CardiacElectroMechanicsProblem< DIM > Class Template Reference

#include <CardiacElectroMechanicsProblem.hpp>

Inheritance diagram for CardiacElectroMechanicsProblem< DIM >:

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Collaboration diagram for CardiacElectroMechanicsProblem< DIM >:

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List of all members.

Public Member Functions

 CardiacElectroMechanicsProblem (ContractionModel contractionModel, TetrahedralMesh< DIM, DIM > *pElectricsMesh, QuadraticMesh< DIM > *pMechanicsMesh, std::vector< unsigned > fixedMechanicsNodes, AbstractCardiacCellFactory< DIM > *pCellFactory, double endTime, double electricsPdeTimeStep, double mechanicsSolveTimestep, double contractionModelOdeTimeStep, 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 SetVariableFibreSheetDirectionsFile (std::string orthoFile, bool definedPerQuadPoint)
std::vector< c_vector< double,
DIM > > & 		rGetDeformedPosition ()
void UseMechanoElectricFeedback ()
c_matrix< double, DIM, DIM > & rGetModifiedConductivityTensor (unsigned elementIndex, const c_matrix< double, DIM, DIM > &rOriginalConductivity)
virtual void PrepareForSolve ()
virtual void OnEndOfTimeStep (unsigned counter)
AbstractNonlinearElasticitySolver
< DIM > * 		GetCardiacMechanicsSolver ()
void SetMaterialLaw (AbstractMaterialLaw< DIM > *pMaterialLaw)

Protected Member Functions

void DetermineWatchedNodes ()
void WriteWatchedLocationData (double time, Vec voltage)

Protected Attributes

ContractionModel mContractionModel
MonodomainProblem< DIM > * mpMonodomainProblem
AbstractCardiacMechanicsSolverInterface
< DIM > * 		mpCardiacMechSolver
AbstractNonlinearElasticitySolver
< DIM > * 		mpMechanicsSolver
double mEndTime
double mElectricsTimeStep
double mMechanicsTimeStep
unsigned mNumElecTimestepsPerMechTimestep
double mContractionModelOdeTimeStep
TetrahedralMesh< DIM, DIM > * mpElectricsMesh
QuadraticMesh< DIM > * mpMechanicsMesh
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< unsigned > mFixedNodes
std::string mFibreSheetDirectionsFile
bool mFibreSheetDirectionsDefinedPerQuadraturePoint
std::vector< double > mStretchesForEachMechanicsElement
std::vector< c_matrix< double,
DIM, DIM > > 		mDeformationGradientsForEachMechanicsElement
std::pair< unsigned, c_matrix
< double, DIM, DIM > > 		mLastModifiedConductivity
bool mConductivityAffectedByDeformationMef
bool mCellModelsAffectedByDeformationMef
AbstractMaterialLaw< DIM > * mpMaterialLaw
bool mAllocatedMaterialLawMemory

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 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

Definition at line 73 of file CardiacElectroMechanicsProblem.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
CardiacElectroMechanicsProblem< DIM >::CardiacElectroMechanicsProblem ( ContractionModel  contractionModel,
TetrahedralMesh< DIM, DIM > *  pElectricsMesh,
QuadraticMesh< DIM > *  pMechanicsMesh,
std::vector< unsigned >  fixedMechanicsNodes,
AbstractCardiacCellFactory< DIM > *  pCellFactory,
double  endTime,
double  electricsPdeTimeStep,
double  mechanicsSolveTimestep,
double  contractionModelOdeTimeStep,
std::string  outputDirectory = "" 
) [inline]

Constructor.

Parameters:
contractionModel contraction model (see the enum "ContractionModel" for the options).
pElectricsMesh Mesh on which to solve electrics (Monodomain)
pMechanicsMesh Mesh (2nd order) on which to solve mechanics
fixedMechanicsNodes Indices of those nodes which a pinned in space
pCellFactory factory to use to create cells
endTime the end time to use
electricsPdeTimeStep timestep used in solving for the electrical activity
mechanicsSolveTimestep how often the mechanics is solved for (should be a multiple of electrics PDE timestep)
contractionModelOdeTimeStep Step size for contraction model (of active tension in cardiac cells) being used.
outputDirectory the output directory

Definition at line 226 of file CardiacElectroMechanicsProblem.cpp.

References GenericEventHandler< 7, MechanicsEventHandler >::BeginEvent(), GenericEventHandler< 13, HeartEventHandler >::Disable(), EXCEPTION, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), LogFile::Instance(), HeartConfig::Instance(), CardiacElectroMechanicsProblem< DIM >::mAllocatedMaterialLawMemory, CardiacElectroMechanicsProblem< DIM >::mCellModelsAffectedByDeformationMef, CardiacElectroMechanicsProblem< DIM >::mConductivityAffectedByDeformationMef, CardiacElectroMechanicsProblem< DIM >::mContractionModel, CardiacElectroMechanicsProblem< DIM >::mContractionModelOdeTimeStep, CardiacElectroMechanicsProblem< DIM >::mDeformationOutputDirectory, CardiacElectroMechanicsProblem< DIM >::mElectricsTimeStep, CardiacElectroMechanicsProblem< DIM >::mEndTime, CardiacElectroMechanicsProblem< DIM >::mFibreSheetDirectionsFile, CardiacElectroMechanicsProblem< DIM >::mFixedNodes, CardiacElectroMechanicsProblem< DIM >::mIsWatchedLocation, CardiacElectroMechanicsProblem< DIM >::mLastModifiedConductivity, CardiacElectroMechanicsProblem< DIM >::mMechanicsTimeStep, CardiacElectroMechanicsProblem< DIM >::mNoElectricsOutput, CardiacElectroMechanicsProblem< DIM >::mNumElecTimestepsPerMechTimestep, CardiacElectroMechanicsProblem< DIM >::mOutputDirectory, CardiacElectroMechanicsProblem< DIM >::mpCardiacMechSolver, CardiacElectroMechanicsProblem< DIM >::mpElectricsMesh, CardiacElectroMechanicsProblem< DIM >::mpMaterialLaw, CardiacElectroMechanicsProblem< DIM >::mpMechanicsMesh, CardiacElectroMechanicsProblem< DIM >::mpMechanicsSolver, CardiacElectroMechanicsProblem< DIM >::mpMonodomainProblem, CardiacElectroMechanicsProblem< DIM >::mWatchedElectricsNodeIndex, CardiacElectroMechanicsProblem< DIM >::mWatchedMechanicsNodeIndex, CardiacElectroMechanicsProblem< DIM >::mWriteOutput, GenericEventHandler< 7, MechanicsEventHandler >::Reset(), LogFile::Set(), HeartConfig::SetOutputDirectory(), HeartConfig::SetOutputFilenamePrefix(), HeartConfig::SetSimulationDuration(), UNSIGNED_UNSET, and LogFile::WriteHeader().

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.

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 343 of file CardiacElectroMechanicsProblem.cpp.

References LogFile::Close(), CardiacElectroMechanicsProblem< DIM >::mAllocatedMaterialLawMemory, CardiacElectroMechanicsProblem< DIM >::mIsWatchedLocation, CardiacElectroMechanicsProblem< DIM >::mpCardiacMechSolver, CardiacElectroMechanicsProblem< DIM >::mpMaterialLaw, 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 55 of file CardiacElectroMechanicsProblem.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), CardiacElectroMechanicsProblem< DIM >::mIsWatchedLocation, CardiacElectroMechanicsProblem< DIM >::mOutputDirectory, CardiacElectroMechanicsProblem< DIM >::mpElectricsMesh, CardiacElectroMechanicsProblem< DIM >::mpMechanicsMesh, CardiacElectroMechanicsProblem< DIM >::mpWatchedLocationFile, CardiacElectroMechanicsProblem< DIM >::mWatchedElectricsNodeIndex, CardiacElectroMechanicsProblem< DIM >::mWatchedLocation, CardiacElectroMechanicsProblem< DIM >::mWatchedMechanicsNodeIndex, NEVER_REACHED, OutputFileHandler::OpenOutputFile(), and UNSIGNED_UNSET.

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

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 139 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().

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 370 of file CardiacElectroMechanicsProblem.cpp.

References CardiacElectroMechanicsProblem< DIM >::DetermineWatchedNodes(), EXCEPTION, MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::GetMonodomainTissue(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), HeartConfig::Instance(), CardiacElectroMechanicsProblem< DIM >::mAllocatedMaterialLawMemory, CardiacElectroMechanicsProblem< DIM >::mCellModelsAffectedByDeformationMef, CardiacElectroMechanicsProblem< DIM >::mConductivityAffectedByDeformationMef, CardiacElectroMechanicsProblem< DIM >::mContractionModel, CardiacElectroMechanicsProblem< DIM >::mDeformationGradientsForEachMechanicsElement, CardiacElectroMechanicsProblem< DIM >::mDeformationOutputDirectory, CardiacElectroMechanicsProblem< DIM >::mFibreSheetDirectionsDefinedPerQuadraturePoint, CardiacElectroMechanicsProblem< DIM >::mFibreSheetDirectionsFile, CardiacElectroMechanicsProblem< DIM >::mFixedNodes, CardiacElectroMechanicsProblem< DIM >::mIsWatchedLocation, CardiacElectroMechanicsProblem< DIM >::mOutputDirectory, CardiacElectroMechanicsProblem< DIM >::mpCardiacMechSolver, CardiacElectroMechanicsProblem< DIM >::mpElectricsMesh, CardiacElectroMechanicsProblem< DIM >::mpMaterialLaw, CardiacElectroMechanicsProblem< DIM >::mpMechanicsMesh, CardiacElectroMechanicsProblem< DIM >::mpMechanicsSolver, CardiacElectroMechanicsProblem< DIM >::mpMeshPair, CardiacElectroMechanicsProblem< DIM >::mpMonodomainProblem, CardiacElectroMechanicsProblem< DIM >::mStretchesForEachMechanicsElement, CardiacElectroMechanicsProblem< DIM >::mWriteOutput, AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SetConductivityModifier(), HeartConfig::SetIntracellularConductivities(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetMesh(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

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

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

Solve the electromechanics problem

Definition at line 475 of file CardiacElectroMechanicsProblem.cpp.

References Hdf5DataWriter::AdvanceAlongUnlimitedDimension(), TimeStepper::AdvanceOneTimeStep(), PetscTools::Barrier(), GenericEventHandler< 7, MechanicsEventHandler >::BeginEvent(), Hdf5DataWriter::Close(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::CreateInitialCondition(), MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::CreateSolver(), GenericEventHandler< 7, MechanicsEventHandler >::EndEvent(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLow(), TimeStepper::GetNextTime(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), HeartConfig::GetOutputDirectory(), TimeStepper::GetTime(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetTissue(), CardiacElectroMechanicsProblem< DIM >::Initialise(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), LogFile::Instance(), HeartConfig::Instance(), TimeStepper::IsTimeAtEnd(), CardiacElectroMechanicsProblem< DIM >::Max(), CardiacElectroMechanicsProblem< DIM >::mCellModelsAffectedByDeformationMef, CardiacElectroMechanicsProblem< DIM >::mConductivityAffectedByDeformationMef, CardiacElectroMechanicsProblem< DIM >::mContractionModelOdeTimeStep, CardiacElectroMechanicsProblem< DIM >::mDeformationGradientsForEachMechanicsElement, CardiacElectroMechanicsProblem< DIM >::mElectricsTimeStep, CardiacElectroMechanicsProblem< DIM >::mEndTime, CardiacElectroMechanicsProblem< DIM >::mIsWatchedLocation, CardiacElectroMechanicsProblem< DIM >::mMechanicsTimeStep, CardiacElectroMechanicsProblem< DIM >::mNoElectricsOutput, CardiacElectroMechanicsProblem< DIM >::mNumElecTimestepsPerMechTimestep, CardiacElectroMechanicsProblem< DIM >::mOutputDirectory, CardiacElectroMechanicsProblem< DIM >::mpCardiacMechSolver, CardiacElectroMechanicsProblem< DIM >::mpElectricsMesh, CardiacElectroMechanicsProblem< DIM >::mpMechanicsMesh, CardiacElectroMechanicsProblem< DIM >::mpMechanicsSolver, CardiacElectroMechanicsProblem< DIM >::mpMeshPair, CardiacElectroMechanicsProblem< DIM >::mpMonodomainProblem, AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpWriter, CardiacElectroMechanicsProblem< DIM >::mStretchesForEachMechanicsElement, CardiacElectroMechanicsProblem< DIM >::mWriteOutput, CardiacElectroMechanicsProblem< DIM >::OnEndOfTimeStep(), CardiacElectroMechanicsProblem< DIM >::PrepareForSolve(), HeartConfig::Reset(), CardiacElectroMechanicsProblem< DIM >::rGetDeformedPosition(), CmguiMeshWriter< DIM, DIM >::SetAdditionalFieldNames(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetBoundaryConditionsContainer(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetInitialCondition(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetMatrixIsNotAssembled(), HeartConfig::SetOutputDirectory(), HeartConfig::SetPrintingTimeStep(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetTimes(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetTimeStep(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), CardiacElectroMechanicsProblem< DIM >::WRITE_EVERY_NTH_TIME, CmguiDeformedSolutionsWriter< DIM >::WriteCmguiScript(), CmguiDeformedSolutionsWriter< DIM >::WriteDeformationPositions(), LogFile::WriteElapsedTime(), CmguiDeformedSolutionsWriter< DIM >::WriteInitialMesh(), MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::WriteOneStep(), and CardiacElectroMechanicsProblem< DIM >::WriteWatchedLocationData().

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 791 of file CardiacElectroMechanicsProblem.cpp.

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

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

Call to not write out voltages

Definition at line 802 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 808 of file CardiacElectroMechanicsProblem.cpp.

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

template<unsigned DIM>
void CardiacElectroMechanicsProblem< DIM >::SetVariableFibreSheetDirectionsFile ( std::string  orthoFile,
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 .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.

Parameters:
orthoFile 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 815 of file CardiacElectroMechanicsProblem.cpp.

References CardiacElectroMechanicsProblem< DIM >::mFibreSheetDirectionsDefinedPerQuadraturePoint, and CardiacElectroMechanicsProblem< DIM >::mFibreSheetDirectionsFile.

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

Returns:
the current deformed position of the nodes

Definition at line 822 of file CardiacElectroMechanicsProblem.cpp.

References CardiacElectroMechanicsProblem< DIM >::mpMechanicsSolver.

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

template<unsigned DIM>
void CardiacElectroMechanicsProblem< DIM >::UseMechanoElectricFeedback (  )  [inline]

By default (at the moment), the deformation does not affect the electrophysiology in any way. Call this to allow it to, then (i) The stretch will be passed back to the cell models for use stretch-activated channels etc (ii) The deformation to alter the conductivity

EMTODO - check these Two 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

Definition at line 284 of file CardiacElectroMechanicsProblem.hpp.

References CardiacElectroMechanicsProblem< DIM >::mCellModelsAffectedByDeformationMef, and CardiacElectroMechanicsProblem< DIM >::mConductivityAffectedByDeformationMef.

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 164 of file CardiacElectroMechanicsProblem.cpp.

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

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

Called in Solve() before the time loop

Definition at line 305 of file CardiacElectroMechanicsProblem.hpp.

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 311 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>
AbstractNonlinearElasticitySolver<DIM>* CardiacElectroMechanicsProblem< DIM >::GetCardiacMechanicsSolver (  )  [inline]

Get the mechanics solver. Needs to be called after Initialise().

///

Todo:
#1756

Definition at line 318 of file CardiacElectroMechanicsProblem.hpp.

References CardiacElectroMechanicsProblem< DIM >::mpMechanicsSolver.

template<unsigned DIM>
void CardiacElectroMechanicsProblem< DIM >::SetMaterialLaw ( AbstractMaterialLaw< DIM > *  pMaterialLaw  )  [inline]

Set the material law. If this isn't called the default material law will be used. Only call before Initialise() and before Solve()

Parameters:
pMaterialLaw the material law

Definition at line 328 of file CardiacElectroMechanicsProblem.hpp.

References CardiacElectroMechanicsProblem< DIM >::mAllocatedMaterialLawMemory, and CardiacElectroMechanicsProblem< DIM >::mpMaterialLaw.

Member Data Documentation

template<unsigned DIM>
ContractionModel CardiacElectroMechanicsProblem< DIM >::mContractionModel [protected]

Contraction model (from enumeration)

Definition at line 82 of file CardiacElectroMechanicsProblem.hpp.

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

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

The cardiac problem class

Definition at line 84 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>
AbstractCardiacMechanicsSolverInterface<DIM>* CardiacElectroMechanicsProblem< DIM >::mpCardiacMechSolver [protected]

Todo:
#1756
The mechanics solver - a pointer to the part that sees the cardiac mechanics interface bit

Definition at line 88 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>
AbstractNonlinearElasticitySolver<DIM>* CardiacElectroMechanicsProblem< DIM >::mpMechanicsSolver [protected]

The mechanics solver - a pointer to the part that sees the solid mechanics solver

Definition at line 90 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>
double CardiacElectroMechanicsProblem< DIM >::mEndTime [protected]

End time. The start time is assumed to be 0.0

Definition at line 93 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 95 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 97 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 99 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>
double CardiacElectroMechanicsProblem< DIM >::mContractionModelOdeTimeStep [protected]

Timestep to use when solving contraction models

Definition at line 101 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 104 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 106 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>
FineCoarseMeshPair<DIM>* CardiacElectroMechanicsProblem< DIM >::mpMeshPair [protected]

Class wrapping both meshes, useful for transferring information

Definition at line 109 of file CardiacElectroMechanicsProblem.hpp.

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

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

Output directory, relative to TEST_OUTPUT

Definition at line 112 of file CardiacElectroMechanicsProblem.hpp.

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

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

Deformation output-sub-directory

Definition at line 114 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 116 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 118 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 121 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 124 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 126 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 128 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 130 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 132 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 135 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>
std::string CardiacElectroMechanicsProblem< DIM >::mFibreSheetDirectionsFile [protected]

.ortho/.orthoquad file from which to read element-wise/quadpoint-wise fibre-sheet-normal-directions

Definition at line 137 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>
bool CardiacElectroMechanicsProblem< DIM >::mFibreSheetDirectionsDefinedPerQuadraturePoint [protected]

Whether the mFibreSheetDirectionsFile file gives the fibre info at each element, or each quadrature point

Definition at line 139 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>
std::vector<double> CardiacElectroMechanicsProblem< DIM >::mStretchesForEachMechanicsElement [protected]

A vector of stretches (in the fibre direction), one for each element in the mechanics mesh

Definition at line 142 of file CardiacElectroMechanicsProblem.hpp.

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

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 144 of file CardiacElectroMechanicsProblem.hpp.

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

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 149 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>
bool CardiacElectroMechanicsProblem< DIM >::mConductivityAffectedByDeformationMef [protected]

Whether the deformation is always to alter the conductivities (ie one part of MEF)

Definition at line 152 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>
bool CardiacElectroMechanicsProblem< DIM >::mCellModelsAffectedByDeformationMef [protected]

Whether the deformation is always to affect the cell models (for example, for use in stretch-activated channels) (ie one part of MEF)

Definition at line 157 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>
AbstractMaterialLaw<DIM>* CardiacElectroMechanicsProblem< DIM >::mpMaterialLaw [protected]

The material law to be used. Defaults to NashHunterPoleZero if an incompressible problem is being solved

Definition at line 160 of file CardiacElectroMechanicsProblem.hpp.

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

template<unsigned DIM>
bool CardiacElectroMechanicsProblem< DIM >::mAllocatedMaterialLawMemory [protected]

Whether a material law was passed in or the default used

Definition at line 163 of file CardiacElectroMechanicsProblem.hpp.

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

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