProblem< DIM >::mNoElectricsOutput.

template<unsigned DIM>

void CardiacElectroMechanicsProblem< DIM >::SetWatchedPosition ( c_vector< double, DIM > watchedLocation ) [inline]

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 796 of file CardiacElectroMechanicsProblem.cpp.

References CardiacElectroMechanicsProblem< DIM >::mIsWatchedLocation, and CardiacElectroMechanicsProblem< DIM >::mWatchedLocation.

template<unsigned DIM>

void CardiacElectroMechanicsProblem< DIM >::Solve ( ) [inline]

Solve the electromechanics problem

Definition at line 454 of file CardiacElectroMechanicsProblem.cpp.

template<unsigned DIM>

void CardiacElectroMechanicsProblem< DIM >::WriteWatchedLocationData	(	double	time,
		Vec	voltage
	)			`[inline, 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 137 of file CardiacElectroMechanicsProblem.cpp.

References CardiacElectroMechanicsProblem< DIM >::mIsWatchedLocation, CardiacElectroMechanicsProblem< DIM >::mpMechanicsSolver, CardiacElectroMechanicsProblem< DIM >::mpWatchedLocationFile, CardiacElectroMechanicsProblem< DIM >::mWatchedElectricsNodeIndex, and CardiacElectroMechanicsProblem< DIM >::mWatchedMechanicsNodeIndex.

Referenced by CardiacElectroMechanicsProblem< DIM >::Solve().

Member Data Documentation

template<unsigned DIM>

CompressibilityType CardiacElectroMechanicsProblem< DIM >::mCompressibilityType [protected]

Either COMPRESSIBLE or INCOMPRESSIBLE

Definition at line 84 of file CardiacElectroMechanicsProblem.hpp.

Referenced by CardiacElectroMechanicsProblem< DIM >::Initialise().

template<unsigned DIM>

std::vector<c_matrix<double,DIM,DIM> > CardiacElectroMechanicsProblem< DIM >::mDeformationGradientsForEachMechanicsElement [protected]

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

Definition at line 138 of file CardiacElectroMechanicsProblem.hpp.

Referenced by CardiacElectroMechanicsProblem< DIM >::Initialise(), CardiacElectroMechanicsProblem< DIM >::rGetModifiedConductivityTensor(), and CardiacElectroMechanicsProblem< DIM >::Solve().

template<unsigned DIM>

std::string CardiacElectroMechanicsProblem< DIM >::mDeformationOutputDirectory [protected]

Deformation output-sub-directory

Definition at line 115 of file CardiacElectroMechanicsProblem.hpp.

Referenced by CardiacElectroMechanicsProblem< DIM >::CardiacElectroMechanicsProblem(), and CardiacElectroMechanicsProblem< DIM >::Initialise().

template<unsigned DIM>

bool CardiacElectroMechanicsProblem< DIM >::mIsWatchedLocation [protected]

Whether any location has been set to be watched (lots of output for that location

Definition at line 125 of file CardiacElectroMechanicsProblem.hpp.

Referenced by CardiacElectroMechanicsProblem< DIM >::DetermineWatchedNodes(), CardiacElectroMechanicsProblem< DIM >::Initialise(), CardiacElectroMechanicsProblem< DIM >::SetWatchedPosition(), CardiacElectroMechanicsProblem< DIM >::Solve(), CardiacElectroMechanicsProblem< DIM >::WriteWatchedLocationData(), and CardiacElectroMechanicsProblem< DIM >::~CardiacElectroMechanicsProblem().

template<unsigned DIM>

std::pair<unsigned, c_matrix<double,DIM,DIM> > CardiacElectroMechanicsProblem< DIM >::mLastModifiedConductivity [protected]

A pair of (element_index, deformed_conductivity) for the last element on which the deformed conductivity sigma_def = F^{-1} sigma_undef F^{-T} has been computed. Used in rGetModifiedConductivityTensor().

Definition at line 143 of file CardiacElectroMechanicsProblem.hpp.

Referenced by CardiacElectroMechanicsProblem< DIM >::CardiacElectroMechanicsProblem(), and CardiacElectroMechanicsProblem< DIM >::rGetModifiedConductivityTensor().

template<unsigned DIM>

bool CardiacElectroMechanicsProblem< DIM >::mNoElectricsOutput [protected]

Whether to not write out voltages

Definition at line 119 of file CardiacElectroMechanicsProblem.hpp.

Referenced by CardiacElectroMechanicsProblem< DIM >::SetNoElectricsOutput(), and CardiacElectroMechanicsProblem< DIM >::Solve().

template<unsigned DIM>

unsigned CardiacElectroMechanicsProblem< DIM >::mNumElecTimestepsPerMechTimestep [protected]

The number of electrics timesteps per mechanics timestep

Definition at line 97 of file CardiacElectroMechanicsProblem.hpp.

Referenced by CardiacElectroMechanicsProblem< DIM >::Initialise(), and CardiacElectroMechanicsProblem< DIM >::Solve().