CardiacSimulation Class Reference

#include <CardiacSimulation.hpp>

Collaboration diagram for CardiacSimulation:

Public Member Functions
	CardiacSimulation (std::string parameterFileName, bool writeProvenanceInfo=false, bool saveProblemInstance=false)
boost::shared_ptr < AbstractUntemplatedCardiacProblem >	GetSavedProblem ()
Private Member Functions
void	ReadParametersFromFile (std::string parameterFileName)
template<class Problem , unsigned SPACE_DIM>
void	CreateAndRun ()
void	Run ()
void	CreateResumeXmlFile (const std::string &rOutputDirectory, const std::string &rArchiveDirectory)
std::string	BoolToString (bool yesNo)
Private Attributes
bool	mSaveProblemInstance
boost::shared_ptr < AbstractUntemplatedCardiacProblem >	mSavedProblem

Detailed Description

A class which encapsulates the executable functionality.

Takes in a chaste parameters XML file and runs the relevant simulation.

The XML Schema, which describes what is allowed in the XML configuration file, can be found at heart/src/io/ChasteParameters_2_0.xsd (for Chaste release 2.0). It contains documentation describing what settings are available. The documentation of the HeartConfig class may also be of use.

Definition at line 76 of file CardiacSimulation.hpp.

Constructor & Destructor Documentation

CardiacSimulation::CardiacSimulation	(	std::string	parameterFileName,
		bool	writeProvenanceInfo = `false`,
		bool	saveProblemInstance = `false`
	)

Constructor

This also runs the simulation immediately.

Parameters:

	parameterFileName	The name of the chaste parameters xml file to use to run a simulation.
	writeProvenanceInfo	Whether to write provanence and machine information files.
	saveProblemInstance	Whether to save a copy of the problem instance for examination by tests.

Definition at line 87 of file CardiacSimulation.cpp.

References EXCEPTION, GenericEventHandler< 16, HeartEventHandler >::Headings(), HeartConfig::Instance(), ReadParametersFromFile(), GenericEventHandler< 16, HeartEventHandler >::Report(), Run(), ExecutableSupport::SetOutputDirectory(), ExecutableSupport::WriteMachineInfoFile(), and ExecutableSupport::WriteProvenanceInfoFile().

Member Function Documentation

std::string CardiacSimulation::BoolToString ( bool yesNo ) [private]

Convert a boolean to a "yes" or "no" string.

Parameters:

yesNo

Definition at line 38 of file CardiacSimulation.cpp.

Referenced by CreateResumeXmlFile().

template<class Problem , unsigned SPACE_DIM>

void CardiacSimulation::CreateAndRun ( ) [inline, private]

Templated method which creates and runs a cardiac simulation, based on the XML file passed to our constructor.

Definition at line 91 of file CardiacSimulation.hpp.

References ABORT_IF_NON0, PetscTools::AmMaster(), OutputDirectoryFifoQueue::CreateNextDir(), CreateResumeXmlFile(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::GetCardiacCell(), HeartConfig::GetCheckpointSimulation(), HeartConfig::GetCheckpointTimestep(), DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLow(), HeartConfig::GetOutputDirectory(), OutputFileHandler::GetOutputDirectoryFullPath(), HeartConfig::GetSimulationDuration(), HeartConfig::Instance(), mSavedProblem, mSaveProblemInstance, HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellIntracellularStimulus(), HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellParameters(), AbstractCardiacCellFactory< SPACE_DIM >::SetMesh(), and HeartConfig::SetSimulationDuration().

void CardiacSimulation::CreateResumeXmlFile	(	const std::string &	rOutputDirectory,
		const std::string &	rArchiveDirectory
	)			`[private]`

Write a ResumeParameters.xml file to the checkpoint directory, to help users in resuming a checkpointed simulation. If the contents of rOutputDirectory are copied to CHASTE_TEST_OUTPUT, and ResumeParameters.xml edited to specify a sensible simulation duration, then it can be used as the input parameters file to resume from the given checkpoint.

Parameters: