#include <AdaptiveBidomainProblem.hpp>

Inheritance diagram for AdaptiveBidomainProblem:

Collaboration diagram for AdaptiveBidomainProblem:

Public Member Functions
	AdaptiveBidomainProblem (AbstractCardiacCellFactory< 3 > *pCellFactory, bool hasBath=false)
	~AdaptiveBidomainProblem ()
void	DoNotAdaptMesh ()
void	AddCurrentSolutionToAdaptiveMesh (Vec solution)
void	InitializeSolutionOnAdaptedMesh (VtkMeshReader< 3, 3 > *reader)
void	AdaptMesh ()
double	GetTargetError ()
double	GetSigma ()
double	GetMaxEdgeLength ()
double	GetMinEdgeLength ()
double	GetGradation ()
unsigned	GetMaxMeshNodes ()
unsigned	GetNumAdaptSweeps ()
void	UseNeumannBoundaryCondition (unsigned index=0)
void	SetNeumannStimulusMagnitudeAndDuration (double magnitude, double duration, double period=DBL_MAX)
void	SetupNeumannBoundaryConditionOnMesh ()
void	LoadSimulationFromVtuFile ()
void	Solve ()
Private Attributes
BidomainSolver< 3, 3 > *	mpSolver
AdaptiveTetrahedralMesh *	mpAdaptiveMesh
bool	mIsMeshAdapting
bool	mInitializeFromVtu
bool	mUseNeumannBoundaryConditions
double	mNeumannStimulusIndex
double	mNeumannStimulusLowerValue
double	mNeumannStimulusUpperValue
double	mNeumannStimulusMagnitude
double	mNeumannStimulusDuration
double	mNeumannStimulusPeriod
AbstractStimulusFunction *	mpNeumannStimulus
StimulusBoundaryCondition< 3 > *	mpNeumannStimulusBoundaryCondition
std::string	mOutputDirectory
std::string	mOutputFilenamePrefix
Friends
class	TestAdaptiveBidomainProblem
class	TestAdaptiveBidomainProblemNightly

Detailed Description

Class which specifies and solves a bidomain problem using adaptivity.

The solution vector is of the form: (V_1, phi_1, V_2, phi_2, ......, V_N, phi_N), where V_j is the voltage at node j and phi_j is the extracellular potential at node j

Adaptivity occurs at each printing time step (to avoid having to add a variable to the XML schema at this stage): this will need tidying up at some point in the future

Definition at line 94 of file AdaptiveBidomainProblem.hpp.

Constructor & Destructor Documentation

AdaptiveBidomainProblem::AdaptiveBidomainProblem	(	AbstractCardiacCellFactory< 3 > *	pCellFactory,
		bool	hasBath = `false`
	)

Constructor

Parameters:

pCellFactory	User defined cell factory which shows how the tissue should create cells.
hasBath	Whether the simulation has a bath (if this is true, all elements with attribute = 1 will be set to be bath elements (the rest should have attribute = 0)).

Definition at line 61 of file AdaptiveBidomainProblem.cpp.

References BidomainProblem< 3 >::mFixedExtracellularPotentialNodes, and mpAdaptiveMesh.

AdaptiveBidomainProblem::~AdaptiveBidomainProblem ( )

Destructor

Definition at line 80 of file AdaptiveBidomainProblem.cpp.

References mpAdaptiveMesh.

Member Function Documentation

void AdaptiveBidomainProblem::AdaptMesh ( )

Adapt the mesh, recontruct the mesh, cell factory, boundary conditions container, bidomain tissue and solver and call InitializeSolutionOnAdaptedMesh()

If the adapt fails for any reason then nothing is done (i.e. we don't recreate objects that remain unchanged)

Definition at line 208 of file AdaptiveBidomainProblem.cpp.

References AdaptiveTetrahedralMesh::AdaptMesh(), GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), AdaptiveTetrahedralMesh::GetAdaptSuccess(), AdaptiveTetrahedralMesh::GetNumNodes(), AdaptiveTetrahedralMesh::GetVtkUnstructuredGrid(), InitializeSolutionOnAdaptedMesh(), HeartConfig::Instance(), mpAdaptiveMesh, BidomainProblem< 3 >::mpBidomainTissue, AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, DIM, 2 >::mpCardiacTissue, AbstractCardiacProblem< DIM, DIM, 2 >::mpCellFactory, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, mpSolver, mUseNeumannBoundaryConditions, AbstractCardiacProblem< DIM, DIM, 2 >::mWriteInfo, NEVER_REACHED, AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetTimeStep(), and SetupNeumannBoundaryConditionOnMesh().

Referenced by Solve().

void AdaptiveBidomainProblem::AddCurrentSolutionToAdaptiveMesh ( Vec solution )

Add the values of all state variables into the adaptive mesh (as VTK node point data) so that they can (a) be used to drive mesh adaption; and/or (b) be interpolated onto the new mesh nodes.

Parameters:

solution The current solution vector

Definition at line 96 of file AdaptiveBidomainProblem.cpp.

References AdaptiveTetrahedralMesh::AddPointData(), GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::GetCardiacCell(), AbstractCardiacCellInterface::GetVoltageIndex(), mpAdaptiveMesh, BidomainProblem< 3 >::mpBidomainTissue, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, and AbstractCardiacCellInterface::rGetStateVariableNames().

Referenced by Solve().

void AdaptiveBidomainProblem::DoNotAdaptMesh ( )

Method to stop any further adapts taking place

Definition at line 85 of file AdaptiveBidomainProblem.cpp.

References mIsMeshAdapting.

double AdaptiveBidomainProblem::GetGradation ( )

Return value of mGradation

Definition at line 301 of file AdaptiveBidomainProblem.cpp.

References HeartConfig::GetGradationForAdaptivity(), and HeartConfig::Instance().

double AdaptiveBidomainProblem::GetMaxEdgeLength ( )

Return value of mMaxEdgeLength

Definition at line 291 of file AdaptiveBidomainProblem.cpp.

References HeartConfig::GetMaxEdgeLengthForAdaptivity(), and HeartConfig::Instance().

unsigned AdaptiveBidomainProblem::GetMaxMeshNodes ( )

Return value of mMaxMeshNodes

Definition at line 306 of file AdaptiveBidomainProblem.cpp.

References HeartConfig::GetMaxNodesForAdaptivity(), and HeartConfig::Instance().

double AdaptiveBidomainProblem::GetMinEdgeLength ( )

Return value of mMinEdgeLength

Definition at line 296 of file AdaptiveBidomainProblem.cpp.

References HeartConfig::GetMinEdgeLengthForAdaptivity(), and HeartConfig::Instance().

unsigned AdaptiveBidomainProblem::GetNumAdaptSweeps ( )

Return value of mNumAdaptSweeps

Definition at line 311 of file AdaptiveBidomainProblem.cpp.

References HeartConfig::GetNumberOfAdaptiveSweeps(), and HeartConfig::Instance().

double AdaptiveBidomainProblem::GetSigma ( )

Return value of mSigma

Definition at line 286 of file AdaptiveBidomainProblem.cpp.

References HeartConfig::GetSigmaForAdaptivity(), and HeartConfig::Instance().

double AdaptiveBidomainProblem::GetTargetError ( )

Return value of mError

Definition at line 281 of file AdaptiveBidomainProblem.cpp.

References HeartConfig::GetTargetErrorForAdaptivity(), and HeartConfig::Instance().

void AdaptiveBidomainProblem::InitializeSolutionOnAdaptedMesh ( VtkMeshReader< 3, 3 > * reader )

Extract the values of state variables from VTK format following adaption and initialize the values of mSolution and the cardiac cell models at each mesh node for simulation on the new mesh

Parameters:

reader

Definition at line 140 of file AdaptiveBidomainProblem.cpp.

References DistributedVector::Begin(), GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), PetscTools::Destroy(), DistributedVector::End(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::GetCardiacCell(), VtkMeshReader< ELEMENT_DIM, SPACE_DIM >::GetPointData(), AbstractCardiacCellInterface::GetVoltageIndex(), BidomainProblem< 3 >::mpBidomainTissue, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, AbstractCardiacProblem< DIM, DIM, 2 >::mSolution, DistributedVector::Restore(), AbstractCardiacCellInterface::rGetStateVariableNames(), and AbstractCardiacCellInterface::SetStateVariable().

Referenced by AdaptMesh(), and Solve().

void AdaptiveBidomainProblem::LoadSimulationFromVtuFile ( )

Restore a simulation previously saved as a .vtu file. Generates mesh and initial conditions (on V, phi and ODE state variables).

Location of .vtu file is assumed to have been set by HeartConfig::SetMesh(). The alternative (constructing its own mesh) doesn't make much sense since the .vtu file must contain a mesh in order to store the variable values at each point of it.

Definition at line 352 of file AdaptiveBidomainProblem.cpp.

References AbstractCardiacProblem< DIM, DIM, 2 >::Initialise(), and mInitializeFromVtu.

void AdaptiveBidomainProblem::SetNeumannStimulusMagnitudeAndDuration	(	double	magnitude,
		double	duration,
		double	period = `DBL_MAX`
	)

Initialize magnitude and duration of a Neumann stimulus (must have called UseNeumannBoundaryConditions() or UseNeumannBoundaryConditions( true ) for this to have any effect)

Parameters:

magnitude	Value of mNeumannStimulusMagnitude
duration	Value of mNeumannStimulusDuration
period	Optional parameter used to specify after how long a regular stimulus is repeated

Definition at line 268 of file AdaptiveBidomainProblem.cpp.

References HeartConfig::Instance(), mNeumannStimulusDuration, mNeumannStimulusMagnitude, and mNeumannStimulusPeriod.

void AdaptiveBidomainProblem::SetupNeumannBoundaryConditionOnMesh ( )

Create a new boundary conditions container to handle the specified Neumann boundary conditions on the mesh. Needs to be called every time a new mesh is constructed (i.e. after every successful adapt)

Todo:: remove magic number? (#1884)

Definition at line 316 of file AdaptiveBidomainProblem.cpp.

References mNeumannStimulusIndex, mNeumannStimulusLowerValue, mNeumannStimulusUpperValue, AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, mpNeumannStimulus, and mpNeumannStimulusBoundaryCondition.

Referenced by AdaptMesh(), and Solve().

void AdaptiveBidomainProblem::Solve ( )

Performs some checks by calling the PreSolveChecks method, creates a solver to which it passes the boundary conditions specified by the user (otherwise it passes the defauls bcc), then at each printing step calls the AdaptMesh method and the Solve method in the solver class to solve the system up until the next printing time step (for the moment, printing time steps and adapt time steps are synonymous)

Also outputs VTK files that record the solution (and the mesh) at each printing time step

Reimplemented from AbstractCardiacProblem< DIM, DIM, 2 >.

Definition at line 358 of file AdaptiveBidomainProblem.cpp.

References AdaptMesh(), AddCurrentSolutionToAdaptiveMesh(), TimeStepper::AdvanceOneTimeStep(), GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), AdaptiveTetrahedralMesh::CalculateSENListAndSids(), AbstractCardiacProblem< DIM, DIM, 2 >::CloseFilesAndPostProcess(), AdaptiveTetrahedralMesh::ConstructFromMesh(), AdaptiveTetrahedralMesh::ConstructFromVtuFile(), BidomainProblem< 3 >::CreateInitialCondition(), PetscTools::Destroy(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), TimeStepper::GetNextTime(), OutputFileHandler::GetOutputDirectoryFullPath(), HeartConfig::GetOutputFilenamePrefix(), TimeStepper::GetTime(), InitializeSolutionOnAdaptedMesh(), HeartConfig::Instance(), TimeStepper::IsTimeAtEnd(), mInitializeFromVtu, mIsMeshAdapting, mNeumannStimulusDuration, mNeumannStimulusIndex, mNeumannStimulusLowerValue, mNeumannStimulusMagnitude, mNeumannStimulusPeriod, mNeumannStimulusUpperValue, mOutputDirectory, mOutputFilenamePrefix, mpAdaptiveMesh, BidomainProblem< 3 >::mpBidomainTissue, AbstractCardiacProblem< DIM, DIM, 2 >::mpBoundaryConditionsContainer, AbstractCardiacProblem< DIM, DIM, 2 >::mpDefaultBoundaryConditionsContainer, AbstractCardiacProblem< DIM, DIM, 2 >::mpMesh, mpNeumannStimulus, AbstractCardiacProblem< DIM, DIM, 2 >::mPrintOutput, mpSolver, AbstractCardiacProblem< DIM, DIM, 2 >::mSolution, mUseNeumannBoundaryConditions, AbstractCardiacProblem< DIM, DIM, 2 >::mWriteInfo, BidomainProblem< 3 >::OnEndOfTimestep(), BidomainProblem< 3 >::PreSolveChecks(), ProgressReporter::PrintFinalising(), PetscTools::ReplicateException(), GenericEventHandler< 16, HeartEventHandler >::Reset(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetInitialCondition(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetTimes(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetTimeStep(), SetupNeumannBoundaryConditionOnMesh(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), ProgressReporter::Update(), BidomainProblem< 3 >::WriteInfo(), and AdaptiveTetrahedralMesh::WriteMeshToFile().

void AdaptiveBidomainProblem::UseNeumannBoundaryCondition ( unsigned index = 0 )

Specify that Neumann boundary conditions will be used. Use with caution: not all Neumann boundary conditions lead to a well-posed problem. Best used only on cuboid geometries, when a stimulus is applied to the face x_i=a and the face x_i=b is grounded.

Parameters:

index The value i when applying the Neumann BCs to x_i=a and x_i=b (a<b) (default = 0)

Definition at line 275 of file AdaptiveBidomainProblem.cpp.

References mNeumannStimulusIndex, and mUseNeumannBoundaryConditions.

Member Data Documentation

bool AdaptiveBidomainProblem::mInitializeFromVtu [private]

Whether or not we are initializing from a .vtu file

Definition at line 112 of file AdaptiveBidomainProblem.hpp.

Referenced by LoadSimulationFromVtuFile(), and Solve().

bool AdaptiveBidomainProblem::mIsMeshAdapting [private]

Whether the mesh is to be adapted or not

Definition at line 110 of file AdaptiveBidomainProblem.hpp.

Referenced by DoNotAdaptMesh(), and Solve().

double AdaptiveBidomainProblem::mNeumannStimulusDuration [private]

Duration of any Neumann stimulus

Definition at line 125 of file AdaptiveBidomainProblem.hpp.

Referenced by SetNeumannStimulusMagnitudeAndDuration(), and Solve().

double AdaptiveBidomainProblem::mNeumannStimulusIndex [private]

The value i when applying Neumann boundary conditions to x_i=a and x_i=b (a<b)

Definition at line 117 of file AdaptiveBidomainProblem.hpp.

Referenced by SetupNeumannBoundaryConditionOnMesh(), Solve(), and UseNeumannBoundaryCondition().

double AdaptiveBidomainProblem::mNeumannStimulusLowerValue [private]

The value a when applying Neumann boundary conditions to x_i=a and x_i=b (a<b)

Definition at line 119 of file AdaptiveBidomainProblem.hpp.

Referenced by SetupNeumannBoundaryConditionOnMesh(), and Solve().

double AdaptiveBidomainProblem::mNeumannStimulusMagnitude [private]

Magnitude of any Neumann stimulus

Definition at line 123 of file AdaptiveBidomainProblem.hpp.

Referenced by SetNeumannStimulusMagnitudeAndDuration(), and Solve().

double AdaptiveBidomainProblem::mNeumannStimulusPeriod [private]

Period of any repeating Neumannn stimulus

Definition at line 127 of file AdaptiveBidomainProblem.hpp.

Referenced by SetNeumannStimulusMagnitudeAndDuration(), and Solve().

double AdaptiveBidomainProblem::mNeumannStimulusUpperValue [private]

The value b when applying Neumann boundary conditions to x_i=a and x_i=b (a<b)

Definition at line 121 of file AdaptiveBidomainProblem.hpp.

Referenced by SetupNeumannBoundaryConditionOnMesh(), and Solve().

std::string AdaptiveBidomainProblem::mOutputDirectory [private]

Determine whether or not an edge of the mesh is of sufficient quality. Edge is "good" if the error metric associated with it is in the range [ 1 - mGoodEdgeRange , 1 + mGoodEdgeRange ] Proportion of edges that must be deemed "bad" (i.e. not good) before an adapt takes place Directory in which output files should be saved.

Definition at line 143 of file AdaptiveBidomainProblem.hpp.

Referenced by Solve().

std::string AdaptiveBidomainProblem::mOutputFilenamePrefix [private]

Filename prefix for output files

Definition at line 146 of file AdaptiveBidomainProblem.hpp.

Referenced by Solve().

AdaptiveTetrahedralMesh* AdaptiveBidomainProblem::mpAdaptiveMesh [private]

Adaptive tetrahedral mesh: used to interface with adaptivity library

Definition at line 108 of file AdaptiveBidomainProblem.hpp.

Referenced by AdaptiveBidomainProblem(), AdaptMesh(), AddCurrentSolutionToAdaptiveMesh(), Solve(), and ~AdaptiveBidomainProblem().