#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)
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)
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
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 260 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 221 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 305 of file AbstractDynamicLinearPdeSolver.hpp.

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), and AdaptiveBidomainProblem::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 480 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 512 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 500 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 506 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 494 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 519 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 486 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 280 of file AbstractDynamicLinearPdeSolver.hpp.

References EXCEPTION.

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), and AdaptiveBidomainProblem::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 294 of file AbstractDynamicLinearPdeSolver.hpp.

References EXCEPTION.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>

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

Dynamic solve method.

Definition at line 326 of file AbstractDynamicLinearPdeSolver.hpp.

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

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), and AdaptiveBidomainProblem::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 312 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 >