#include <CellBasedParabolicPdeSolver.hpp>

Inheritance diagram for CellBasedParabolicPdeSolver< DIM >:

Collaboration diagram for CellBasedParabolicPdeSolver< DIM >:

Public Member Functions
	CellBasedParabolicPdeSolver (TetrahedralMesh< DIM, DIM > pMesh, AbstractLinearParabolicPde< DIM, DIM > pPde, BoundaryConditionsContainer< DIM, DIM, 1 > *pBoundaryConditions)

virtual	~CellBasedParabolicPdeSolver ()

Public Member Functions inherited from SimpleLinearParabolicSolver< DIM, DIM >
	SimpleLinearParabolicSolver (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, AbstractLinearParabolicPde< ELEMENT_DIM, SPACE_DIM > pPde, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 1 > *pBoundaryConditions)

Public Member Functions inherited from AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, 1, NORMAL >
	AbstractAssemblerSolverHybrid (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > pMesh, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > pBoundaryConditions)

virtual	~AbstractAssemblerSolverHybrid ()

void	SetupGivenLinearSystem (Vec currentSolution, bool computeMatrix, LinearSystem *pLinearSystem)

Public Member Functions inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >
	AbstractFeVolumeIntegralAssembler (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

virtual	~AbstractFeVolumeIntegralAssembler ()

Public Member Functions inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
	AbstractFeAssemblerCommon ()

void	SetCurrentSolution (Vec currentSolution)

virtual	~AbstractFeAssemblerCommon ()

Public Member Functions inherited from AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
	AbstractFeAssemblerInterface ()

void	SetMatrixToAssemble (Mat &rMatToAssemble, bool zeroMatrixBeforeAssembly=true)

void	SetVectorToAssemble (Vec &rVecToAssemble, bool zeroVectorBeforeAssembly)

void	Assemble ()

void	AssembleMatrix ()

void	AssembleVector ()

virtual	~AbstractFeAssemblerInterface ()

Public Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 >
	AbstractDynamicLinearPdeSolver (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

void	SetTimes (double tStart, double tEnd)

void	SetTimeStep (double dt)

void	SetInitialCondition (Vec initialCondition)

virtual Vec	Solve ()

void	SetMatrixIsNotAssembled ()

void	SetTimeAdaptivityController (AbstractTimeAdaptivityController *pTimeAdaptivityController)

void	SetOutputToVtk (bool output)

void	SetOutputToParallelVtk (bool output)

void	SetOutputToTxt (bool output)

void	SetOutputDirectoryAndPrefix (std::string outputDirectory, std::string prefix)

void	SetPrintingTimestepMultiple (unsigned multiple)

Public Member Functions inherited from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
	AbstractLinearPdeSolver (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)

virtual	~AbstractLinearPdeSolver ()

virtual void	InitialiseForSolve (Vec initialSolution=nullptr)

virtual void	PrepareForSetupLinearSystem (Vec currentSolution)

virtual void	FinaliseLinearSystem (Vec currentSolution)

virtual void	FollowingSolveLinearSystem (Vec currentSolution)

LinearSystem *	GetLinearSystem ()

Protected Member Functions
virtual c_vector< double, 1 *(DIM+1)>	ComputeVectorTerm (c_vector< double, DIM+1 > &rPhi, c_matrix< double, DIM, DIM+1 > &rGradPhi, ChastePoint< DIM > &rX, c_vector< double, 1 > &rU, c_matrix< double, 1, DIM > &rGradU, Element< DIM, DIM > *pElement)

virtual c_matrix< double, 1 (DIM+1), 1 (DIM+1)>	ComputeMatrixTerm (c_vector< double, DIM+1 > &rPhi, c_matrix< double, DIM, DIM+1 > &rGradPhi, ChastePoint< DIM > &rX, c_vector< double, 1 > &rU, c_matrix< double, 1, DIM > &rGradU, Element< DIM, DIM > *pElement)

void	ResetInterpolatedQuantities ()

void	IncrementInterpolatedQuantities (double phiI, const Node< DIM > *)

Protected Member Functions inherited from SimpleLinearParabolicSolver< DIM, DIM >
virtual c_matrix< double, 1 (ELEMENT_DIM+1), 1 (ELEMENT_DIM+1)>	ComputeMatrixTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 1 > &rU, c_matrix< double, 1, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

virtual c_vector< double, 1 *(ELEMENT_DIM+1)>	ComputeVectorTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, 1 > &rU, c_matrix< double, 1, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

void	SetupLinearSystem (Vec currentSolution, bool computeMatrix)

Protected Member Functions inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >
void	ComputeTransformedBasisFunctionDerivatives (const ChastePoint< ELEMENT_DIM > &rPoint, const c_matrix< double, ELEMENT_DIM, SPACE_DIM > &rInverseJacobian, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rReturnValue)

void	DoAssemble ()

virtual c_matrix< double, PROBLEM_DIM (ELEMENT_DIM+1), PROBLEM_DIM (ELEMENT_DIM+1)>	ComputeMatrixTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

virtual c_vector< double, PROBLEM_DIM *(ELEMENT_DIM+1)>	ComputeVectorTerm (c_vector< double, ELEMENT_DIM+1 > &rPhi, c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU, Element< ELEMENT_DIM, SPACE_DIM > *pElement)

virtual void	AssembleOnElement (Element< ELEMENT_DIM, SPACE_DIM > &rElement, c_matrix< double, PROBLEM_DIM (ELEMENT_DIM+1), PROBLEM_DIM (ELEMENT_DIM+1) > &rAElem, c_vector< double, PROBLEM_DIM *(ELEMENT_DIM+1)> &rBElem)

virtual bool	ElementAssemblyCriterion (Element< ELEMENT_DIM, SPACE_DIM > &rElement)

Protected Member Functions inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
virtual double	GetCurrentSolutionOrGuessValue (unsigned nodeIndex, unsigned indexOfUnknown)

virtual void	IncrementInterpolatedQuantities (double phiI, const Node< SPACE_DIM > *pNode)

virtual void	IncrementInterpolatedGradientQuantities (const c_matrix< double, SPACE_DIM, ELEMENT_DIM+1 > &rGradPhi, unsigned phiIndex, const Node< SPACE_DIM > *pNode)

Protected Member Functions inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 >
void	InitialiseHdf5Writer ()

void	WriteOneStep (double time, Vec solution)

Private Attributes
double	mInterpolatedSourceTerm

Additional Inherited Members
Protected Types inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >
typedef LinearBasisFunction< ELEMENT_DIM >	BasisFunction

Protected Attributes inherited from SimpleLinearParabolicSolver< DIM, DIM >
AbstractLinearParabolicPde< ELEMENT_DIM, SPACE_DIM > *	mpParabolicPde

Protected Attributes inherited from AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, 1, NORMAL >
NaturalNeumannSurfaceTermAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >	mNaturalNeumannSurfaceTermAssembler

BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *	mpBoundaryConditions

Protected Attributes inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh

GaussianQuadratureRule< ELEMENT_DIM > *	mpQuadRule

Protected Attributes inherited from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >
ReplicatableVector	mCurrentSolutionOrGuessReplicated

Protected Attributes inherited from AbstractFeAssemblerInterface< CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >
Vec	mVectorToAssemble

Mat	mMatrixToAssemble

bool	mAssembleMatrix

bool	mAssembleVector

bool	mZeroMatrixBeforeAssembly

bool	mZeroVectorBeforeAssembly

PetscInt	mOwnershipRangeLo

PetscInt	mOwnershipRangeHi

Protected Attributes inherited from AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 >
double	mTstart

double	mTend

bool	mTimesSet

Vec	mInitialCondition

bool	mMatrixIsAssembled

bool	mMatrixIsConstant

double	mIdealTimeStep

double	mLastWorkingTimeStep

AbstractTimeAdaptivityController *	mpTimeAdaptivityController

bool	mOutputToVtk

bool	mOutputToParallelVtk

bool	mOutputToTxt

std::string	mOutputDirectory

std::string	mFilenamePrefix

unsigned	mPrintingTimestepMultiple

Hdf5DataWriter *	mpHdf5Writer

std::vector< int >	mVariableColumnIds

Protected Attributes inherited from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
LinearSystem *	mpLinearSystem

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh

Detailed Description

template<unsigned DIM>
class CellBasedParabolicPdeSolver< DIM >

A purpose-made parabolic solver that interpolates the source terms from node onto Gauss points, as for a cell-based simulation with PDEs the source will only be known at the cells (nodes), not the Gauss points.

Definition at line 48 of file CellBasedParabolicPdeSolver.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

CellBasedParabolicPdeSolver< DIM >::CellBasedParabolicPdeSolver	(	TetrahedralMesh< DIM, DIM > *	pMesh,
		AbstractLinearParabolicPde< DIM, DIM > *	pPde,
		BoundaryConditionsContainer< DIM, DIM, 1 > *	pBoundaryConditions
	)

Constructor.

Parameters

pMesh	pointer to the mesh
pPde	pointer to the PDE
pBoundaryConditions	pointer to the boundary conditions

Definition at line 39 of file CellBasedParabolicPdeSolver.cpp.

template<unsigned DIM>

CellBasedParabolicPdeSolver< DIM >::~CellBasedParabolicPdeSolver ( )

virtual

Destructor.

Definition at line 47 of file CellBasedParabolicPdeSolver.cpp.

Member Function Documentation

template<unsigned DIM>

c_matrix< double, 1 (DIM+1), 1 (DIM+1)> CellBasedParabolicPdeSolver< DIM >::ComputeMatrixTerm	(	c_vector< double, DIM+1 > &	rPhi,
		c_matrix< double, DIM, DIM+1 > &	rGradPhi,
		ChastePoint< DIM > &	rX,
		c_vector< double, 1 > &	rU,
		c_matrix< double, 1, DIM > &	rGradU,
		Element< DIM, DIM > *	pElement
	)

protectedvirtual

The SimpleLinearParabolicSolver version of this method is overloaded using the interpolated source term.

Parameters

rPhi	The basis functions, rPhi(i) = phi_i, i=1..numBases
rGradPhi	Basis gradients, rGradPhi(i,j) = d(phi_j)/d(X_i)
rX	The point in space
rU	The unknown as a vector, u(i) = u_i
rGradU	The gradient of the unknown as a matrix, rGradU(i,j) = d(u_i)/d(X_j)
pElement	Pointer to the element

Returns: The matrix term for the stiffness matrix

Definition at line 65 of file CellBasedParabolicPdeSolver.cpp.

References PdeSimulationTime::GetPdeTimeStepInverse(), and SimpleLinearParabolicSolver< DIM, DIM >::mpParabolicPde.

template<unsigned DIM>

c_vector< double, 1 *(DIM+1)> CellBasedParabolicPdeSolver< DIM >::ComputeVectorTerm	(	c_vector< double, DIM+1 > &	rPhi,
		c_matrix< double, DIM, DIM+1 > &	rGradPhi,
		ChastePoint< DIM > &	rX,
		c_vector< double, 1 > &	rU,
		c_matrix< double, 1, DIM > &	rGradU,
		Element< DIM, DIM > *	pElement
	)

protectedvirtual

The SimpleLinearParabolicSolver version of this method is overloaded using the interpolated source term.

Parameters

rPhi	The basis functions, rPhi(i) = phi_i, i=1..numBases
rGradPhi	Basis gradients, rGradPhi(i,j) = d(phi_j)/d(X_i)
rX	The point in space
rU	The unknown as a vector, u(i) = u_i
rGradU	The gradient of the unknown as a matrix, rGradU(i,j) = d(u_i)/d(X_j)
pElement	Pointer to the element