ElectroMechanicsProblemDefinition< DIM > Class Template Reference

#include <ElectroMechanicsProblemDefinition.hpp>

Inherits SolidMechanicsProblemDefinition< DIM >.

Collaboration diagram for ElectroMechanicsProblemDefinition< DIM >:
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List of all members.

Public Member Functions

 ElectroMechanicsProblemDefinition (QuadraticMesh< DIM > &rMesh)
virtual ~ElectroMechanicsProblemDefinition ()
void SetContractionModel (ContractionModelName contractionModel, double timestep)
void SetContractionCellFactory (AbstractContractionCellFactory< DIM > *pCellFactory)
void SetUseDefaultCardiacMaterialLaw (CompressibilityType compressibilityType)
void SetSolverType (SolverType solver)
void SetDeformationAffectsElectrophysiology (bool deformationAffectsConductivity, bool deformationAffectsCellModels)
void SetMechanicsSolveTimestep (double timestep)
void SetVariableFibreSheetDirectionsFile (const FileFinder &rFibreSheetDirectionsFile, bool definedPerQuadPoint)
void SetApplyIsotropicCrossFibreTension (bool applyCrossFibreTension, double crossFibreTensionFraction)
void SetApplyAnisotropicCrossFibreTension (bool applyCrossFibreTension, double sheetTensionFraction, double sheetNormalTensionFraction)
AbstractContractionCellFactory
< DIM > * 
GetContractionCellFactory ()
void SetContractionModelOdeTimestep (double timestep)
double GetContractionModelOdeTimestep ()
double GetMechanicsSolveTimestep ()
bool GetDeformationAffectsConductivity ()
bool GetDeformationAffectsCellModels ()
SolverType GetSolverType ()
bool ReadFibreSheetDirectionsFromFile ()
FileFinder GetFibreSheetDirectionsFile ()
bool GetFibreSheetDirectionsDefinedPerQuadraturePoint ()
void SetNumIncrementsForInitialDeformation (unsigned numIncrements)
unsigned GetNumIncrementsForInitialDeformation ()
double GetApplyCrossFibreTension ()
double GetSheetTensionFraction ()
double GetSheetNormalTensionFraction ()
virtual void Validate ()

Private Attributes

double mContractionModelOdeTimeStep
double mMechanicsSolveTimestep
bool mDeformationAffectsConductivity
bool mDeformationAffectsCellModels
AbstractMaterialLaw< DIM > * mpDefaultMaterialLaw
bool mReadFibreSheetInformationFromFile
FileFinder mFibreSheetDirectionsFile
bool mFibreSheetDirectionsDefinedPerQuadraturePoint
unsigned mNumIncrementsForInitialDeformation
bool mApplyCrossFibreTension
double mSheetTensionFraction
double mSheetNormalTensionFraction
AbstractContractionCellFactory
< DIM > * 
mpContractionCellFactory
bool mWeMadeCellFactory
SolverType mSolverType

Friends

class TestExplicitCardiacMechanicsSolver
class TestImplicitCardiacMechanicsSolver
class TestElectroMechanicsProblemDefinition

Detailed Description

template<unsigned DIM>
class ElectroMechanicsProblemDefinition< DIM >

Subclass of SolidMechanicsProblemDefinition with some cardiac-electro-mechanics-specific methods.

Definition at line 52 of file ElectroMechanicsProblemDefinition.hpp.


Constructor & Destructor Documentation

template<unsigned DIM>
ElectroMechanicsProblemDefinition< DIM >::ElectroMechanicsProblemDefinition ( QuadraticMesh< DIM > &  rMesh  )  [inline]

Constructor

Parameters:
rMesh the mesh

Definition at line 40 of file ElectroMechanicsProblemDefinition.cpp.

template<unsigned DIM>
ElectroMechanicsProblemDefinition< DIM >::~ElectroMechanicsProblemDefinition (  )  [inline, virtual]

Member Function Documentation

template<unsigned DIM>
double ElectroMechanicsProblemDefinition< DIM >::GetApplyCrossFibreTension (  )  [inline]
Returns:
true if cross-fibre tension is applied.

Definition at line 375 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mApplyCrossFibreTension.

template<unsigned DIM>
AbstractContractionCellFactory<DIM>* ElectroMechanicsProblemDefinition< DIM >::GetContractionCellFactory (  )  [inline]
Returns:
A pointer to the contraction cell factory that should be applied to the mechanics mesh.

Definition at line 257 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mpContractionCellFactory.

template<unsigned DIM>
double ElectroMechanicsProblemDefinition< DIM >::GetContractionModelOdeTimestep (  )  [inline]
Returns:
the contraction model time step.

Definition at line 278 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mContractionModelOdeTimeStep.

template<unsigned DIM>
bool ElectroMechanicsProblemDefinition< DIM >::GetDeformationAffectsCellModels (  )  [inline]
Returns:
whether the deformation affects the cardiac cell models, for example if there are stretch-activated channels in the cell model.

Definition at line 306 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mDeformationAffectsCellModels.

template<unsigned DIM>
bool ElectroMechanicsProblemDefinition< DIM >::GetDeformationAffectsConductivity (  )  [inline]
Returns:
whether the deformation affects the electrical physiological conductivity (or whether this effect is neglected).

Definition at line 297 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mDeformationAffectsConductivity.

template<unsigned DIM>
bool ElectroMechanicsProblemDefinition< DIM >::GetFibreSheetDirectionsDefinedPerQuadraturePoint (  )  [inline]
Returns:
whether the fibre-sheet info is defined for each quadrature point in the mesh (if not, if it defined for each element in the mesh). (Should only be called if ReadFibreSheetDirectionsFromFile() returns true).

Definition at line 342 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mFibreSheetDirectionsDefinedPerQuadraturePoint, and ElectroMechanicsProblemDefinition< DIM >::mReadFibreSheetInformationFromFile.

template<unsigned DIM>
FileFinder ElectroMechanicsProblemDefinition< DIM >::GetFibreSheetDirectionsFile (  )  [inline]
template<unsigned DIM>
double ElectroMechanicsProblemDefinition< DIM >::GetMechanicsSolveTimestep (  )  [inline]
Returns:
how often the mechanics PDEs are solved.

Definition at line 287 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mMechanicsSolveTimestep.

template<unsigned DIM>
unsigned ElectroMechanicsProblemDefinition< DIM >::GetNumIncrementsForInitialDeformation (  )  [inline]
Returns:
the number of increments to be used in the initial deformation (see SetNumIncrementsForInitialDeformation() for more details).

Definition at line 367 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mNumIncrementsForInitialDeformation.

template<unsigned DIM>
double ElectroMechanicsProblemDefinition< DIM >::GetSheetNormalTensionFraction (  )  [inline]
Returns:
the value of the cross-fibre sheet-normal tension fraction.

Definition at line 391 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mSheetNormalTensionFraction.

template<unsigned DIM>
double ElectroMechanicsProblemDefinition< DIM >::GetSheetTensionFraction (  )  [inline]
Returns:
the value of the cross-fibre sheet tension fraction.

Definition at line 383 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mSheetTensionFraction.

template<unsigned DIM>
SolverType ElectroMechanicsProblemDefinition< DIM >::GetSolverType (  )  [inline]
Returns:
Whether to use an implicit or explicit mechanics solver.

Definition at line 314 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mSolverType.

template<unsigned DIM>
bool ElectroMechanicsProblemDefinition< DIM >::ReadFibreSheetDirectionsFromFile (  )  [inline]
Returns:
whether the fibre-sheet info should be read from file (if not the defaults should be used).

Definition at line 322 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mReadFibreSheetInformationFromFile.

template<unsigned DIM>
void ElectroMechanicsProblemDefinition< DIM >::SetApplyAnisotropicCrossFibreTension ( bool  applyCrossFibreTension,
double  sheetTensionFraction,
double  sheetNormalTensionFraction 
) [inline]

Set if active tension should be applied in the cross-fibre directions. This only makes sense in 3D.

By default active tension is only applied in the fibre direction. This method allows the user to specify that a proportion of the active tension should also be applied in the cross-fibre directions. The fraction of the active tension that is applied in the two cross-fibre direction should be specified.

Parameters:
applyCrossFibreTension active tension is applied in the cross-fibre directions if set to true.
sheetTensionFraction The fraction of the active tension to apply in the sheet direction.
sheetNormalTensionFraction The fraction of the active tension to apply in the sheet-normal direction.

Definition at line 143 of file ElectroMechanicsProblemDefinition.cpp.

References EXCEPTION, ElectroMechanicsProblemDefinition< DIM >::mApplyCrossFibreTension, ElectroMechanicsProblemDefinition< DIM >::mSheetNormalTensionFraction, and ElectroMechanicsProblemDefinition< DIM >::mSheetTensionFraction.

template<unsigned DIM>
void ElectroMechanicsProblemDefinition< DIM >::SetApplyIsotropicCrossFibreTension ( bool  applyCrossFibreTension,
double  crossFibreTensionFraction 
) [inline]

Set if active tension should be applied in the cross-fibre directions. This can be done in 2D or 3D.

By default active tension is only applied in the fibre direction. This method allows the user to specify that a proportion of the active tension should also be applied in the cross-fibre directions (both in the sheet and sheet-normal directions equally). The fraction of the active tension that is applied in the cross-fibre direction should be specified.

Parameters:
applyCrossFibreTension active tension is applied in the cross-fibre directions if set to true.
crossFibreTensionFraction The fraction of the active tension to apply in the cross-fibre directions.

Definition at line 135 of file ElectroMechanicsProblemDefinition.cpp.

References ElectroMechanicsProblemDefinition< DIM >::mApplyCrossFibreTension, ElectroMechanicsProblemDefinition< DIM >::mSheetNormalTensionFraction, and ElectroMechanicsProblemDefinition< DIM >::mSheetTensionFraction.

template<unsigned DIM>
void ElectroMechanicsProblemDefinition< DIM >::SetContractionCellFactory ( AbstractContractionCellFactory< DIM > *  pCellFactory  )  [inline]

We provide an interface to set heterogeneous contraction cells via a cell factory, which allows different models (or parameters) to be set per element.

Note you also need to call SetContractionModelOdeTimestep() before solving.

Parameters:
pCellFactory The contraction cell factory to be used.

Definition at line 155 of file ElectroMechanicsProblemDefinition.cpp.

References ElectroMechanicsProblemDefinition< DIM >::mpContractionCellFactory, and ContinuumMechanicsProblemDefinition< DIM >::mrMesh.

Referenced by ElectroMechanicsProblemDefinition< DIM >::SetContractionModel().

template<unsigned DIM>
void ElectroMechanicsProblemDefinition< DIM >::SetContractionModel ( ContractionModelName  contractionModel,
double  timestep 
) [inline]

Set the contraction model to be used (throughout the tissue).

Note the timestep should be set to a (typical) ODE time-step even if the contraction model is not going to solve ODEs.

Parameters:
contractionModel contraction model (from the enumeration ContractionModelName)
timestep timestep to be used in solving (ODE-based) contraction models.

Definition at line 73 of file ElectroMechanicsProblemDefinition.cpp.

References ElectroMechanicsProblemDefinition< DIM >::mpContractionCellFactory, ElectroMechanicsProblemDefinition< DIM >::mWeMadeCellFactory, ElectroMechanicsProblemDefinition< DIM >::SetContractionCellFactory(), ElectroMechanicsProblemDefinition< DIM >::SetContractionModelOdeTimestep(), and ElectroMechanicsProblemDefinition< DIM >::SetSolverType().

template<unsigned DIM>
void ElectroMechanicsProblemDefinition< DIM >::SetContractionModelOdeTimestep ( double  timestep  )  [inline]

Set the timestep to be used when solving contraction models. Note that you will need to use the finest timestep that any of the models requires, it is not set on a per-model basis.

Parameters:
timestep Timestep to use.

Definition at line 270 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mContractionModelOdeTimeStep.

Referenced by ElectroMechanicsProblemDefinition< DIM >::SetContractionModel().

template<unsigned DIM>
void ElectroMechanicsProblemDefinition< DIM >::SetDeformationAffectsElectrophysiology ( bool  deformationAffectsConductivity,
bool  deformationAffectsCellModels 
) [inline]

Set if and how the deformation should affect the electro-physiology.

Parameters:
deformationAffectsConductivity Whether the deformation should affect the electrical physiological conductivity (or whether this effect is neglected)
deformationAffectsCellModels Whether the deformation should affect the cardiac cell models, for example if there are stretch-activated channels in the cell model.

Several important things to note: (i) this can't be called if fibre-sheet directions have been defined from file for each quadrature point (as opposed to each mechanics element) - this is because if the stretch is to be passed back to the electric mesh nodes, the fibre direction has to be defined at those nodes (ii) currently the set-up stage (computing mechanics mesh elements and weights for electrics mesh nodes) is inefficiently implemented - setup will be very slow for big meshes (iii) if deformationAffectsCellModels is true, the cell model ought to be one for which AbstractCardiacCell::SetStretch() has been implemented to do something (i.e. not generated automatically from CellML). (iv) deformationAffectsConductivity is not currently allowed in the compressible material law case as the effect of the determinant of the deformation gradient on the conductivity has not currently been implemented.

Definition at line 113 of file ElectroMechanicsProblemDefinition.cpp.

References ElectroMechanicsProblemDefinition< DIM >::mDeformationAffectsCellModels, and ElectroMechanicsProblemDefinition< DIM >::mDeformationAffectsConductivity.

template<unsigned DIM>
void ElectroMechanicsProblemDefinition< DIM >::SetMechanicsSolveTimestep ( double  timestep  )  [inline]

Set how often the mechanics is solved for.

Parameters:
timestep timestep

Definition at line 120 of file ElectroMechanicsProblemDefinition.cpp.

References ElectroMechanicsProblemDefinition< DIM >::mMechanicsSolveTimestep.

template<unsigned DIM>
void ElectroMechanicsProblemDefinition< DIM >::SetNumIncrementsForInitialDeformation ( unsigned  numIncrements  )  [inline]

The first deformation (to find the equilibrium state given the loading) may require the loading to be incremented, in order for the Solve() to converge. Set the number of increments to be used.

Parameters:
numIncrements number of increments

Definition at line 354 of file ElectroMechanicsProblemDefinition.hpp.

References EXCEPTION, and ElectroMechanicsProblemDefinition< DIM >::mNumIncrementsForInitialDeformation.

template<unsigned DIM>
void ElectroMechanicsProblemDefinition< DIM >::SetSolverType ( SolverType  solver  )  [inline]

Decide which type of solver to attempt to use. Default value is IMPLICIT if this method is not called.

Parameters:
solver The solver type to use (EXPLICIT or IMPLICIT).

Definition at line 175 of file ElectroMechanicsProblemDefinition.hpp.

References ElectroMechanicsProblemDefinition< DIM >::mSolverType.

Referenced by ElectroMechanicsProblemDefinition< DIM >::SetContractionModel().

template<unsigned DIM>
void ElectroMechanicsProblemDefinition< DIM >::SetUseDefaultCardiacMaterialLaw ( CompressibilityType  compressibilityType  )  [inline]

Use the default material law (NashHunter in the incompressible case, exponential in the compressible case), throughout the tissue.

Parameters:
compressibilityType Either INCOMPRESSIBLE or COMPRESSIBLE

Definition at line 93 of file ElectroMechanicsProblemDefinition.cpp.

References ElectroMechanicsProblemDefinition< DIM >::mpDefaultMaterialLaw, and SolidMechanicsProblemDefinition< DIM >::SetMaterialLaw().

template<unsigned DIM>
void ElectroMechanicsProblemDefinition< DIM >::SetVariableFibreSheetDirectionsFile ( const FileFinder rFibreSheetDirectionsFile,
bool  definedPerQuadPoint 
) [inline]

Set a variable fibre-sheet-normal direction (matrices), from file. If the second parameter is false, there should be one fibre-sheet definition for each element; otherwise there should be one fibre-sheet definition for each *quadrature point* in the mesh. In the first case, the file should be a standard .ortho file (ie each line has the fibre dir, sheet dir, normal dir for that element), in the second it should have .orthoquad as the format.

If this method is not called, the default fibre-sheet directions are used - ie fibres parallel to X-axis, sheets parallel to Y-axis.

Parameters:
rFibreSheetDirectionsFile the file containing the fibre/sheet directions
definedPerQuadPoint whether the fibre-sheet definitions are for each quadrature point in the mesh (if not, one for each element is assumed).

Definition at line 127 of file ElectroMechanicsProblemDefinition.cpp.

References ElectroMechanicsProblemDefinition< DIM >::mFibreSheetDirectionsDefinedPerQuadraturePoint, ElectroMechanicsProblemDefinition< DIM >::mFibreSheetDirectionsFile, and ElectroMechanicsProblemDefinition< DIM >::mReadFibreSheetInformationFromFile.

template<unsigned DIM>
void ElectroMechanicsProblemDefinition< DIM >::Validate (  )  [inline, virtual]

Member Data Documentation

template<unsigned DIM>
bool ElectroMechanicsProblemDefinition< DIM >::mApplyCrossFibreTension [private]
template<unsigned DIM>
double ElectroMechanicsProblemDefinition< DIM >::mContractionModelOdeTimeStep [private]
template<unsigned DIM>
bool ElectroMechanicsProblemDefinition< DIM >::mDeformationAffectsCellModels [private]

Whether the deformation should affect the cardiac cell models, for example if there are stretch-activated channels in the cell model.

Definition at line 75 of file ElectroMechanicsProblemDefinition.hpp.

Referenced by ElectroMechanicsProblemDefinition< DIM >::GetDeformationAffectsCellModels(), ElectroMechanicsProblemDefinition< DIM >::SetDeformationAffectsElectrophysiology(), and ElectroMechanicsProblemDefinition< DIM >::Validate().

Whether the deformation should affect the electrical physiological conductivity (or whether this effect is neglected)

Definition at line 69 of file ElectroMechanicsProblemDefinition.hpp.

Referenced by ElectroMechanicsProblemDefinition< DIM >::GetDeformationAffectsConductivity(), ElectroMechanicsProblemDefinition< DIM >::SetDeformationAffectsElectrophysiology(), and ElectroMechanicsProblemDefinition< DIM >::Validate().

.ortho/.orthoquad file from which to read element-wise, or quadrature-point-wise fibre-sheet-normal-directions

Definition at line 90 of file ElectroMechanicsProblemDefinition.hpp.

Referenced by ElectroMechanicsProblemDefinition< DIM >::GetFibreSheetDirectionsFile(), and ElectroMechanicsProblemDefinition< DIM >::SetVariableFibreSheetDirectionsFile().

template<unsigned DIM>
double ElectroMechanicsProblemDefinition< DIM >::mMechanicsSolveTimestep [private]

The first deformation (to find the equilibrium state given the loading) may require the loading to be incremented, in order for the Solve() to converge - this stores the number of increments to be used (initialised to 1)

Definition at line 103 of file ElectroMechanicsProblemDefinition.hpp.

Referenced by ElectroMechanicsProblemDefinition< DIM >::GetNumIncrementsForInitialDeformation(), and ElectroMechanicsProblemDefinition< DIM >::SetNumIncrementsForInitialDeformation().

template<unsigned DIM>
AbstractMaterialLaw<DIM>* ElectroMechanicsProblemDefinition< DIM >::mpDefaultMaterialLaw [private]
template<unsigned DIM>
double ElectroMechanicsProblemDefinition< DIM >::mSheetNormalTensionFraction [private]
template<unsigned DIM>
double ElectroMechanicsProblemDefinition< DIM >::mSheetTensionFraction [private]
template<unsigned DIM>
SolverType ElectroMechanicsProblemDefinition< DIM >::mSolverType [private]
template<unsigned DIM>
bool ElectroMechanicsProblemDefinition< DIM >::mWeMadeCellFactory [private]

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

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