LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > Class Template Reference

#include <LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp>

Inheritance diagram for LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >:

Collaboration diagram for LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >:

Public Member Functions
	LinearParabolicPdeSystemWithCoupledOdeSystemSolver (TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, AbstractLinearParabolicPdeSystemForCoupledOdeSystem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *pPdeSystem, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *pBoundaryConditions, std::vector< AbstractOdeSystemForCoupledPdeSystem * > odeSystemsAtNodes=std::vector< AbstractOdeSystemForCoupledPdeSystem * >(), boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver=boost::shared_ptr< AbstractIvpOdeSolver >())
	~LinearParabolicPdeSystemWithCoupledOdeSystemSolver ()
void	PrepareForSetupLinearSystem (Vec currentPdeSolution)
void	SetOutputDirectory (std::string outputDirectory, bool clearDirectory=false)
void	SetSamplingTimeStep (double samplingTimeStep)
void	SolveAndWriteResultsToFile ()
void	WriteVtkResultsToFile (Vec solution, unsigned numTimeStepsElapsed)
AbstractOdeSystemForCoupledPdeSystem *	GetOdeSystemAtNode (unsigned index)
Public Member Functions inherited from AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, INTERPOLATION_LEVEL >
	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, PROBLEM_DIM >
	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	FinaliseLinearSystem (Vec currentSolution)
virtual void	FollowingSolveLinearSystem (Vec currentSolution)
LinearSystem *	GetLinearSystem ()

Private Member Functions
void	WriteVtkResultsToFile ()
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)
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)
void	ResetInterpolatedQuantities ()
void	IncrementInterpolatedQuantities (double phiI, const Node< SPACE_DIM > *pNode)
void	InitialiseForSolve (Vec initialSolution=NULL)
void	SetupLinearSystem (Vec currentSolution, bool computeMatrix)

Private Attributes
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh
AbstractLinearParabolicPdeSystemForCoupledOdeSystem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *	mpPdeSystem
std::vector< AbstractOdeSystemForCoupledPdeSystem * >	mOdeSystemsAtNodes
std::vector< double >	mInterpolatedOdeStateVariables
boost::shared_ptr< AbstractIvpOdeSolver >	mpOdeSolver
double	mSamplingTimeStep
bool	mOdeSystemsPresent
out_stream	mpVtkMetaFile
bool	mClearOutputDirectory

Additional Inherited Members
Protected Types inherited from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >
typedef LinearBasisFunction< ELEMENT_DIM >	BasisFunction
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 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	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, PROBLEM_DIM >
void	InitialiseHdf5Writer ()
void	WriteOneStep (double time, Vec solution)
Protected Attributes inherited from AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, INTERPOLATION_LEVEL >
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, PROBLEM_DIM >
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 ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM, unsigned PROBLEM_DIM = 1>
class LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >

A class for solving systems of parabolic PDEs and ODEs, which may be coupled via their source terms:

d/dt (u_i) = div (D(x) grad (u_i)) + f_i (x, u_1, ..., u_p, v_1, ..., v_q), i=1,...,p, d/dt (v_j) = g_j(x, u_1, ..., u_p, v_1, ..., v_q), j=1,...,q.

The solver class is templated over spatial dimension and PDE problem dimension (p).

Definition at line 60 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

Constructor & Destructor Documentation

LinearParabolicPdeSystemWithCoupledOdeSystemSolver()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LinearParabolicPdeSystemWithCoupledOdeSystemSolver	(	TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	pMesh,
		AbstractLinearParabolicPdeSystemForCoupledOdeSystem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *	pPdeSystem,
		BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > *	pBoundaryConditions,
		std::vector< AbstractOdeSystemForCoupledPdeSystem * >	odeSystemsAtNodes = std::vector<AbstractOdeSystemForCoupledPdeSystem*>(),
		boost::shared_ptr< AbstractIvpOdeSolver >	pOdeSolver = boost::shared_ptr<AbstractIvpOdeSolver>()
	)

Constructor.

Parameters

pMesh	pointer to the mesh
pPdeSystem	pointer to the PDE system
pBoundaryConditions	pointer to the boundary conditions.
odeSystemsAtNodes	optional vector of pointers to ODE systems, defined at nodes
pOdeSolver	optional pointer to an ODE solver (defaults to NULL)

Definition at line 368 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

References LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mOdeSystemsAtNodes, LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mOdeSystemsPresent, AbstractAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, INTERPOLATION_LEVEL >::mpBoundaryConditions, LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh, and LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpOdeSolver.

~LinearParabolicPdeSystemWithCoupledOdeSystemSolver()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~LinearParabolicPdeSystemWithCoupledOdeSystemSolver

(

)

Destructor. If an ODE system is present, the pointers to the ODE system objects are deleted here.

Definition at line 408 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

Member Function Documentation

ComputeMatrixTerm()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

c_matrix< double, PROBLEM_DIM *(ELEMENT_DIM+1), PROBLEM_DIM *(ELEMENT_DIM+1)> LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::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  )

privatevirtual

Returns

the term to be added to the element stiffness matrix.

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

Reimplemented from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >.

Definition at line 250 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

References AbstractLinearParabolicPdeSystemForCoupledOdeSystem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeDiffusionTerm(), AbstractLinearParabolicPdeSystemForCoupledOdeSystem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeDuDtCoefficientFunction(), and PdeSimulationTime::GetPdeTimeStepInverse().

ComputeVectorTerm()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

c_vector< double, PROBLEM_DIM *(ELEMENT_DIM+1)> LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::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  )

privatevirtual

Returns

the term to be added to the element stiffness vector.

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

Reimplemented from AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, true, true, INTERPOLATION_LEVEL >.

Definition at line 280 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

References AbstractLinearParabolicPdeSystemForCoupledOdeSystem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeDuDtCoefficientFunction(), AbstractLinearParabolicPdeSystemForCoupledOdeSystem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeSourceTerm(), and PdeSimulationTime::GetPdeTimeStepInverse().

GetOdeSystemAtNode()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractOdeSystemForCoupledPdeSystem * LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetOdeSystemAtNode

(

unsigned

index

)

Get a pointer to the ODE system defined at a given node.

Parameters

index

the global index of a node in the mpMesh

Returns

mOdeSystemsAtNodes[index]

Definition at line 615 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

IncrementInterpolatedQuantities()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::IncrementInterpolatedQuantities ( double  phiI, const Node< SPACE_DIM > *  pNode  )

privatevirtual

Update the member variable mInterpolatedOdeStateVariables by computing the interpolated value of each ODE state variable at each Gauss point.

Parameters

phiI
pNode	pointer to a Node

Reimplemented from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >.

Definition at line 322 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

References Node< SPACE_DIM >::GetIndex().

InitialiseForSolve()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseForSolve ( Vec  initialSolution = NULL )

privatevirtual

Initialise method: sets up the linear system (using the mesh to determine the number of unknowns per row to preallocate) if it is not already set up. Can use an initial solution as PETSc template, or base it on the mesh size.

Parameters

initialSolution

Initial solution (defaults to NULL) for PETSc to use as a template.

Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 336 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMaximumContainingElementsPerProcess().

PrepareForSetupLinearSystem()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PrepareForSetupLinearSystem ( Vec  currentPdeSolution )

virtual

Overridden PrepareForSetupLinearSystem() method. Pass the current solution to the PDE system to the ODE system and solve it over the next timestep.

Parameters

currentPdeSolution

the solution to the PDE system at the current time

Reimplemented from AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 420 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

References PdeSimulationTime::GetNextTime(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), PdeSimulationTime::GetPdeTimeStep(), and PdeSimulationTime::GetTime().

ResetInterpolatedQuantities()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ResetInterpolatedQuantities ( void  )

privatevirtual

Reset the member variable mInterpolatedOdeStateVariables.

Reimplemented from AbstractFeAssemblerCommon< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >.

Definition at line 310 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

SetOutputDirectory()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetOutputDirectory	(	std::string	outputDirectory,
		bool	clearDirectory = false
	)

Set mOutputDirectory.

Parameters

outputDirectory	the output directory to use
clearDirectory	whether to clear outputDirectory or not. Note that the actual clearing happens when you call SolveAndWriteResultsToFile(). False by default.

Definition at line 451 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

SetSamplingTimeStep()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetSamplingTimeStep

(

double

samplingTimeStep

)

Set mSamplingTimeStep.

Parameters

samplingTimeStep

the sampling timestep to use

Definition at line 458 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

SetupLinearSystem()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetupLinearSystem ( Vec  currentSolution, bool  computeMatrix  )

privatevirtual

Completely set up the linear system that has to be solved each timestep.

Parameters

currentSolution	The current solution which can be used in setting up the linear system if needed (NULL if there isn't a current solution)
computeMatrix	Whether to compute the LHS matrix of the linear system (mainly for dynamic solves).

Implements AbstractLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.

Definition at line 362 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

SolveAndWriteResultsToFile()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SolveAndWriteResultsToFile

(

)

Solve the coupled PDE/ODE system over the pre-specified time interval, and record results using mSamplingTimeStep.

Definition at line 465 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

References TimeStepper::AdvanceOneTimeStep(), PetscTools::Destroy(), DOUBLE_UNSET, EXCEPTION, TimeStepper::GetNextTime(), TimeStepper::GetTime(), TimeStepper::GetTotalTimeStepsTaken(), TimeStepper::IsTimeAtEnd(), and OutputFileHandler::OpenOutputFile().

WriteVtkResultsToFile() [1/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM, unsigned PROBLEM_DIM = 1>

void LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteVtkResultsToFile ( )

private

Write the current results to mpVtkMetaFile.

WriteVtkResultsToFile() [2/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteVtkResultsToFile	(	Vec	solution,
		unsigned	numTimeStepsElapsed
	)

Write the solution to VTK. Called by SolveAndWriteResultsToFile().

Parameters

solution	the solution of the coupled PDE/ODE system
numTimeStepsElapsed	the number of timesteps that have elapsed

Definition at line 540 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

References VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::AddPointData(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

Member Data Documentation

mClearOutputDirectory

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM, unsigned PROBLEM_DIM = 1>

bool LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mClearOutputDirectory

private

Whether the output directory should be cleared before solve or not. False by default. Can be changed when setting the output directory

Definition at line 98 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

mInterpolatedOdeStateVariables

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM, unsigned PROBLEM_DIM = 1>

std::vector<double> LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mInterpolatedOdeStateVariables

private

The values of the ODE system state variables, interpolated at a quadrature point.

Definition at line 76 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

mOdeSystemsAtNodes

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM, unsigned PROBLEM_DIM = 1>

std::vector<AbstractOdeSystemForCoupledPdeSystem*> LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mOdeSystemsAtNodes

private

Vector of pointers to ODE systems, defined at nodes.

Definition at line 73 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

Referenced by LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LinearParabolicPdeSystemWithCoupledOdeSystemSolver().

mOdeSystemsPresent

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM, unsigned PROBLEM_DIM = 1>

bool LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mOdeSystemsPresent

private

Whether ODE systems are present (if not, then the system comprises coupled PDEs only).

Definition at line 89 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

Referenced by LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LinearParabolicPdeSystemWithCoupledOdeSystemSolver().

mpMesh

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM, unsigned PROBLEM_DIM = 1>

AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpMesh

private

Pointer to the mesh.

Definition at line 67 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

Referenced by LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LinearParabolicPdeSystemWithCoupledOdeSystemSolver().

mpOdeSolver

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM, unsigned PROBLEM_DIM = 1>

boost::shared_ptr<AbstractIvpOdeSolver> LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpOdeSolver

private

The ODE solver.

Definition at line 79 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

Referenced by LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::LinearParabolicPdeSystemWithCoupledOdeSystemSolver().

mpPdeSystem

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM, unsigned PROBLEM_DIM = 1>

AbstractLinearParabolicPdeSystemForCoupledOdeSystem<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>* LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpPdeSystem

private

The PDE system to be solved.

Definition at line 70 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

mpVtkMetaFile

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM, unsigned PROBLEM_DIM = 1>

out_stream LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpVtkMetaFile

private

Meta results file for VTK.

Definition at line 92 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

mSamplingTimeStep

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM, unsigned PROBLEM_DIM = 1>

double LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mSamplingTimeStep

private

A sampling timestep for writing results to file. Set to PdeSimulationTime::GetPdeTimeStep() in the constructor; may be overwritten using the SetSamplingTimeStep() method.

Definition at line 86 of file LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp.

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

• pde/src/solver/LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp