#include <AbstractDynamicLinearPdeSolver.hpp>

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

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

Public Member Functions
	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)

virtual void	SetupLinearSystem (Vec currentSolution, bool computeMatrix)=0

LinearSystem *	GetLinearSystem ()

Protected Member Functions
void	InitialiseHdf5Writer ()

void	WriteOneStep (double time, Vec solution)

Protected Attributes
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

Friends
class	TestSimpleLinearParabolicSolver

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >

Abstract class for dynamic linear PDE solves. This class defines the Solve() method. The concrete class should implement the SetupLinearSystem() method (defined in AbstractLinearPdeSolver), based on the PDE being solved and the numerical method.

Definition at line 56 of file AbstractDynamicLinearPdeSolver.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractDynamicLinearPdeSolver ( AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * pMesh )

Constructor.

Parameters

pMesh the mesh

Definition at line 262 of file AbstractDynamicLinearPdeSolver.hpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseHdf5Writer ( )

protected

Create and initialise the HDF5 writer. Called by Solve() if results are to be output.

Note: For now, writing variable names as 'Variable_0' etc; in the future, could allow user to specify units of time and names and units of dependent variables to be passed to the writer using DefineVariable() and DefineUnlimitedDimension()

Definition at line 223 of file AbstractDynamicLinearPdeSolver.hpp.

References EXCEPTION.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetInitialCondition ( Vec initialCondition )

Set the initial condition.

Note: We do *not* take responsibility for destroying this vector - the caller must do so once the solver is no longer in use.

Parameters

initialCondition the initial condition

Definition at line 307 of file AbstractDynamicLinearPdeSolver.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetMatrixIsNotAssembled ( )

Tell the solver to assemble the matrix again next timestep.

Definition at line 500 of file AbstractDynamicLinearPdeSolver.hpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetOutputDirectoryAndPrefix	(	std::string	outputDirectory,
		std::string	prefix
	)

Parameters

outputDirectory	the output directory
prefix	the filename prefix

Definition at line 532 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetOutputToParallelVtk ( bool output )

Parameters

output whether to output to parallel VTK (.pvtu) file

Definition at line 520 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetOutputToTxt ( bool output )

Parameters

output whether to output to a .txt format that is readable by Matlab

Definition at line 526 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetOutputToVtk ( bool output )

Parameters

output whether to output to VTK (.vtu) file

Definition at line 514 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetPrintingTimestepMultiple ( unsigned multiple )

Parameters

multiple the ratio of the number of actual timesteps to the number of timesteps at which results are output to HDF5 and other files.

Definition at line 539 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetTimeAdaptivityController ( AbstractTimeAdaptivityController * pTimeAdaptivityController )

Set a controller class which alters the dt used.

Parameters

pTimeAdaptivityController the controller

Definition at line 506 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetTimes	(	double	tStart,
		double	tEnd
	)

Set the times to solve between.

Parameters

tStart	the start time
tEnd	the end time

Definition at line 282 of file AbstractDynamicLinearPdeSolver.hpp.

References EXCEPTION.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetTimeStep ( double dt )

Set (or reset) the timestep to use.

Parameters

dt timestep

Definition at line 296 of file AbstractDynamicLinearPdeSolver.hpp.

References EXCEPTION.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

Vec AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve ( )

virtual

Dynamic solve method.

Returns: solution vector

Definition at line 328 of file AbstractDynamicLinearPdeSolver.hpp.

References TimeStepper::AdvanceOneTimeStep(), GenericEventHandler< 16, HeartEventHandler >::BeginEvent(), RelativeTo::ChasteTestOutput, PetscTools::Destroy(), GenericEventHandler< 16, HeartEventHandler >::EndEvent(), EXCEPTION, TimeStepper::GetNextTime(), TimeStepper::GetNextTimeStep(), TimeStepper::GetTime(), TimeStepper::GetTotalTimeStepsTaken(), TimeStepper::IsTimeAtEnd(), NEVER_REACHED, TimeStepper::ResetTimeStep(), PdeSimulationTime::SetPdeTimeStepAndNextTime(), and PdeSimulationTime::SetTime().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

void AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteOneStep	(	double	time,
		Vec	solution
	)

protected

Write one timestep of output data to HDF5 file.

Parameters

time	the time
solution	the solution vector to write

Definition at line 314 of file AbstractDynamicLinearPdeSolver.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

std::string AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mFilenamePrefix

protected

Filename prefix for HDF5 and other files.

Definition at line 116 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

double AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mIdealTimeStep

protected

The timestep to use. This is either the last timestep passed in in SetTimeStep, or the last timestep suggested by the time adaptivity controller.

Definition at line 86 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

Vec AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mInitialCondition

protected

The initial condition vector.

Definition at line 71 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

double AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mLastWorkingTimeStep

protected

The last actual timestep used.

Definition at line 89 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mMatrixIsAssembled

protected

Whether the matrix has been assembled for the current time step.

Definition at line 74 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mMatrixIsConstant

protected

Whether the matrix is constant in time (if so the system need not be assembled at each time step). Defaults to false.

Definition at line 80 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

std::string AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mOutputDirectory

protected

Output directory (a subfolder of tmp/[USERNAME]/testoutput).

Definition at line 113 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mOutputToParallelVtk

protected

Flag to say if we need to output to VTK parallel (.pvtu). Defaults to false in the constructor.

Definition at line 104 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mOutputToTxt

protected

Flag to say if we need to output to a .txt format that is readable by Matlab. Defaults to false in the constructor.

Definition at line 110 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mOutputToVtk

protected

Flag to say if we need to output to VTK. Defaults to false in the constructor.

Definition at line 98 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

Hdf5DataWriter* AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpHdf5Writer

protected

The object used to write results to HDF5 file.

Definition at line 126 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

unsigned AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mPrintingTimestepMultiple

protected

The ratio of the number of actual timesteps to the number of timesteps at which results are output to HDF5 and other files. Defaults to 1 in the constructor.

Definition at line 123 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

AbstractTimeAdaptivityController* AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpTimeAdaptivityController

protected

A controller which determines what timestep to use (defaults to NULL).

Definition at line 92 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

double AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mTend

protected

Simulation end time.

Definition at line 65 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

bool AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mTimesSet

protected

Whether SetTimes has been called with suitable parameters.

Definition at line 68 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

double AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mTstart

protected

Simulation start time.

Definition at line 62 of file AbstractDynamicLinearPdeSolver.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

std::vector<int> AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mVariableColumnIds

protected

List of variable column IDs as written to HDF5 file.

Definition at line 129 of file AbstractDynamicLinearPdeSolver.hpp.

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

pde/src/solver/AbstractDynamicLinearPdeSolver.hpp

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM> class AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >