CardiacElectroMechanicsProblem< DIM > Class Template Reference

#include <CardiacElectroMechanicsProblem.hpp>

Inheritance diagram for CardiacElectroMechanicsProblem< DIM >:

Collaboration diagram for CardiacElectroMechanicsProblem< DIM >:

List of all members.

Public Member Functions

CardiacElectroMechanicsProblem (TetrahedralMesh< DIM, DIM > *pElectricsMesh, QuadraticMesh< DIM > *pMechanicsMesh, std::vector< unsigned > fixedMechanicsNodes, AbstractCardiacCellFactory< DIM > *pCellFactory, double endTime, unsigned numElecTimeStepsPerMechTimestep, double nhsOdeTimeStep, 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 ()

Protected Member Functions

void DetermineWatchedNodes ()

void WriteWatchedLocationData (double time, Vec voltage)

Protected Attributes

MonodomainProblem< DIM > * mpMonodomainProblem

ImplicitCardiacMechanicsAssembler
< DIM > * mpCardiacMechAssembler

double mEndTime

double mElectricsTimeStep

double mMechanicsTimeStep

unsigned mNumElecTimestepsPerMechTimestep

double mNhsOdeTimeStep

TetrahedralMesh< DIM, DIM > * mpElectricsMesh

QuadraticMesh< DIM > * mpMechanicsMesh

std::vector< ElementAndWeights
< DIM > > mElementAndWeightsForQuadPoints

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< unsigned > mFixedNodes

Static Protected Attributes

static const int WRITE_EVERY_NTH_TIME = 1

Friends

class TestCardiacElectroMechanicsProblem

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 NHS cell models) 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 NHS 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 NHS models
integrate NHS models implicity for active tension
use this active tension in computing the stress for that guess of the deformation end

Note: invC is not used in the monodomain equations (code added but commented out) we have shown that this does not affect the mechanics results (might affect the electrics).

Definition at line 99 of file CardiacElectroMechanicsProblem.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

CardiacElectroMechanicsProblem< DIM >::CardiacElectroMechanicsProblem	(	TetrahedralMesh< DIM, DIM > *	pElectricsMesh,
		QuadraticMesh< DIM > *	pMechanicsMesh,
		std::vector< unsigned >	fixedMechanicsNodes,
		AbstractCardiacCellFactory< DIM > *	pCellFactory,
		double	endTime,
		unsigned	numElecTimeStepsPerMechTimestep,
		double	nhsOdeTimeStep,
		std::string	outputDirectory = `""`
	)			`[inline]`

Constructor

Definition at line 162 of file CardiacElectroMechanicsProblem.cpp.

template<unsigned DIM>

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

Delete allocated memory and close the watched location file

Definition at line 247 of file CardiacElectroMechanicsProblem.cpp.

References LogFile::Close(), CardiacElectroMechanicsProblem< DIM >::mIsWatchedLocation, CardiacElectroMechanicsProblem< DIM >::mpCardiacMechAssembler, CardiacElectroMechanicsProblem< DIM >::mpMechanicsMesh, 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 >::WriteWatchedLocationData	(	double	time,
		Vec	voltage
	)			`[inline, protected]`

Write info (x, y, V, and Ca) for the watched node. Note: the Ca is written, but this ASSUMES LUO-RUDY IS USED

Todo:: Rather inefficient

Todo:: :

Definition at line 137 of file CardiacElectroMechanicsProblem.cpp.

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

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

template<unsigned DIM>

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

Initialise the class. Calls ConstructMeshes() and ConstructMechanicsAssembler(). Initialises the MonodomainProblem and sets up the electrics mesh to mechanics mesh data.

Definition at line 265 of file CardiacElectroMechanicsProblem.cpp.

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

template<unsigned DIM>

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

Solve the electromechanics problem

Definition at line 334 of file CardiacElectroMechanicsProblem.cpp.

template<unsigned DIM>

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

Call to not write out voltages

Definition at line 543 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

Definition at line 549 of file CardiacElectroMechanicsProblem.cpp.

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

template<unsigned DIM>

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

Get the current deformed position of the nodes

Definition at line 556 of file CardiacElectroMechanicsProblem.cpp.

References CardiacElectroMechanicsProblem< DIM >::mpCardiacMechAssembler.

Member Data Documentation

template<unsigned DIM>

MonodomainProblem<DIM>* CardiacElectroMechanicsProblem< DIM >::mpMonodomainProblem [protected]

The cardiac problem class

Definition at line 106 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

ImplicitCardiacMechanicsAssembler<DIM>* CardiacElectroMechanicsProblem< DIM >::mpCardiacMechAssembler [protected]

The mechanics assembler

Definition at line 108 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

double CardiacElectroMechanicsProblem< DIM >::mEndTime [protected]

End time. The start time is assumed to be 0.0

Definition at line 111 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

double CardiacElectroMechanicsProblem< DIM >::mElectricsTimeStep [protected]

The electrics timestep.

Definition at line 113 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

double CardiacElectroMechanicsProblem< DIM >::mMechanicsTimeStep [protected]

The mechanics timestep. Needs to be a multiple of the electrics timestep

Definition at line 115 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

unsigned CardiacElectroMechanicsProblem< DIM >::mNumElecTimestepsPerMechTimestep [protected]

The number of electrics timesteps per mechanics timestep

Definition at line 117 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

double CardiacElectroMechanicsProblem< DIM >::mNhsOdeTimeStep [protected]

Timestep to use when solving NHS models (for implicit version)

Definition at line 119 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

TetrahedralMesh<DIM,DIM>* CardiacElectroMechanicsProblem< DIM >::mpElectricsMesh [protected]

The mesh for the electrics

Definition at line 122 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

QuadraticMesh<DIM>* CardiacElectroMechanicsProblem< DIM >::mpMechanicsMesh [protected]

The mesh for the mechanics

Definition at line 124 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

std::vector<ElementAndWeights<DIM> > CardiacElectroMechanicsProblem< DIM >::mElementAndWeightsForQuadPoints [protected]

The (electrics-mesh) element numbers saying which element each (mechanics-mesh) gauss point is in, and the weight of that gauss point for that particular element.

Definition at line 131 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

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

Output directory, relative to TEST_OUTPUT

Definition at line 134 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

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

Deformation output-sub-directory

Definition at line 136 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

bool CardiacElectroMechanicsProblem< DIM >::mWriteOutput [protected]

Whether to write any output

Definition at line 138 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

bool CardiacElectroMechanicsProblem< DIM >::mNoElectricsOutput [protected]

Whether to not write out voltages

Definition at line 140 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

const int CardiacElectroMechanicsProblem< DIM >::WRITE_EVERY_NTH_TIME = 1 [static, protected]

when to write output

Definition at line 143 of file CardiacElectroMechanicsProblem.hpp.

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

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 146 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

c_vector<double,DIM> CardiacElectroMechanicsProblem< DIM >::mWatchedLocation [protected]

The watched location if there is one

Definition at line 148 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

unsigned CardiacElectroMechanicsProblem< DIM >::mWatchedElectricsNodeIndex [protected]

The node in the electrics mesh corresponding to the watched location

Definition at line 150 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

unsigned CardiacElectroMechanicsProblem< DIM >::mWatchedMechanicsNodeIndex [protected]

The node in the mechanics mesh corresponding to the watched location

Definition at line 152 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

out_stream CardiacElectroMechanicsProblem< DIM >::mpWatchedLocationFile [protected]

File where watched location info is written

Definition at line 154 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>

std::vector<unsigned> CardiacElectroMechanicsProblem< DIM >::mFixedNodes [protected]

Nodes for which the deformation is fixed to zero

Definition at line 157 of file CardiacElectroMechanicsProblem.hpp.

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

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

/tmp/release_1/heart/src/problem/CardiacElectroMechanicsProblem.hpp
/tmp/release_1/heart/src/problem/CardiacElectroMechanicsProblem.cpp


Public Member Functions
	CardiacElectroMechanicsProblem (TetrahedralMesh< DIM, DIM > pElectricsMesh, QuadraticMesh< DIM > pMechanicsMesh, std::vector< unsigned > fixedMechanicsNodes, AbstractCardiacCellFactory< DIM > *pCellFactory, double endTime, unsigned numElecTimeStepsPerMechTimestep, double nhsOdeTimeStep, 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 ()
Protected Member Functions
void	DetermineWatchedNodes ()
void	WriteWatchedLocationData (double time, Vec voltage)
Protected Attributes
MonodomainProblem< DIM > *	mpMonodomainProblem
ImplicitCardiacMechanicsAssembler < DIM > *	mpCardiacMechAssembler
double	mEndTime
double	mElectricsTimeStep
double	mMechanicsTimeStep
unsigned	mNumElecTimestepsPerMechTimestep
double	mNhsOdeTimeStep
TetrahedralMesh< DIM, DIM > *	mpElectricsMesh
QuadraticMesh< DIM > *	mpMechanicsMesh
std::vector< ElementAndWeights < DIM > >	mElementAndWeightsForQuadPoints
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< unsigned >	mFixedNodes
Static Protected Attributes
static const int	WRITE_EVERY_NTH_TIME = 1
Friends
class	TestCardiacElectroMechanicsProblem

CardiacElectroMechanicsProblem< DIM > Class Template Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Friends

Detailed Description

template<unsigned DIM> class CardiacElectroMechanicsProblem< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class CardiacElectroMechanicsProblem< DIM >