HeartConfig Class Reference

#include <HeartConfig.hpp>

Collaboration diagram for HeartConfig:

Public Types
typedef std::map< std::string, std::string >	SchemaLocationsMap
Public Member Functions
void	SetUseFixedSchemaLocation (bool useFixedSchemaLocation)
void	SetFixedSchemaLocations (const SchemaLocationsMap &rSchemaLocations)
void	SetParametersFile (const std::string &rFileName)
void	Write (bool useArchiveLocationInfo=false, std::string subfolderName="output")
void	CopySchema (const std::string &rToDirectory)
boost::shared_ptr < cp::chaste_parameters_type >	ReadFile (const std::string &rFileName)
	~HeartConfig ()
unsigned	GetVersionFromNamespace (const std::string &rNamespaceUri)
FileFinder	GetParametersFilePath ()
bool	IsSimulationDefined () const
bool	IsSimulationResumed () const
unsigned	GetSpaceDimension () const
double	GetSimulationDuration () const
cp::domain_type	GetDomain () const
cp::ionic_model_selection_type	GetDefaultIonicModel () const
template<unsigned DIM>
void	GetIonicModelRegions (std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &rDefinedRegions, std::vector< cp::ionic_model_selection_type > &rIonicModels) const
void	SetIonicModelRegions (std::vector< ChasteCuboid< 3 > > &rDefinedRegions, std::vector< cp::ionic_model_selection_type > &rIonicModels) const
bool	IsMeshProvided () const
bool	GetCreateMesh () const
bool	GetCreateSlab () const
bool	GetCreateSheet () const
bool	GetCreateFibre () const
bool	GetLoadMesh () const
void	GetSlabDimensions (c_vector< double, 3 > &slabDimensions) const
void	GetSheetDimensions (c_vector< double, 2 > &sheetDimensions) const
void	GetFibreLength (c_vector< double, 1 > &fibreLength) const
double	GetInterNodeSpace () const
std::string	GetMeshName () const
cp::media_type	GetConductivityMedia () const
template<unsigned DIM>
void	GetStimuli (std::vector< boost::shared_ptr< AbstractStimulusFunction > > &rStimuliApplied, std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &rStimulatedAreas) const
template<unsigned DIM>
void	GetCellHeterogeneities (std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &rCellHeterogeneityRegions, std::vector< double > &rScaleFactorGks, std::vector< double > &rScaleFactorIto, std::vector< double > &rScaleFactorGkr, std::vector< std::map< std::string, double > > *pParameterSettings)
bool	GetConductivityHeterogeneitiesProvided () const
bool	AreCellularTransmuralHeterogeneitiesRequested ()
double	GetEpiLayerFraction ()
double	GetEndoLayerFraction ()
double	GetMidLayerFraction ()
unsigned	GetEpiLayerIndex ()
unsigned	GetEndoLayerIndex ()
unsigned	GetMidLayerIndex ()
template<unsigned DIM>
void	GetConductivityHeterogeneities (std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &conductivitiesHeterogeneityAreas, std::vector< c_vector< double, 3 > > &intraConductivities, std::vector< c_vector< double, 3 > > &extraConductivities) const
std::string	GetOutputDirectory () const
std::string	GetOutputFilenamePrefix () const
bool	GetOutputVariablesProvided () const
void	GetOutputVariables (std::vector< std::string > &rOutputVariables) const
bool	GetOutputUsingOriginalNodeOrdering ()
bool	GetCheckpointSimulation () const
double	GetCheckpointTimestep () const
unsigned	GetMaxCheckpointsOnDisk () const
HeartFileFinder	GetArchivedSimulationDir () const
void	GetIntracellularConductivities (c_vector< double, 3 > &intraConductivities) const
void	GetIntracellularConductivities (c_vector< double, 2 > &intraConductivities) const
void	GetIntracellularConductivities (c_vector< double, 1 > &intraConductivities) const
void	GetExtracellularConductivities (c_vector< double, 3 > &extraConductivities) const
void	GetExtracellularConductivities (c_vector< double, 2 > &extraConductivities) const
void	GetExtracellularConductivities (c_vector< double, 1 > &extraConductivities) const
double	GetBathConductivity (unsigned bathRegion=UINT_MAX) const
const std::set< unsigned > &	rGetTissueIdentifiers ()
const std::set< unsigned > &	rGetBathIdentifiers ()
double	GetSurfaceAreaToVolumeRatio () const
double	GetCapacitance () const
double	GetOdeTimeStep () const
double	GetPdeTimeStep () const
double	GetPrintingTimeStep () const
bool	GetUseAbsoluteTolerance () const
double	GetAbsoluteTolerance () const
bool	GetUseRelativeTolerance () const
double	GetRelativeTolerance () const
const char *	GetKSPSolver () const
const char *	GetKSPPreconditioner () const
DistributedTetrahedralMeshPartitionType::type	GetMeshPartitioning () const
bool	IsAdaptivityParametersPresent () const
bool	IsPostProcessingSectionPresent () const
void	EnsurePostProcessingSectionPresent ()
bool	IsPostProcessingRequested () const
bool	IsApdMapsRequested () const
void	GetApdMaps (std::vector< std::pair< double, double > > &rApdMaps) const
bool	IsUpstrokeTimeMapsRequested () const
void	GetUpstrokeTimeMaps (std::vector< double > &rUpstrokeTimeMaps) const
bool	IsMaxUpstrokeVelocityMapRequested () const
void	GetMaxUpstrokeVelocityMaps (std::vector< double > &rUpstrokeVelocityMaps) const
bool	IsConductionVelocityMapsRequested () const
void	GetConductionVelocityMaps (std::vector< unsigned > &rConductionVelocityMaps) const
bool	IsAnyNodalTimeTraceRequested () const
void	GetNodalTimeTraceRequested (std::vector< unsigned > &rRequestedNodes) const
bool	IsPseudoEcgCalculationRequested () const
template<unsigned SPACE_DIM>
void	GetPseudoEcgElectrodePositions (std::vector< ChastePoint< SPACE_DIM > > &rPseudoEcgElectrodePositions) const
bool	GetUseStateVariableInterpolation () const
bool	IsOutputVisualizerPresent () const
bool	GetVisualizeWithMeshalyzer () const
bool	GetVisualizeWithCmgui () const
bool	GetVisualizeWithVtk () const
bool	GetVisualizeWithParallelVtk () const
unsigned	GetVisualizerOutputPrecision ()
bool	IsElectrodesPresent () const
void	GetElectrodeParameters (bool &rGroundSecondElectrode, unsigned &rIndex, double &rMagnitude, double &rStartTime, double &rDuration)
bool	GetUseMassLumping ()
bool	GetUseMassLumpingForPrecond ()
bool	GetUseReactionDiffusionOperatorSplitting ()
bool	GetUseFixedNumberIterationsLinearSolver ()
unsigned	GetEvaluateNumItsEveryNSolves ()
void	SetSpaceDimension (unsigned spaceDimension)
void	SetSimulationDuration (double simulationDuration)
void	SetDomain (const cp::domain_type &rDomain)
void	SetDefaultIonicModel (const cp::ionic_models_available_type &rIonicModel)
void	SetSlabDimensions (double x, double y, double z, double inter_node_space)
void	SetSheetDimensions (double x, double y, double inter_node_space)
void	SetFibreLength (double x, double inter_node_space)
void	SetMeshFileName (std::string meshPrefix, cp::media_type fibreDefinition=cp::media_type::NoFibreOrientation)
void	SetConductivityHeterogeneities (std::vector< ChasteCuboid< 3 > > &rConductivityAreas, std::vector< c_vector< double, 3 > > &rIntraConductivities, std::vector< c_vector< double, 3 > > &rExtraConductivities)
void	SetConductivityHeterogeneitiesEllipsoid (std::vector< ChasteEllipsoid< 3 > > &conductivityAreas, std::vector< c_vector< double, 3 > > &intraConductivities, std::vector< c_vector< double, 3 > > &extraConductivities)
void	SetOutputDirectory (const std::string &rOutputDirectory)
void	SetOutputFilenamePrefix (const std::string &rOutputFilenamePrefix)
void	SetOutputVariables (const std::vector< std::string > &rOutputVariables)
void	SetOutputUsingOriginalNodeOrdering (bool useOriginal)
void	SetCheckpointSimulation (bool checkpointSimulation, double checkpointTimestep=-1.0, unsigned maxCheckpointsOnDisk=UINT_MAX)
void	SetIntracellularConductivities (const c_vector< double, 3 > &rIntraConductivities)
void	SetIntracellularConductivities (const c_vector< double, 2 > &rIntraConductivities)
void	SetIntracellularConductivities (const c_vector< double, 1 > &rIntraConductivities)
void	SetExtracellularConductivities (const c_vector< double, 3 > &rExtraConductivities)
void	SetExtracellularConductivities (const c_vector< double, 2 > &rExtraConductivities)
void	SetExtracellularConductivities (const c_vector< double, 1 > &rExtraConductivities)
void	SetBathConductivity (double bathConductivity)
void	SetBathMultipleConductivities (std::map< unsigned, double > bathConductivities)
void	SetTissueAndBathIdentifiers (const std::set< unsigned > &tissueIds, const std::set< unsigned > &bathIds)
void	SetSurfaceAreaToVolumeRatio (double ratio)
void	SetCapacitance (double capacitance)
void	SetOdePdeAndPrintingTimeSteps (double odeTimeStep, double pdeTimeStep, double printingTimeStep)
void	SetOdeTimeStep (double odeTimeStep)
void	SetPdeTimeStep (double pdeTimeStep)
void	SetPrintingTimeStep (double printingTimeStep)
void	SetUseRelativeTolerance (double relativeTolerance)
void	SetUseAbsoluteTolerance (double absoluteTolerance)
void	SetKSPSolver (const char *kspSolver, bool warnOfChange=false)
void	SetKSPPreconditioner (const char *kspPreconditioner)
void	SetMeshPartitioning (const char *meshPartioningMethod)
void	SetApdMaps (const std::vector< std::pair< double, double > > &rApdMaps)
void	SetUpstrokeTimeMaps (std::vector< double > &rUpstrokeTimeMaps)
void	SetMaxUpstrokeVelocityMaps (std::vector< double > &rMaxUpstrokeVelocityMaps)
void	SetConductionVelocityMaps (std::vector< unsigned > &rConductionVelocityMaps)
void	SetRequestedNodalTimeTraces (std::vector< unsigned > &requestedNodes)
template<unsigned SPACE_DIM>
void	SetPseudoEcgElectrodePositions (const std::vector< ChastePoint< SPACE_DIM > > &rPseudoEcgElectrodePositions)
void	EnsureOutputVisualizerExists (void)
void	SetVisualizeWithMeshalyzer (bool useMeshalyzer=true)
void	SetVisualizeWithCmgui (bool useCmgui=true)
void	SetVisualizeWithVtk (bool useVtk=true)
void	SetVisualizeWithParallelVtk (bool useParallelVtk=true)
void	SetVisualizerOutputPrecision (unsigned numberOfDigits)
void	SetElectrodeParameters (bool groundSecondElectrode, unsigned index, double magnitude, double startTime, double duration)
void	SetUseStateVariableInterpolation (bool useStateVariableInterpolation=true)
void	SetUseMassLumping (bool useMassLumping=true)
void	SetUseMassLumpingForPrecond (bool useMassLumping=true)
void	SetUseReactionDiffusionOperatorSplitting (bool useOperatorSplitting=true)
void	SetUseFixedNumberIterationsLinearSolver (bool useFixedNumberIterations=true, unsigned evaluateNumItsEveryNSolves=UINT_MAX)
bool	HasDrugDose () const
double	GetDrugDose () const
void	SetDrugDose (double drugDose)
void	SetIc50Value (const std::string &rCurrentName, double ic50, double hill=1.0)
std::map< std::string, std::pair< double, double > >	GetIc50Values ()
bool	HasPurkinje ()
double	GetPurkinjeCapacitance ()
void	SetPurkinjeCapacitance (double capacitance)
double	GetPurkinjeSurfaceAreaToVolumeRatio ()
void	SetPurkinjeSurfaceAreaToVolumeRatio (double ratio)
double	GetPurkinjeConductivity ()
void	SetPurkinjeConductivity (double conductivity)
Static Public Member Functions
static HeartConfig *	Instance ()
static void	Reset ()
Private Member Functions
void	CheckTimeSteps () const
template<class Archive >
void	save (Archive &archive, const unsigned int version) const
template<class Archive >
void	load (Archive &archive, const unsigned int version)
void	LoadFromCheckpoint ()
void	UpdateParametersFromResumeSimulation (boost::shared_ptr< cp::chaste_parameters_type > pResumeParameters)
void	SetDefaultSchemaLocations ()
	HeartConfig ()
void	CheckSimulationIsDefined (std::string callingMethod="") const
void	CheckResumeSimulationIsDefined (std::string callingMethod="") const
Private Attributes
SchemaLocationsMap	mSchemaLocations
boost::shared_ptr < cp::chaste_parameters_type >	mpParameters
FileFinder	mParametersFilePath
bool	mUseFixedSchemaLocation
double	mEpiFraction
double	mEndoFraction
double	mMidFraction
unsigned	mIndexMid
unsigned	mIndexEpi
unsigned	mIndexEndo
bool	mUserAskedForCellularTransmuralHeterogeneities
bool	mUseMassLumping
bool	mUseMassLumpingForPrecond
bool	mUseReactionDiffusionOperatorSplitting
std::map< unsigned, double >	mBathConductivities
std::set< unsigned >	mTissueIdentifiers
std::set< unsigned >	mBathIdentifiers
bool	mUseFixedNumberIterations
unsigned	mEvaluateNumItsEveryNSolves
Static Private Attributes
static std::auto_ptr< HeartConfig >	mpInstance
Friends
class	boost::serialization::access
class	TestHeartConfig

Detailed Description

A singleton class containing configuration parameters for heart simulations.

This class wraps the settings from the XML configuration file in a more friendly interface, providing methods to read and write all the settings, and round-trip them to/from XML format. It also deals with the complexities of supporting multiple versions of CodeSynthesis XSD.

chaste_parameters_type is a convenience class created by CodeSynthesis XSD

Definition at line 78 of file HeartConfig.hpp.

Member Typedef Documentation

typedef std::map<std::string, std::string> HeartConfig::SchemaLocationsMap

Our type for specifying schema location properties: a map from namespace URI to schema URI. The default namespace is specified by an empty namespace URI.

Definition at line 140 of file HeartConfig.hpp.

Constructor & Destructor Documentation

HeartConfig::~HeartConfig ( )

Destructor

Definition at line 247 of file HeartConfig.cpp.

HeartConfig::HeartConfig ( ) [private]

Todo:: #1703 This defaults should be set in HeartConfigDefaults.hpp

Definition at line 215 of file HeartConfig.cpp.

References CreateDefaultParameters(), mBathIdentifiers, mEndoFraction, mEpiFraction, mIndexEndo, mIndexEpi, mIndexMid, mMidFraction, mpInstance, mpParameters, mTissueIdentifiers, mUseFixedSchemaLocation, mUserAskedForCellularTransmuralHeterogeneities, mUseReactionDiffusionOperatorSplitting, and SetDefaultSchemaLocations().

Member Function Documentation

bool HeartConfig::AreCellularTransmuralHeterogeneitiesRequested ( )

Returns:: the value of the flag that tells whether the user asked for cellular transmural heterogeneities

Definition at line 1247 of file HeartConfig.cpp.

References mUserAskedForCellularTransmuralHeterogeneities.

void HeartConfig::CheckResumeSimulationIsDefined ( std::string callingMethod = "" ) const [private]

CheckSimulationIsDefined is a convenience method for checking if the "<"ResumeSimulation">" element has been defined and therefore is safe to use the ResumeSimulation().get() pointer to access other data.

Throws an exception if not.

Parameters:

callingMethod

string describing the get method performing the check.

Definition at line 678 of file HeartConfig.cpp.

References EXCEPTION, and IsSimulationDefined().

Referenced by GetArchivedSimulationDir().

void HeartConfig::CheckSimulationIsDefined ( std::string callingMethod = "" ) const [private]

CheckSimulationIsDefined is a convenience method for checking if the "<"Simulation">" element has been defined and therefore is safe to use the Simulation().get() pointer to access other data.

Throws an exception if not.

Parameters:

callingMethod

string describing the get method performing the check.

Definition at line 670 of file HeartConfig.cpp.

References EXCEPTION, and IsSimulationResumed().

Referenced by GetCellHeterogeneities(), GetConductivityHeterogeneities(), GetConductivityHeterogeneitiesProvided(), GetConductivityMedia(), GetCreateFibre(), GetCreateMesh(), GetCreateSheet(), GetCreateSlab(), GetDefaultIonicModel(), GetFibreLength(), GetInterNodeSpace(), GetIonicModelRegions(), GetLoadMesh(), GetMeshName(), GetOutputDirectory(), GetOutputFilenamePrefix(), GetOutputUsingOriginalNodeOrdering(), GetOutputVariablesProvided(), GetSheetDimensions(), GetSlabDimensions(), GetStimuli(), HasPurkinje(), IsMeshProvided(), and IsOutputVisualizerPresent().

void HeartConfig::CheckTimeSteps ( ) const [private]

Throws if the time steps don't obey constraints (within machine precision) ode_step > 0.0 pde_step = n1 * ode_step (where n1 is a positive integer) printing_step = n2 * pde_step (where n2 is a positive integer)

Definition at line 2376 of file HeartConfig.cpp.

References EXCEPTION, GetCheckpointSimulation(), GetCheckpointTimestep(), GetOdeTimeStep(), GetPdeTimeStep(), and GetPrintingTimeStep().

Referenced by LoadFromCheckpoint(), SetCheckpointSimulation(), SetOdePdeAndPrintingTimeSteps(), and SetParametersFile().

void HeartConfig::CopySchema ( const std::string & rToDirectory )

Try to copy the latest version of the schema to the given directory. If we can't find the latest version of the schema, generate a warning.

Note:: Must be called by the master only, preferably in a TRY_IF_MASTER() in case of failure, to handle exceptions nicely.

Parameters:

rToDirectory

directory to copy to

Definition at line 360 of file HeartConfig.cpp.

References RelativeTo::Absolute, RelativeTo::ChasteSourceRoot, FileFinder::CopyTo(), RelativeTo::CWD, FileFinder::Exists(), and FileFinder::SetPath().

Referenced by Write().

void HeartConfig::EnsureOutputVisualizerExists ( void )

Create the OutputVisualizer element if it doesn't exist

Definition at line 2663 of file HeartConfig.cpp.

References mpParameters.

Referenced by SetVisualizerOutputPrecision(), SetVisualizeWithCmgui(), SetVisualizeWithMeshalyzer(), SetVisualizeWithParallelVtk(), and SetVisualizeWithVtk().

void HeartConfig::EnsurePostProcessingSectionPresent ( )

Create a PostProcessing section in the user parameters if one doesn't exist.

Definition at line 1715 of file HeartConfig.cpp.

References mpParameters.

Referenced by SetApdMaps(), SetConductionVelocityMaps(), SetMaxUpstrokeVelocityMaps(), SetPseudoEcgElectrodePositions(), SetRequestedNodalTimeTraces(), SetUpstrokeTimeMaps(), and UpdateParametersFromResumeSimulation().

double HeartConfig::GetAbsoluteTolerance ( ) const

Returns:: KSP absolute tolerance (or throw if we are using relative)

Definition at line 1602 of file HeartConfig.cpp.

References EXCEPTION, GetUseAbsoluteTolerance(), and mpParameters.

Referenced by AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::DisplayRun(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

void HeartConfig::GetApdMaps ( std::vector< std::pair< double, double > > & rApdMaps ) const

Parameters:

rApdMaps

each entry is a request for a map with

a percentage in the range [1, 100)
a threshold (in mV)

Definition at line 1748 of file HeartConfig.cpp.

References IsApdMapsRequested(), and mpParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

HeartFileFinder HeartConfig::GetArchivedSimulationDir ( ) const

Returns:: directory where the archived simulation to resume is defined

Definition at line 1431 of file HeartConfig.cpp.

References CheckResumeSimulationIsDefined(), and mpParameters.

double HeartConfig::GetBathConductivity ( unsigned bathRegion = UINT_MAX ) const

Returns bath conductivities for different regions of the bath. When called without a region identifier, it will return whatever has been defined as BathConductivity

Parameters:

bathRegion

region identifier

Returns:: bath conductivity (mS/cm)

Definition at line 1521 of file HeartConfig.cpp.

References HeartRegionCode::IsRegionBath(), mBathConductivities, and mpParameters.

Referenced by BidomainWithBathAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm().

double HeartConfig::GetCapacitance ( ) const

Returns:: surface capacitance Cm for PDE (uF/cm^2)

Definition at line 1572 of file HeartConfig.cpp.

References mpParameters.

Referenced by BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), CorriasBuistICCModified::CorriasBuistICCModified(), CorriasBuistSMCModified::CorriasBuistSMCModified(), CML_noble_varghese_kohl_noble_1998_basic_with_sac::GetIIonic(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and BidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

template<unsigned DIM>

void HeartConfig::GetCellHeterogeneities	(	std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &	rCellHeterogeneityRegions,
		std::vector< double > &	rScaleFactorGks,
		std::vector< double > &	rScaleFactorIto,
		std::vector< double > &	rScaleFactorGkr,
		std::vector< std::map< std::string, double > > *	pParameterSettings
	)			`[inline]`

Reads from the XML file the cellular hetrogeneities. It fugures out whether the user specified a cuboid or a transmural-type of hetrogeneities. In the latter case, it stores the percentage values of Epi and Endo layers in two member variables, accessible via get methods. It also checks if the user-supplied numbers are consistent (i.e., positive and add up to less than 1) Return a number of heterogeneous regions for special gating variable changes

Todo:

do we assume the vectors are initially empty? The returned std::vectors are all of the same length

Parameters:

	rCellHeterogeneityRegions	cellHeterogeneityAreas[0] is the first region
	rScaleFactorGks	scaleFactorGks[0] is a scaling factor for the first region
	rScaleFactorIto	scaleFactorIto[0] is a scaling factor for the first region
	rScaleFactorGkr	scaleFactorGkr[0] is a scaling factor for the first region
	pParameterSettings	specification of named parameters to set on the cell models; each entry is a map from parameter name to value.

Todo:: There is no set method

Definition at line 1109 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), EXCEPTION, mEndoFraction, mEpiFraction, mIndexEndo, mIndexEpi, mIndexMid, mMidFraction, mpParameters, and mUserAskedForCellularTransmuralHeterogeneities.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().

bool HeartConfig::GetCheckpointSimulation ( ) const

Get whether simulation should be checkpointed or not

Returns:: archive simulation

Definition at line 1413 of file HeartConfig.cpp.

References IsSimulationDefined(), and mpParameters.

Referenced by CheckTimeSteps(), CardiacSimulation::CreateAndRun(), HeartConfigRelatedCellFactory< SPACE_DIM >::CreateCellWithIntracellularStimulus(), GetCheckpointTimestep(), and GetMaxCheckpointsOnDisk().

double HeartConfig::GetCheckpointTimestep ( ) const

Get checkpointing timestep

Returns:: checkpointing timestep

Definition at line 1418 of file HeartConfig.cpp.

References GetCheckpointSimulation(), and mpParameters.

Referenced by CheckTimeSteps(), CardiacSimulation::CreateAndRun(), and CardiacSimulation::CreateResumeXmlFile().

void HeartConfig::GetConductionVelocityMaps ( std::vector< unsigned > & rConductionVelocityMaps ) const

Parameters:

rConductionVelocityMaps

each entry is a request for a map with

an index to treat as the source for wave propagation

Definition at line 1833 of file HeartConfig.cpp.

References IsConductionVelocityMapsRequested(), and mpParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

template<unsigned DIM>

void HeartConfig::GetConductivityHeterogeneities	(	std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &	conductivitiesHeterogeneityAreas,
		std::vector< c_vector< double, 3 > > &	intraConductivities,
		std::vector< c_vector< double, 3 > > &	extraConductivities
	)			const `[inline]`

Return a number of heterogeneous regions (Axis-aligned boxes)

Todo:

do we assume the vectors are initially empty? The returned std::vectors are all of the same length

Parameters:

	conductivitiesHeterogeneityAreas	conductivitiesHeterogeneityAreas[0] is the first region
	intraConductivities	intraConductivities[0] is conductivity vector for the first region
	extraConductivities	extraConductivities[0] is conductivity vector for the first region

Todo:: When this is implemented, then we require an example in ChasteParametersFullFormat.xml

Definition at line 1289 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), EXCEPTION, GetConductivityHeterogeneitiesProvided(), GetExtracellularConductivities(), GetIntracellularConductivities(), and mpParameters.

Referenced by ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), and ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell().

bool HeartConfig::GetConductivityHeterogeneitiesProvided ( ) const

Returns:: true if there are conductivity heterogeneities for GetConductivityHeterogeneities to return

Definition at line 1282 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), and mpParameters.

Referenced by ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell(), and GetConductivityHeterogeneities().

cp::media_type HeartConfig::GetConductivityMedia ( ) const

Returns:: media (Orthotropic/Axisymmetric/NoFibreOrientation) so that we know whether to read a .ortho/.axi file

Definition at line 963 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), GetLoadMesh(), and mpParameters.

Referenced by ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), and ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell().

bool HeartConfig::GetCreateFibre ( ) const

Returns:: true if it's a cuboid simulation (no mesh on disk)

Definition at line 868 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), IsMeshProvided(), and mpParameters.

Referenced by GetFibreLength(), and GetInterNodeSpace().

bool HeartConfig::GetCreateMesh ( ) const

Returns:: true if it's a cuboid simulation (no mesh on disk)

Definition at line 844 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), IsMeshProvided(), and mpParameters.

bool HeartConfig::GetCreateSheet ( ) const

Returns:: true if it's a cuboid simulation (no mesh on disk)

Definition at line 860 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), IsMeshProvided(), and mpParameters.

Referenced by GetInterNodeSpace(), and GetSheetDimensions().

bool HeartConfig::GetCreateSlab ( ) const

Returns:: true if it's a cuboid simulation (no mesh on disk)

Definition at line 852 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), IsMeshProvided(), and mpParameters.

Referenced by GetInterNodeSpace(), and GetSlabDimensions().

cp::ionic_model_selection_type HeartConfig::GetDefaultIonicModel ( ) const

Default cardiac cell model to use at all mesh nodes (unless otherwise specified by GetIonicModelRegions). cp::ionic_model_selection_type is generated automatically from the XML Schema.

Returns:: type of model

Definition at line 725 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), and mpParameters.

cp::domain_type HeartConfig::GetDomain ( ) const

cp::domain_type is an xsd convenience class type

Returns:: domain type of simulation: bi- or mono-domain

Definition at line 712 of file HeartConfig.cpp.

References IsSimulationDefined(), and mpParameters.

Referenced by CardiacSimulation::CreateResumeXmlFile(), and UpdateParametersFromResumeSimulation().

double HeartConfig::GetDrugDose ( ) const

Returns:: the dose of the drug (in the same units as the IC50s)

Definition at line 2810 of file HeartConfig.cpp.

References HasDrugDose(), and mpParameters.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellParameters().

void HeartConfig::GetElectrodeParameters	(	bool &	rGroundSecondElectrode,
		unsigned &	rIndex,
		double &	rMagnitude,
		double &	rStartTime,
		double &	rDuration
	)

Get electrode parameters.

Parameters:

	rGroundSecondElectrode	Whether to ground the second electrode (see class documentation)
	rIndex	The value i when applying the electrodes to x_i=a and x_i=b (a<b)
	rMagnitude	Magnitude of the stimulus
	rStartTime	Switch on time
	rDuration	Duration of the stimulus.

Definition at line 2747 of file HeartConfig.cpp.

References EXCEPTION, IsElectrodesPresent(), and mpParameters.

Referenced by Electrodes< DIM >::Electrodes().

double HeartConfig::GetEndoLayerFraction ( )

Returns:: the fraction of endocardial layer

Definition at line 1257 of file HeartConfig.cpp.

References mEndoFraction.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas().

unsigned HeartConfig::GetEndoLayerIndex ( )

Returns:: the index with which the endocardial layer is supplied (i.e., the order it comes in the XML file)

Definition at line 1272 of file HeartConfig.cpp.

References mIndexEndo.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas().

double HeartConfig::GetEpiLayerFraction ( )

Returns:: the fraction of epicardial layer

Definition at line 1252 of file HeartConfig.cpp.

References mEpiFraction.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas().

unsigned HeartConfig::GetEpiLayerIndex ( )

Returns:: the index with which the epicardial layer is supplied (i.e., the order it comes in the XML file)

Definition at line 1267 of file HeartConfig.cpp.

References mIndexEpi.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas().

unsigned HeartConfig::GetEvaluateNumItsEveryNSolves ( )

Returns:: how often perform a solve with residual-based stop criteria in order to decide how many iterations to perform in following linear solves.

Definition at line 2924 of file HeartConfig.cpp.

References mEvaluateNumItsEveryNSolves.

void HeartConfig::GetExtracellularConductivities ( c_vector< double, 1 > & extraConductivities ) const

1D version

Parameters:

extraConductivities

DIM-vector for returning extracellular conductivities (mS/cm)

Definition at line 1511 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::GetExtracellularConductivities ( c_vector< double, 2 > & extraConductivities ) const

2D version

Parameters:

extraConductivities

DIM-vector for returning extracellular conductivities (mS/cm)

Definition at line 1497 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::GetExtracellularConductivities ( c_vector< double, 3 > & extraConductivities ) const

3D version

Parameters:

extraConductivities

DIM-vector for returning extracellular conductivities (mS/cm)

Definition at line 1480 of file HeartConfig.cpp.

References mpParameters.

Referenced by ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), and GetConductivityHeterogeneities().

void HeartConfig::GetFibreLength ( c_vector< double, 1 > & fibreLength ) const

Parameters:

fibreLength

return vector for the (cuboid) mesh dimensions (cm)

Definition at line 915 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), EXCEPTION, GetCreateFibre(), GetSpaceDimension(), and mpParameters.

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

std::map< std::string, std::pair< double, double > > HeartConfig::GetIc50Values ( )

Get the parameters for the model of "conductance-block" drug action on a set of ion channels.

Returns:: A map between the current/channel name, and a pair giving IC50 value and hill coefficient.

Definition at line 2829 of file HeartConfig.cpp.

References HasDrugDose(), and mpParameters.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellParameters().

double HeartConfig::GetInterNodeSpace ( ) const

Returns:: internode space of cuboid mesh (cm)

Definition at line 929 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), GetCreateFibre(), GetCreateSheet(), GetCreateSlab(), GetSpaceDimension(), mpParameters, and NEVER_REACHED.

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

void HeartConfig::GetIntracellularConductivities ( c_vector< double, 1 > & intraConductivities ) const

1D version

Parameters:

intraConductivities

DIM-vector for returning intracellular conductivities (mS/cm)

Definition at line 1470 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::GetIntracellularConductivities ( c_vector< double, 2 > & intraConductivities ) const

2D version

Parameters:

intraConductivities

DIM-vector for returning intracellular conductivities (mS/cm)

Definition at line 1456 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::GetIntracellularConductivities ( c_vector< double, 3 > & intraConductivities ) const

3D version

Parameters:

intraConductivities

DIM-vector for returning intracellular conductivities (mS/cm)

Definition at line 1439 of file HeartConfig.cpp.

References mpParameters.

Referenced by ExtendedBidomainProblem< DIM >::CreateCardiacTissue(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell(), and GetConductivityHeterogeneities().

template<unsigned DIM>

void HeartConfig::GetIonicModelRegions	(	std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &	rDefinedRegions,
		std::vector< cp::ionic_model_selection_type > &	rIonicModels
	)			const `[inline]`

Regions where we need to use a different cell model (think infarction). cp::ionic_model_selection_type is generated automatically from the XML Schema.

The supplied vectors are first cleared, then filled in with the information from the parameters files. On return, both vectors will be the same length (one entry per region).

Parameters:

	rDefinedRegions	vector of axis-aligned box regions (one per cellular heterogeneity)
	rIonicModels	vector of models (one per cellular heterogeneity)

Todo:: When this is implemented, then we require an example in ChasteParametersFullFormat.xml

Definition at line 733 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), EXCEPTION, mpParameters, and NEVER_REACHED.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().

const char * HeartConfig::GetKSPPreconditioner ( ) const

Returns:: name of -pc_type from {"jacobi", "bjacobi", "hypre", "ml", "spai", "blockdiagonal", "ldufactorisation", "none"}

Definition at line 1647 of file HeartConfig.cpp.

References EXCEPTION, and mpParameters.

const char * HeartConfig::GetKSPSolver ( ) const

Returns:: name of -ksp_type from {"gmres", "cg", "symmlq"}

Definition at line 1628 of file HeartConfig.cpp.

References EXCEPTION, and mpParameters.

Referenced by SetKSPSolver().

bool HeartConfig::GetLoadMesh ( ) const

Returns:: true if a mesh file name is given and we are expecting to load a mesh from file

Definition at line 877 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), IsMeshProvided(), and mpParameters.

Referenced by ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell(), GetConductivityMedia(), and GetMeshName().

unsigned HeartConfig::GetMaxCheckpointsOnDisk ( ) const

Get number of checkpoints to keep on disk

Returns:: checkpointing timestep

Definition at line 1424 of file HeartConfig.cpp.

References GetCheckpointSimulation(), and mpParameters.

Referenced by CardiacSimulation::CreateResumeXmlFile().

void HeartConfig::GetMaxUpstrokeVelocityMaps ( std::vector< double > & rUpstrokeVelocityMaps ) const

Parameters:

rUpstrokeVelocityMaps

each entry is a request for a map with

a threshold (in mV, defaulted to -30 mV)

Definition at line 1805 of file HeartConfig.cpp.

References IsMaxUpstrokeVelocityMapRequested(), and mpParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

std::string HeartConfig::GetMeshName ( ) const

Returns:: path/basename of mesh files

Definition at line 955 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), GetLoadMesh(), and mpParameters.

Referenced by AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::AbstractCardiacTissue(), HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), and AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::ReadJunctionsFile().

DistributedTetrahedralMeshPartitionType::type HeartConfig::GetMeshPartitioning ( ) const

Returns:: the mesh partitioning method to use

Definition at line 1677 of file HeartConfig.cpp.

References EXCEPTION, and mpParameters.

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

double HeartConfig::GetMidLayerFraction ( )

Returns:: the fraction of endocardial layer

Definition at line 1262 of file HeartConfig.cpp.

References mMidFraction.

unsigned HeartConfig::GetMidLayerIndex ( )

Returns:: the index with which the midmyocardial layer is supplied (i.e., the order it comes in the XML file)

Definition at line 1277 of file HeartConfig.cpp.

References mIndexMid.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas().

void HeartConfig::GetNodalTimeTraceRequested ( std::vector< unsigned > & rRequestedNodes ) const

Parameters:

rRequestedNodes

vector of indices of requested nodes that will be filled in by this function

Definition at line 1861 of file HeartConfig.cpp.

References IsAnyNodalTimeTraceRequested(), and mpParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

double HeartConfig::GetOdeTimeStep ( ) const

Returns:: ODE time-step (ms)

Definition at line 1578 of file HeartConfig.cpp.

References mpParameters.

Referenced by CheckTimeSteps(), SetPdeTimeStep(), and SetPrintingTimeStep().

std::string HeartConfig::GetOutputDirectory ( ) const

Returns:: output directory path name

Definition at line 1364 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), and mpParameters.

Referenced by CardiacSimulation::CreateAndRun(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh(), and Write().

std::string HeartConfig::GetOutputFilenamePrefix ( ) const

Returns:: Prefix for files If set to "res" this produces [path]/res.h5 [path]/output/res_mesh.pts [path]/output/res_mesh.tri [path]/output/res_parameters.xml (a copy of this configuration at the end of the simulation) [path]/output/res_times.info [path]/output/res_V.dat

Definition at line 1371 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), and mpParameters.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), and Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::WriteCmguiScript().

bool HeartConfig::GetOutputUsingOriginalNodeOrdering ( )

Returns:: whether to write output HDF5 file using the original mesh permutation (in situations where a parallel partition may have permuted the node). The default is to use the new, not original permutation,

Definition at line 1402 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), and mpParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteVariablesOverTimeAtNodes().

void HeartConfig::GetOutputVariables ( std::vector< std::string > & rOutputVariables ) const

Returns:: the extra output variables from the xml file.

Parameters:

rOutputVariables

reference to std::vector to contain the output variables requested. Note: will be cleared before being filled.

Definition at line 1384 of file HeartConfig.cpp.

References GetOutputVariablesProvided(), and mpParameters.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineExtraVariablesWriterColumns(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep().

bool HeartConfig::GetOutputVariablesProvided ( ) const

Returns:: true iff any extra output variables have been requested

Definition at line 1378 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), and mpParameters.

Referenced by GetOutputVariables().

FileFinder HeartConfig::GetParametersFilePath ( )

Returns:: where the user parameters were read from. The result is undefined if no parameters file has been read.

Definition at line 534 of file HeartConfig.cpp.

References mParametersFilePath.

double HeartConfig::GetPdeTimeStep ( ) const

Returns:: PDE time-step (ms)

Definition at line 1584 of file HeartConfig.cpp.

References mpParameters.

Referenced by CheckTimeSteps(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForNode(), CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Initialise(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks(), SetOdeTimeStep(), SetPrintingTimeStep(), and CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve().

double HeartConfig::GetPrintingTimeStep ( ) const

Returns:: priting time-step (ms)

Definition at line 1590 of file HeartConfig.cpp.

References mpParameters.

Referenced by CheckTimeSteps(), AbstractCvodeCell::Compute(), SetOdeTimeStep(), and SetPdeTimeStep().

template<unsigned SPACE_DIM>

void HeartConfig::GetPseudoEcgElectrodePositions ( std::vector< ChastePoint< SPACE_DIM > > & rPseudoEcgElectrodePositions ) const [inline]

Parameters:

rPseudoEcgElectrodePositions

will be filled in with the positions of electrodes to use in calculating pseudo-ECGs (if any)

Definition at line 1891 of file HeartConfig.cpp.

References mpParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

double HeartConfig::GetPurkinjeCapacitance ( )

Returns:: the surface capacitance for Purkinje myocytes.

Definition at line 2939 of file HeartConfig.cpp.

References mpParameters.

double HeartConfig::GetPurkinjeConductivity ( )

Returns:: the default conductivity for Purkinje fibres.

Definition at line 2970 of file HeartConfig.cpp.

References mpParameters.

double HeartConfig::GetPurkinjeSurfaceAreaToVolumeRatio ( )

Returns:: the surface area to volume ratio for Purkinje fibres.

Definition at line 2955 of file HeartConfig.cpp.

References mpParameters.

Referenced by AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateJunction().

double HeartConfig::GetRelativeTolerance ( ) const

Returns:: KSP relative tolerance (or throw if we are using absolute)

Definition at line 1618 of file HeartConfig.cpp.

References EXCEPTION, GetUseRelativeTolerance(), and mpParameters.

Referenced by AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::DisplayRun(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

void HeartConfig::GetSheetDimensions ( c_vector< double, 2 > & sheetDimensions ) const

Parameters:

sheetDimensions

return vector for the (cuboid) mesh dimensions (cm)

Definition at line 900 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), EXCEPTION, GetCreateSheet(), GetSpaceDimension(), and mpParameters.

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

double HeartConfig::GetSimulationDuration ( ) const

Returns:: duration of the simulation (ms)

Definition at line 699 of file HeartConfig.cpp.

References IsSimulationDefined(), and mpParameters.

Referenced by CardiacSimulation::CreateAndRun(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks().

void HeartConfig::GetSlabDimensions ( c_vector< double, 3 > & slabDimensions ) const

Parameters:

slabDimensions

return vector for the (cuboid) mesh dimensions (cm)

Definition at line 884 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), EXCEPTION, GetCreateSlab(), GetSpaceDimension(), and mpParameters.

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

unsigned HeartConfig::GetSpaceDimension ( ) const

Returns:: space dimension 1, 2 or 3.

Definition at line 686 of file HeartConfig.cpp.

References IsSimulationDefined(), and mpParameters.

Referenced by CardiacSimulation::CreateResumeXmlFile(), GetFibreLength(), GetInterNodeSpace(), GetSheetDimensions(), GetSlabDimensions(), and UpdateParametersFromResumeSimulation().

template<unsigned DIM>

void HeartConfig::GetStimuli	(	std::vector< boost::shared_ptr< AbstractStimulusFunction > > &	rStimuliApplied,
		std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &	rStimulatedAreas
	)			const `[inline]`

Return a number of stimulated regions (Axis-aligned boxes)

Todo:

do we assume the vectors are initially empty? The returned std::vectors are all of the same length

Parameters:

	rStimuliApplied	rStimuliApplied[0] is stimulus for the first region
	rStimulatedAreas	rStimulatedAreas[0] is the first region to be stimulated

Todo:: There is no set method

Definition at line 972 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), EXCEPTION, mpParameters, and NEVER_REACHED.

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory().

double HeartConfig::GetSurfaceAreaToVolumeRatio ( ) const

Returns:: surface area to volume ratio chi a.k.a Am for PDE (1/cm)

Definition at line 1566 of file HeartConfig.cpp.

References mpParameters.

Referenced by BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), MonodomainCorrectionTermAssembler< ELEM_DIM, SPACE_DIM >::ComputeVectorTerm(), BidomainCorrectionTermAssembler< ELEM_DIM, SPACE_DIM >::ComputeVectorTerm(), AbstractCardiacCellInterface::GetIntracellularAreaStimulus(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and BidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

void HeartConfig::GetUpstrokeTimeMaps ( std::vector< double > & rUpstrokeTimeMaps ) const

Parameters:

rUpstrokeTimeMaps

each entry is a request for a map with

a threshold (in mV)

Definition at line 1777 of file HeartConfig.cpp.

References IsUpstrokeTimeMapsRequested(), and mpParameters.

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WritePostProcessingFiles().

bool HeartConfig::GetUseAbsoluteTolerance ( ) const

Returns:: true if we are using KSP absolute tolerance

Definition at line 1596 of file HeartConfig.cpp.

References mpParameters.

Referenced by AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::DisplayRun(), and GetAbsoluteTolerance().

bool HeartConfig::GetUseFixedNumberIterationsLinearSolver ( )

Returns:: whether to use a fixed number of iterations in the linear solver

Definition at line 2919 of file HeartConfig.cpp.

References mUseFixedNumberIterations.

bool HeartConfig::GetUseMassLumping ( )

Returns:: whether to use mass lumping in the FE solver or not.

Definition at line 2888 of file HeartConfig.cpp.

References mUseMassLumping.

bool HeartConfig::GetUseMassLumpingForPrecond ( )

Returns:: whether to use mass lumping in the construction of the preconditioner of the FE solver or not.

Definition at line 2898 of file HeartConfig.cpp.

References mUseMassLumpingForPrecond.

bool HeartConfig::GetUseReactionDiffusionOperatorSplitting ( )

Returns:: whether to use Strang operator splitting of the reaction and diffusion terms (see Set method documentation).

Definition at line 2908 of file HeartConfig.cpp.

References mUseReactionDiffusionOperatorSplitting.

bool HeartConfig::GetUseRelativeTolerance ( ) const

Returns:: true if we are using KSP relative tolerance

Definition at line 1612 of file HeartConfig.cpp.

References mpParameters.

Referenced by GetRelativeTolerance(), ExtendedBidomainProblem< DIM >::PreSolveChecks(), and BidomainProblem< DIM >::PreSolveChecks().

bool HeartConfig::GetUseStateVariableInterpolation ( ) const

Returns:: true if state variable interpolation is used

Definition at line 2780 of file HeartConfig.cpp.

References mpParameters.

Referenced by BidomainCorrectionTermAssembler< ELEM_DIM, SPACE_DIM >::BidomainCorrectionTermAssembler(), BidomainSolver< ELEMENT_DIM, SPACE_DIM >::BidomainSolver(), MonodomainProblem< ELEMENT_DIM, SPACE_DIM >::CreateCardiacTissue(), BidomainProblem< DIM >::CreateCardiacTissue(), and MonodomainCorrectionTermAssembler< ELEM_DIM, SPACE_DIM >::MonodomainCorrectionTermAssembler().

unsigned HeartConfig::GetVersionFromNamespace ( const std::string & rNamespaceUri )

Returns:: the Chaste version of a parameters file, given its namespace URI. The version will be encoded as major*1000+minor.

Parameters:

rNamespaceUri

the namespace URI of the parameters file

Definition at line 404 of file HeartConfig.cpp.

References EXCEPTION.

Referenced by ReadFile().

unsigned HeartConfig::GetVisualizerOutputPrecision ( )

Returns:: the number of digits to be output in the converted solution data files.

Definition at line 1964 of file HeartConfig.cpp.

References IsOutputVisualizerPresent(), and mpParameters.

bool HeartConfig::GetVisualizeWithCmgui ( ) const

Returns:: whether to convert the output from HDF5 to Cmgui readable format

Definition at line 1928 of file HeartConfig.cpp.

References IsOutputVisualizerPresent(), and mpParameters.

bool HeartConfig::GetVisualizeWithMeshalyzer ( ) const

Returns:: whether to convert the output from HDF5 to meshalyzer readable format

Definition at line 1916 of file HeartConfig.cpp.

References IsOutputVisualizerPresent(), and mpParameters.

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

bool HeartConfig::GetVisualizeWithParallelVtk ( ) const

Returns:: whether to convert the output from HDF5 to parallel Vtk readable format

Definition at line 1940 of file HeartConfig.cpp.

References IsOutputVisualizerPresent(), and mpParameters.

bool HeartConfig::GetVisualizeWithVtk ( ) const

Returns:: whether to convert the output from HDF5 to Vtk readable format

Definition at line 1952 of file HeartConfig.cpp.

References IsOutputVisualizerPresent(), and mpParameters.

bool HeartConfig::HasDrugDose ( ) const

Returns:: whether HeartConfig has a drug concentration and any IC50s set up

Definition at line 2805 of file HeartConfig.cpp.

References mpParameters.

Referenced by GetDrugDose(), and GetIc50Values().

bool HeartConfig::HasPurkinje ( )

Returns:: whether this simulation contains a Purkinje system.

Definition at line 2933 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), and mpParameters.

HeartConfig * HeartConfig::Instance ( ) [static]

Call this method to access the global parameters holder.

Returns:: a single instance of the class

Definition at line 206 of file HeartConfig.cpp.

References mpInstance.

bool HeartConfig::IsAdaptivityParametersPresent ( ) const

Adaptivity is now deprecated. This method now gives a warning before returning true.

Returns:: true if there is an adaptivity section

Definition at line 1696 of file HeartConfig.cpp.

References mpParameters.

bool HeartConfig::IsAnyNodalTimeTraceRequested ( ) const

Returns:: true if any nodal time trace is requested

Definition at line 1849 of file HeartConfig.cpp.

References IsPostProcessingSectionPresent(), and mpParameters.

Referenced by GetNodalTimeTraceRequested(), and IsPostProcessingRequested().

bool HeartConfig::IsApdMapsRequested ( ) const

Returns:: true if APD maps have been requested

Definition at line 1736 of file HeartConfig.cpp.

References IsPostProcessingSectionPresent(), and mpParameters.

Referenced by GetApdMaps(), and IsPostProcessingRequested().

bool HeartConfig::IsConductionVelocityMapsRequested ( ) const

Returns:: true if conduction velocity maps have been requested

Definition at line 1821 of file HeartConfig.cpp.

References IsPostProcessingSectionPresent(), and mpParameters.

Referenced by GetConductionVelocityMaps(), and IsPostProcessingRequested().

bool HeartConfig::IsElectrodesPresent ( ) const

Returns:: true if there is an electrodes section

Definition at line 1977 of file HeartConfig.cpp.

References mpParameters.

Referenced by GetElectrodeParameters(), HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory(), and SetElectrodeParameters().

bool HeartConfig::IsMaxUpstrokeVelocityMapRequested ( ) const

Returns:: true maximum upstroke velocity maps have been requested

Definition at line 1793 of file HeartConfig.cpp.

References IsPostProcessingSectionPresent(), and mpParameters.

Referenced by GetMaxUpstrokeVelocityMaps(), and IsPostProcessingRequested().

bool HeartConfig::IsMeshProvided ( ) const

Returns:: true if a mesh file name is given. (Otherwise it's assumed that this is a cuboid simulation.)

Definition at line 838 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), and mpParameters.

Referenced by ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell(), GetCreateFibre(), GetCreateMesh(), GetCreateSheet(), GetCreateSlab(), and GetLoadMesh().

bool HeartConfig::IsOutputVisualizerPresent ( ) const

Returns:: whether there is an OutputVisualizer element present.

Definition at line 1909 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), and mpParameters.

Referenced by GetVisualizerOutputPrecision(), GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithParallelVtk(), and GetVisualizeWithVtk().

bool HeartConfig::IsPostProcessingRequested ( ) const

Returns:: true if any post-processing information has been requested

Definition at line 1720 of file HeartConfig.cpp.

References IsAnyNodalTimeTraceRequested(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), IsMaxUpstrokeVelocityMapRequested(), IsPostProcessingSectionPresent(), IsPseudoEcgCalculationRequested(), and IsUpstrokeTimeMapsRequested().

bool HeartConfig::IsPostProcessingSectionPresent ( ) const

Returns:: true if there is a post-processing section

Definition at line 1710 of file HeartConfig.cpp.

References mpParameters.

Referenced by IsAnyNodalTimeTraceRequested(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), IsMaxUpstrokeVelocityMapRequested(), IsPostProcessingRequested(), IsPseudoEcgCalculationRequested(), and IsUpstrokeTimeMapsRequested().

bool HeartConfig::IsPseudoEcgCalculationRequested ( ) const

Returns:: true iff pseudo-ECG calculation has been requested

Definition at line 1878 of file HeartConfig.cpp.

References IsPostProcessingSectionPresent(), and mpParameters.

Referenced by IsPostProcessingRequested().

bool HeartConfig::IsSimulationDefined ( ) const

Returns whether the configuration file defines a new simulation.

Returns:: is a new simulation?

Definition at line 659 of file HeartConfig.cpp.

References mpParameters.

Referenced by CheckResumeSimulationIsDefined(), GetCheckpointSimulation(), GetDomain(), GetSimulationDuration(), GetSpaceDimension(), and SetParametersFile().

bool HeartConfig::IsSimulationResumed ( ) const

Returns whether the configuration file resumes an archived simulation.

Returns:: is a resumed simulation?

Definition at line 664 of file HeartConfig.cpp.

References mpParameters.

Referenced by CheckSimulationIsDefined().

bool HeartConfig::IsUpstrokeTimeMapsRequested ( ) const

Returns:: true if upstroke time maps have been requested

Definition at line 1766 of file HeartConfig.cpp.

References IsPostProcessingSectionPresent(), and mpParameters.

Referenced by GetUpstrokeTimeMaps(), and IsPostProcessingRequested().

template<class Archive >

void HeartConfig::load	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Un-archive the object.

Parameters:

	archive
	version

Definition at line 115 of file HeartConfig.hpp.

References LoadFromCheckpoint().

void HeartConfig::LoadFromCheckpoint ( ) [private]

This method is called by load() to do the actual work - we don't need the Boost archives since we load from our serialised XML.

Definition at line 315 of file HeartConfig.cpp.

References RelativeTo::AbsoluteOrCwd, CheckTimeSteps(), ArchiveLocationInfo::GetArchiveDirectory(), Instance(), MergeDefaults(), mParametersFilePath, mpParameters, ReadFile(), SetCheckpointSimulation(), FileFinder::SetPath(), and UpdateParametersFromResumeSimulation().

Referenced by load().

boost::shared_ptr< cp::chaste_parameters_type > HeartConfig::ReadFile ( const std::string & rFileName )

Utility method to parse an XML parameters file.

Parameters:

rFileName

Name of XML file

Returns:: a pointer to the parameters in a convenience class created by CodeSynthesis XSD

Definition at line 449 of file HeartConfig.cpp.

References XmlTransforms::CheckForIluPreconditioner(), XmlTools::EscapeSpaces(), EXCEPTION, GetVersionFromNamespace(), XmlTransforms::MoveConductivityHeterogeneities(), mpParameters, mSchemaLocations, mUseFixedSchemaLocation, XmlTools::ReadXmlFile(), XmlTransforms::SetDefaultVisualizer(), XmlTools::SetNamespace(), XmlTransforms::TransformArchiveDirectory(), and XmlTransforms::TransformIonicModelDefinitions().

Referenced by LoadFromCheckpoint(), and SetParametersFile().

void HeartConfig::Reset ( ) [static]

Throw away the current instance by resetting auto_ptr mpInstance to NULL. "New" another mpInstance

Definition at line 651 of file HeartConfig.cpp.

References mpInstance.

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

const std::set< unsigned > & HeartConfig::rGetBathIdentifiers ( )

Gets region identifiers that have to be considered as bath.

Returns:: set of identifiers

Definition at line 1561 of file HeartConfig.cpp.

References mBathIdentifiers.

Referenced by BidomainProblem< DIM >::AnalyseMeshForBath(), and HeartRegionCode::GetValidBathId().

const std::set< unsigned > & HeartConfig::rGetTissueIdentifiers ( )

Gets region identifiers that have to be considered as cardiac tissue.

Returns:: set of identifiers

Definition at line 1556 of file HeartConfig.cpp.

References mTissueIdentifiers.

Referenced by HeartRegionCode::GetValidTissueId().

template<class Archive >

void HeartConfig::save	(	Archive &	archive,
		const unsigned int	version
	)			const `[inline, private]`

Archive the object.

Parameters:

	archive
	version

Definition at line 98 of file HeartConfig.hpp.

References PetscTools::AmMaster(), PetscTools::Barrier(), and mpInstance.

void HeartConfig::SetApdMaps ( const std::vector< std::pair< double, double > > & rApdMaps )

Set the parameters of the apd map requested

Parameters:

rApdMaps

each entry is a request for a map with

a percentage in the range [1, 100) (ranges are not checked by this method, but during the calculation)
a threshold (in mV)

Definition at line 2550 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpParameters.

void HeartConfig::SetBathConductivity ( double bathConductivity )

Set bath default conductivity

Parameters:

bathConductivity

default conductivity for perfusing bath (mS/cm)

Todo:: Is this used anywhere?

Definition at line 2300 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetBathMultipleConductivities ( std::map< unsigned, double > bathConductivities )

Set multiple bath conductivities based on element region label (mS/cm)

Parameters:

bathConductivities

map between different bath region identifier and their conductivity (if different from default)

Todo:: : This implementation is temporary until we incorporate the bath heterogeneities to the XML schema

Definition at line 2306 of file HeartConfig.cpp.

References mBathConductivities.

void HeartConfig::SetCapacitance ( double capacitance )

Set surface capacitance Cm (for PDE)

Parameters:

capacitance

(uF/cm^2)

Definition at line 2345 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetCheckpointSimulation	(	bool	checkpointSimulation,
		double	checkpointTimestep = `-1.0`,
		unsigned	maxCheckpointsOnDisk = `UINT_MAX`
	)

Set whether the simulation should be checkpointed or not.

Parameters:

	checkpointSimulation	whether to do checkpointing
	checkpointTimestep	checkpointing timestep
	maxCheckpointsOnDisk	maximum number of checkpoint archives to keep on disk

Definition at line 2216 of file HeartConfig.cpp.

References CheckTimeSteps(), and mpParameters.

Referenced by LoadFromCheckpoint(), and UpdateParametersFromResumeSimulation().

void HeartConfig::SetConductionVelocityMaps ( std::vector< unsigned > & rConductionVelocityMaps )

Set the parameters of the conduction velocity map requested

Parameters:

rConductionVelocityMaps

is a list of origin node indices. One map is created for each origin node.

Definition at line 2607 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpParameters.

void HeartConfig::SetConductivityHeterogeneities	(	std::vector< ChasteCuboid< 3 > > &	rConductivityAreas,
		std::vector< c_vector< double, 3 > > &	rIntraConductivities,
		std::vector< c_vector< double, 3 > > &	rExtraConductivities
	)

Set a number of heterogeneous regions (Axis-aligned boxes) It is assumed that the std::vectors are all of the same length

Parameters:

	rConductivityAreas	conductivityAreas[0] is the first region
	rIntraConductivities	intraConductivities[0] is conductivity vector for the first region
	rExtraConductivities	extraConductivities[0] is conductivity vector for the first region

Definition at line 2084 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetConductivityHeterogeneitiesEllipsoid	(	std::vector< ChasteEllipsoid< 3 > > &	conductivityAreas,
		std::vector< c_vector< double, 3 > > &	intraConductivities,
		std::vector< c_vector< double, 3 > > &	extraConductivities
	)

Set a number of heterogeneous regions (Axis-aligned ellipsoids) It is assumed that the std::vectors are all of the same length

Parameters:

	conductivityAreas	conductivityAreas[0] is the first region
	intraConductivities	intraConductivities[0] is conductivity vector for the first region
	extraConductivities	extraConductivities[0] is conductivity vector for the first region

Definition at line 2132 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetDefaultIonicModel ( const cp::ionic_models_available_type & rIonicModel )

Set the configuration to place the given cardiac cell models at all mesh nodes (unless otherwise specified by SetIonicModelRegions). cp::ionic_models_available_type is generated automatically from the XML Schema.

Parameters:

rIonicModel

type of model

Definition at line 2001 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetDefaultSchemaLocations ( ) [private]

Set default schema locations in the Chaste source tree.

Definition at line 387 of file HeartConfig.cpp.

References ChasteBuildInfo::GetRootDir(), and mSchemaLocations.

Referenced by HeartConfig().

void HeartConfig::SetDomain ( const cp::domain_type & rDomain )

Set the configuration to run mono or bidomain cp::domain_type is an xsd convenience class type

Parameters:

rDomain

type of simulation bi- mono-domain

Definition at line 1996 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetDrugDose ( double drugDose )

Parameters:

drugDose

The dose of the drug to use (should be in units consistent with the IC50s).

Definition at line 2816 of file HeartConfig.cpp.

References mpParameters.

Referenced by SetIc50Value().

void HeartConfig::SetElectrodeParameters	(	bool	groundSecondElectrode,
		unsigned	index,
		double	magnitude,
		double	startTime,
		double	duration
	)

Setup electrode parameters.

Parameters:

	groundSecondElectrode	Whether to ground the second electrode (see class documentation)
	index	The value i when applying the electrodes to x_i=a and x_i=b (a<b)
	magnitude	Magnitude of the stimulus
	startTime	Switch on time
	duration	Duration of the stimulus.

Definition at line 2708 of file HeartConfig.cpp.

References IsElectrodesPresent(), and mpParameters.

void HeartConfig::SetExtracellularConductivities ( const c_vector< double, 1 > & rExtraConductivities )

1D version

Parameters:

rExtraConductivities

DIM-vector of extracellular conductivities (mS/cm)

Definition at line 2291 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetExtracellularConductivities ( const c_vector< double, 2 > & rExtraConductivities )

2D version

Parameters:

rExtraConductivities

DIM-vector of extracellular conductivities (mS/cm)

Definition at line 2281 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetExtracellularConductivities ( const c_vector< double, 3 > & rExtraConductivities )

3D version

Parameters:

rExtraConductivities

DIM-vector of extracellular conductivities (mS/cm)

Definition at line 2270 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetFibreLength	(	double	x,
		double	inter_node_space
	)

Set dimensions of simulation for use with a cuboid mesh generated on the fly. 1-D.

Parameters:

	x	length in 1st dimension (cm)
	inter_node_space	Spacing in cartesian direction (cm).

Definition at line 2033 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetFixedSchemaLocations ( const SchemaLocationsMap & rSchemaLocations )

Set the schema files to use. Also calls SetUseFixedSchemaLocation(true).

Parameters:

rSchemaLocations

map from namespace URI to schema URI

Definition at line 438 of file HeartConfig.cpp.

References mSchemaLocations, and SetUseFixedSchemaLocation().

void HeartConfig::SetIc50Value	(	const std::string &	rCurrentName,
		double	ic50,
		double	hill = `1.0`
	)

Add a new conductance block model for a particular channel.

Parameters:

	rCurrentName	The Oxford metadata name of the current (e.g. membrane_fast_sodium_current)
	ic50	The IC50 value for this channel (should be in consistent units with drug dose)
	hill	The hill coefficient to use (usually default to 1)

Definition at line 2849 of file HeartConfig.cpp.

References mpParameters, and SetDrugDose().

void HeartConfig::SetIntracellularConductivities ( const c_vector< double, 1 > & rIntraConductivities )

1D version

Parameters:

rIntraConductivities

DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2261 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetIntracellularConductivities ( const c_vector< double, 2 > & rIntraConductivities )

2D version

Parameters:

rIntraConductivities

DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2251 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetIntracellularConductivities ( const c_vector< double, 3 > & rIntraConductivities )

3D version

Parameters:

rIntraConductivities

DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2240 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetIonicModelRegions	(	std::vector< ChasteCuboid< 3 > > &	rDefinedRegions,
		std::vector< cp::ionic_model_selection_type > &	rIonicModels
	)			const

Set the regions where we need to use a different cell model (think infarction). Unlike the get method, this is currently only supported in 3d. cp::ionic_model_selection_type is generated automatically from the XML Schema.

The input standard vectors must be of the same length (one entry per region) otherwise the method throws.

Parameters:

	rDefinedRegions	vector of axis-aligned box regions (one per cellular heterogeneity)
	rIonicModels	vector of models (one per cellular heterogeneity)

Definition at line 2057 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetKSPPreconditioner ( const char * kspPreconditioner )

Set the type of preconditioner as with the flag "-pc_type"

Parameters:

kspPreconditioner

a string from {"jacobi", "bjacobi", "hypre", "ml", "spai", "blockdiagonal", "ldufactorisation", "none"}

Definition at line 2470 of file HeartConfig.cpp.

References EXCEPTION, and mpParameters.

void HeartConfig::SetKSPSolver	(	const char *	kspSolver,
		bool	warnOfChange = `false`
	)

Set the type of KSP solver as with the flag "-ksp_type"

Parameters:

	kspSolver	a string from {"gmres", "cg", "symmlq"}
	warnOfChange	Warn if this set is changing the current value because the calling code may be (silently) overwriting a user setting

Definition at line 2437 of file HeartConfig.cpp.

References EXCEPTION, GetKSPSolver(), and mpParameters.

Referenced by AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem(), and AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::FinaliseLinearSystem().

void HeartConfig::SetMaxUpstrokeVelocityMaps ( std::vector< double > & rMaxUpstrokeVelocityMaps )

Set the parameters of the maximal upstroke velocity map requested

Parameters:

rMaxUpstrokeVelocityMaps

is the list of thresholds (mV) with respect to which the upstroke velocity maps are calculated. The threshold is used for determining when an action potential occurs.

Definition at line 2586 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpParameters.

void HeartConfig::SetMeshFileName	(	std::string	meshPrefix,
		cp::media_type	fibreDefinition = `cp::media_type::NoFibreOrientation`
	)

Sets the name of a mesh to be read from disk for this simulation

Parameters:

	meshPrefix	path and basename of a set of mesh files (.nodes .ele etc) in triangle/tetget format
	fibreDefinition	if set (Orthotropic/Axisymmetric) then a (.ortho/.axi) file should also be read

Todo:: There is no Get method

Definition at line 2045 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetMeshPartitioning ( const char * meshPartioningMethod )

Set the type of mesh partitioning method

Parameters:

meshPartioningMethod

a string from {"dumb", "metis", "parmetis", "petsc"}

Definition at line 2522 of file HeartConfig.cpp.

References EXCEPTION, and mpParameters.

void HeartConfig::SetOdePdeAndPrintingTimeSteps	(	double	odeTimeStep,
		double	pdeTimeStep,
		double	printingTimeStep
	)

Set the configuration to use ode, pde and printing times of given values

The ODE step is used by explicit solver schemes such as ForwardEuler to evolve the ODE system at each node in the mesh. AbstractCardiacCells set their internal timestep to this value in their constructors. (AbstractCvodeCells will ignore this setting and use an adaptive time step scheme between PDE or sampling times.)

The PDE time step dictates how long a PDE solve should run before re-evaluating the ODE and cell model states and recalculating current contributions. The ODE time step should be a subdivision of this PDE timestep.

The sampling timestep should be a multiple of the PDE timestep, and dictates how frequently the output to file of results should occur.

This method calls CheckTimeSteps() to ensure the above compatibility conditions are met.

Parameters:

	odeTimeStep	ode value to use
	pdeTimeStep	pde value to use
	printingTimeStep	printing value to use

Definition at line 2353 of file HeartConfig.cpp.

References CheckTimeSteps(), and mpParameters.

Referenced by AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), SetOdeTimeStep(), SetPdeTimeStep(), and SetPrintingTimeStep().

void HeartConfig::SetOdeTimeStep ( double odeTimeStep )

Set the configuration to use ode time step of given value, for explicit solver schemes such as ForwardEuler. AbstractCardiacCells set their internal timestep to this in their constructors.

AbstractCvodeCells will ignore this setting and use an adaptive time step scheme between PDE or sampling times.

Calls CheckTimeSteps via SetOdePdeAndPrintingTimeSteps

Parameters:

odeTimeStep

the value to use

Definition at line 2361 of file HeartConfig.cpp.

References GetPdeTimeStep(), GetPrintingTimeStep(), and SetOdePdeAndPrintingTimeSteps().

void HeartConfig::SetOutputDirectory ( const std::string & rOutputDirectory )

Parameters:

rOutputDirectory

Full path to output directory (will be created if necessary)

Definition at line 2180 of file HeartConfig.cpp.

References mpParameters.

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::CardiacElectroMechanicsProblem(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), and VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().

void HeartConfig::SetOutputFilenamePrefix ( const std::string & rOutputFilenamePrefix )

Parameters:

rOutputFilenamePrefix

Prefix for files If set to "res" this will produce [path]/res.h5 [path]/output/res_mesh.pts [path]/output/res_mesh.tri [path]/output/res_parameters.xml (a copy of this configuration at the end of the simulation) [path]/output/res_times.info [path]/output/res_V.dat

Definition at line 2185 of file HeartConfig.cpp.

References mpParameters.

Referenced by CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::CardiacElectroMechanicsProblem(), and AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge().

void HeartConfig::SetOutputUsingOriginalNodeOrdering ( bool useOriginal )

This method may set the output HDF5 file to be written using the original mesh permutation (in situations where a parallel partition may have permuted the node). The default is to use the new, not original permutation, i.e. useOriginal=false

Parameters:

useOriginal

whether to use the original permutation

Definition at line 2210 of file HeartConfig.cpp.

References mpParameters.

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

void HeartConfig::SetOutputVariables ( const std::vector< std::string > & rOutputVariables )

Parameters:

rOutputVariables

a vector of std::strings of the names of each variable that should be outputted at each time step.

USING THIS METHOD WILL OVERRIDE THE ANY OUTPUT VARIABLES SET IN THE XML FILE

Definition at line 2190 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetParametersFile ( const std::string & rFileName )

mpParameters is set to a new context associated with a parameters file

Parameters:

rFileName

The name of the parameters file

Definition at line 522 of file HeartConfig.cpp.

References RelativeTo::AbsoluteOrCwd, CheckTimeSteps(), CreateDefaultParameters(), IsSimulationDefined(), MergeDefaults(), mParametersFilePath, mpParameters, ReadFile(), and FileFinder::SetPath().

Referenced by CardiacSimulation::ReadParametersFromFile().

void HeartConfig::SetPdeTimeStep ( double pdeTimeStep )

Set the configuration to use pde time of given value Calls CheckTimeSteps via SetOdePdeAndPrintingTimeSteps

Parameters:

pdeTimeStep

the value to use

Definition at line 2366 of file HeartConfig.cpp.

References GetOdeTimeStep(), GetPrintingTimeStep(), and SetOdePdeAndPrintingTimeSteps().

void HeartConfig::SetPrintingTimeStep ( double printingTimeStep )

Set the configuration to use printing time of given value. The printing time step is how long between timesteps that are written to the HDF5 file.

Calls CheckTimeSteps via SetOdePdeAndPrintingTimeSteps

Parameters:

printingTimeStep

the value to use

Definition at line 2371 of file HeartConfig.cpp.

References GetOdeTimeStep(), GetPdeTimeStep(), and SetOdePdeAndPrintingTimeSteps().

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

template<unsigned SPACE_DIM>

void HeartConfig::SetPseudoEcgElectrodePositions ( const std::vector< ChastePoint< SPACE_DIM > > & rPseudoEcgElectrodePositions ) [inline]

Set the parameters for pseudo-ECG calculation.

Parameters:

rPseudoEcgElectrodePositions

should contan the positions of electrodes to use in calculating pseudo-ECGs (if any)

Definition at line 2640 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpParameters.

void HeartConfig::SetPurkinjeCapacitance ( double capacitance )

Set the surface capacitance for Purkinje myocytes.

Parameters:

capacitance

Purkinje capacitance (Cm) (units uF/cm^2)

Definition at line 2947 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetPurkinjeConductivity ( double conductivity )

Set the default conductivity for Purkinje fibres.

Parameters:

conductivity

Purkinje conductivity (units mS/cm)

Definition at line 2978 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetPurkinjeSurfaceAreaToVolumeRatio ( double ratio )

Set the surface area to volume ratio for Purkinje fibres.

Parameters:

ratio

the ratio (Am) (units 1/cm)

Definition at line 2963 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetRequestedNodalTimeTraces ( std::vector< unsigned > & requestedNodes )

Sets some requested nodes for printing of their variables over time in separate files. The node numbering is referred to the original numbering (unpermuted).

Parameters:

requestedNodes

the node indices (in the unpermuted mesh) where we want the plot over time

Definition at line 2623 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpParameters.

void HeartConfig::SetSheetDimensions	(	double	x,
		double	y,
		double	inter_node_space
	)

Set dimensions of simulation for use with a cuboid mesh generated on the fly. 2-D.

Parameters:

	x	length in 1st dimension (cm)
	y	length in 2nd dimension (cm)
	inter_node_space	Spacing in cartesian direction (cm). Diagonals will be longer.

Definition at line 2021 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetSimulationDuration ( double simulationDuration )

Set the configuration simulation end time.

Parameters:

simulationDuration

end time for the next call to Solve() (in ms).

Definition at line 1990 of file HeartConfig.cpp.

References mpParameters.

Referenced by AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), CardiacSimulation::CreateAndRun(), and UpdateParametersFromResumeSimulation().

void HeartConfig::SetSlabDimensions	(	double	x,
		double	y,
		double	z,
		double	inter_node_space
	)

Set dimensions of simulation for use with a cuboid mesh generated on the fly. 3-D.

Parameters:

	x	length in 1st dimension (cm)
	y	length in 2nd dimension (cm)
	z	length in 3rd dimension (cm)
	inter_node_space	Spacing in cartesian direction (cm). Diagonals will be longer.

Definition at line 2009 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetSpaceDimension ( unsigned spaceDimension )

Set the configuration dimension

Parameters:

spaceDimension

1, 2 or 3.

Definition at line 1985 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetSurfaceAreaToVolumeRatio ( double ratio )

Sets which region identifiers have to be considered cardiac tissue.

param tissueIds set of identifiers

Todo:: #1703 Think about adding this convenience method either copying the existing BathIds, resetting them out of the way, or making them empty...

Set surface area to volume ratio Am (for PDE)

Parameters:

ratio

(1/cm)

Definition at line 2339 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetTissueAndBathIdentifiers	(	const std::set< unsigned > &	tissueIds,
		const std::set< unsigned > &	bathIds
	)

Sets which region identifiers have to be considered cardiac tissue and bath.

Parameters:

	tissueIds	set of identifiers
	bathIds	set of identifiers

Definition at line 2318 of file HeartConfig.cpp.

References EXCEPTION, mBathIdentifiers, and mTissueIdentifiers.

void HeartConfig::SetUpstrokeTimeMaps ( std::vector< double > & rUpstrokeTimeMaps )

Set the parameters of the upstroke time map requested

Parameters:

rUpstrokeTimeMaps

is the list of thresholds (mV) with respect to which the upstroke time maps are calculated. The threshold is used for determining when an action potential occurs.

Definition at line 2568 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpParameters.

void HeartConfig::SetUseAbsoluteTolerance ( double absoluteTolerance )

Set the configuration to use KSP absolute tolerance of given value

Parameters:

absoluteTolerance

the value to use

Definition at line 2429 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetUseFixedNumberIterationsLinearSolver	(	bool	useFixedNumberIterations = `true`,
		unsigned	evaluateNumItsEveryNSolves = `UINT_MAX`
	)

Set the use of fixed number of iterations in the linear solver

Parameters:

	useFixedNumberIterations	Whether to use a fixed number of iterations for the linear solver
	evaluateNumItsEveryNSolves	Perform a solve with convergence-based stop criteria every n solves to decide how many iterations perform for the next n-1 solves. Default is perfoming a single evaluation at the beginning of the simulation.

Definition at line 2913 of file HeartConfig.cpp.

References mEvaluateNumItsEveryNSolves, and mUseFixedNumberIterations.

void HeartConfig::SetUseFixedSchemaLocation ( bool useFixedSchemaLocation )

Parameters:

useFixedSchemaLocation

whether to read the schema location from the XML file (false) or use the schema located at heart/src/io/ChasteParameters.xsd in the Chaste source tree (or specified with SetFixedSchemaLocations()) (true).

Definition at line 444 of file HeartConfig.cpp.

References mUseFixedSchemaLocation.

Referenced by CardiacSimulation::ReadParametersFromFile(), and SetFixedSchemaLocations().

void HeartConfig::SetUseMassLumping ( bool useMassLumping = true )

Set the use of mass lumping in the FE solver.

Parameters:

useMassLumping

Whether to use it

Definition at line 2883 of file HeartConfig.cpp.

References mUseMassLumping.

Referenced by MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

void HeartConfig::SetUseMassLumpingForPrecond ( bool useMassLumping = true )

Set the use of mass lumping in the construction of the preconditioner in the FE solver.

Parameters:

useMassLumping

Whether to use it

Definition at line 2893 of file HeartConfig.cpp.

References mUseMassLumpingForPrecond.

void HeartConfig::SetUseReactionDiffusionOperatorSplitting ( bool useOperatorSplitting = true )

Use Strang operator splitting of the diffusion (conductivity) term and the reaction (ionic current) term, instead of solving the full reaction-diffusion PDE. This does NOT refer to operator splitting of the two PDEs in the bidomain equations. For details see for example Sundnes et al "Computing the Electrical Activity of the Heart".

Parameters:

useOperatorSplitting

Whether to use operator splitting (defaults to true).

Definition at line 2903 of file HeartConfig.cpp.

References mUseReactionDiffusionOperatorSplitting.

void HeartConfig::SetUseRelativeTolerance ( double relativeTolerance )

Set the configuration to use KSP relative tolerance of given value

Parameters:

relativeTolerance

the value to use

Definition at line 2421 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetUseStateVariableInterpolation ( bool useStateVariableInterpolation = true )

Set the use of State Variable Interpolation in the computation of ionic currents. See documentation page ChasteGuides/StateVariableInterpolation.

Parameters:

useStateVariableInterpolation

Whether to use it.

Definition at line 2791 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetVisualizerOutputPrecision ( unsigned numberOfDigits )

Set the precision with which to output textual visualizer formats (e.g. meshalyzer). Use '0' for the implementation-defined default precision.

Parameters:

numberOfDigits

how many digits of precision to use

Definition at line 2700 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpParameters.

void HeartConfig::SetVisualizeWithCmgui ( bool useCmgui = true )

Set whether to convert the output from HDF5 to Cmgui readable format

Parameters:

useCmgui

Definition at line 2676 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpParameters.

Referenced by UpdateParametersFromResumeSimulation().

void HeartConfig::SetVisualizeWithMeshalyzer ( bool useMeshalyzer = true )

Set whether to convert the output from HDF5 to meshalyzer readable format

Parameters:

useMeshalyzer

Definition at line 2668 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpParameters.

Referenced by UpdateParametersFromResumeSimulation().

void HeartConfig::SetVisualizeWithParallelVtk ( bool useParallelVtk = true )

Set whether to convert the output from HDF5 to parallel Vtk readable format

Parameters:

useParallelVtk

Definition at line 2692 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpParameters.

Referenced by UpdateParametersFromResumeSimulation().

void HeartConfig::SetVisualizeWithVtk ( bool useVtk = true )

Set whether to convert the output from HDF5 to Vtk readable format

Parameters:

useVtk

Definition at line 2684 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpParameters.

Referenced by UpdateParametersFromResumeSimulation().

void HeartConfig::UpdateParametersFromResumeSimulation ( boost::shared_ptr< cp::chaste_parameters_type > pResumeParameters ) [private]

When loading a simulation from archive, some parameters can get overridden by the content of the ResumeSimulation element. This method does that.

Parameters:

pResumeParameters

the parameters containing the ResumeSimulation element.

Definition at line 539 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), EXCEPTION, GetDomain(), GetSpaceDimension(), Instance(), mpParameters, SetCheckpointSimulation(), SetSimulationDuration(), SetVisualizeWithCmgui(), SetVisualizeWithMeshalyzer(), SetVisualizeWithParallelVtk(), and SetVisualizeWithVtk().

Referenced by LoadFromCheckpoint().

void HeartConfig::Write	(	bool	useArchiveLocationInfo = `false`,
		std::string	subfolderName = `"output"`
	)

Write out the complete configuration set (ChasteParameters and ChasteDefaults) as an XML file. Note that the location of ChasteParameters.xsd (schema definition) will be hard-coded in the XML file.

Parameters:

	useArchiveLocationInfo	if false, then use self's GetOutputDirectory() and open in named subfolder if true, then use ArchiveLocationInfo
	subfolderName	-- where to store with respect to GetOutputDirectory()

Note:: This method is collective if useArchiveLocationInfo is false

Definition at line 252 of file HeartConfig.cpp.

References PetscTools::AmMaster(), CopySchema(), EXCEPTION, ArchiveLocationInfo::GetArchiveDirectory(), GetOutputDirectory(), OutputFileHandler::GetOutputDirectoryFullPath(), and mpParameters.

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

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Definition at line 90 of file HeartConfig.hpp.

Member Data Documentation

std::map<unsigned, double> HeartConfig::mBathConductivities [private]

Map defining bath conductivity for multiple bath regions

Definition at line 1299 of file HeartConfig.hpp.

Referenced by GetBathConductivity(), and SetBathMultipleConductivities().

std::set<unsigned> HeartConfig::mBathIdentifiers [private]

Mesh region identifiers to be considered as Bath

Definition at line 1309 of file HeartConfig.hpp.

Referenced by HeartConfig(), rGetBathIdentifiers(), and SetTissueAndBathIdentifiers().

double HeartConfig::mEndoFraction [private]

Fraction of endocardial layer

Definition at line 1253 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), GetEndoLayerFraction(), and HeartConfig().

double HeartConfig::mEpiFraction [private]

Fraction of epicardial layer

Definition at line 1248 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), GetEpiLayerFraction(), and HeartConfig().

unsigned HeartConfig::mEvaluateNumItsEveryNSolves [private]

Perform a solve with convergence-based stop criteria every n solves to decide how many iterations perform for the next n-1 solves. Default is performing a single evaluation at the beginning of the simulation.

Definition at line 1321 of file HeartConfig.hpp.

Referenced by GetEvaluateNumItsEveryNSolves(), and SetUseFixedNumberIterationsLinearSolver().

unsigned HeartConfig::mIndexEndo [private]

Order index in which the endocardial heterogeneities are supplied

Definition at line 1273 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), GetEndoLayerIndex(), and HeartConfig().

unsigned HeartConfig::mIndexEpi [private]

Order index in which the epicardial heterogeneities are supplied

Definition at line 1268 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), GetEpiLayerIndex(), and HeartConfig().

unsigned HeartConfig::mIndexMid [private]

Order index in which the midmyocardial heterogeneities are supplied

Definition at line 1263 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), GetMidLayerIndex(), and HeartConfig().

double HeartConfig::mMidFraction [private]

Fraction of midmyocardial layer

Definition at line 1258 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), GetMidLayerFraction(), and HeartConfig().

FileFinder HeartConfig::mParametersFilePath [private]

Where the user parameters were read from.

Definition at line 1237 of file HeartConfig.hpp.

Referenced by GetParametersFilePath(), LoadFromCheckpoint(), and SetParametersFile().

std::auto_ptr< HeartConfig > HeartConfig::mpInstance [static, private]

The single instance of the class

Definition at line 1232 of file HeartConfig.hpp.

Referenced by HeartConfig(), Instance(), Reset(), and save().

boost::shared_ptr<cp::chaste_parameters_type> HeartConfig::mpParameters [private]

Pointer to parameters read from the user's input XML file

Definition at line 1229 of file HeartConfig.hpp.

Referenced by EnsureOutputVisualizerExists(), EnsurePostProcessingSectionPresent(), GetAbsoluteTolerance(), GetApdMaps(), GetArchivedSimulationDir(), GetBathConductivity(), GetCapacitance(), GetCellHeterogeneities(), GetCheckpointSimulation(), GetCheckpointTimestep(), GetConductionVelocityMaps(), GetConductivityHeterogeneities(), GetConductivityHeterogeneitiesProvided(), GetConductivityMedia(), GetCreateFibre(), GetCreateMesh(), GetCreateSheet(), GetCreateSlab(), GetDefaultIonicModel(), GetDomain(), GetDrugDose(), GetElectrodeParameters(), GetExtracellularConductivities(), GetFibreLength(), GetIc50Values(), GetInterNodeSpace(), GetIntracellularConductivities(), GetIonicModelRegions(), GetKSPPreconditioner(), GetKSPSolver(), GetLoadMesh(), GetMaxCheckpointsOnDisk(), GetMaxUpstrokeVelocityMaps(), GetMeshName(), GetMeshPartitioning(), GetNodalTimeTraceRequested(), GetOdeTimeStep(), GetOutputDirectory(), GetOutputFilenamePrefix(), GetOutputUsingOriginalNodeOrdering(), GetOutputVariables(), GetOutputVariablesProvided(), GetPdeTimeStep(), GetPrintingTimeStep(), GetPseudoEcgElectrodePositions(), GetPurkinjeCapacitance(), GetPurkinjeConductivity(), GetPurkinjeSurfaceAreaToVolumeRatio(), GetRelativeTolerance(), GetSheetDimensions(), GetSimulationDuration(), GetSlabDimensions(), GetSpaceDimension(), GetStimuli(), GetSurfaceAreaToVolumeRatio(), GetUpstrokeTimeMaps(), GetUseAbsoluteTolerance(), GetUseRelativeTolerance(), GetUseStateVariableInterpolation(), GetVisualizerOutputPrecision(), GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithParallelVtk(), GetVisualizeWithVtk(), HasDrugDose(), HasPurkinje(), HeartConfig(), IsAdaptivityParametersPresent(), IsAnyNodalTimeTraceRequested(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), IsElectrodesPresent(), IsMaxUpstrokeVelocityMapRequested(), IsMeshProvided(), IsOutputVisualizerPresent(), IsPostProcessingSectionPresent(), IsPseudoEcgCalculationRequested(), IsSimulationDefined(), IsSimulationResumed(), IsUpstrokeTimeMapsRequested(), LoadFromCheckpoint(), ReadFile(), SetApdMaps(), SetBathConductivity(), SetCapacitance(), SetCheckpointSimulation(), SetConductionVelocityMaps(), SetConductivityHeterogeneities(), SetConductivityHeterogeneitiesEllipsoid(), SetDefaultIonicModel(), SetDomain(), SetDrugDose(), SetElectrodeParameters(), SetExtracellularConductivities(), SetFibreLength(), SetIc50Value(), SetIntracellularConductivities(), SetIonicModelRegions(), SetKSPPreconditioner(), SetKSPSolver(), SetMaxUpstrokeVelocityMaps(), SetMeshFileName(), SetMeshPartitioning(), SetOdePdeAndPrintingTimeSteps(), SetOutputDirectory(), SetOutputFilenamePrefix(), SetOutputUsingOriginalNodeOrdering(), SetOutputVariables(), SetParametersFile(), SetPseudoEcgElectrodePositions(), SetPurkinjeCapacitance(), SetPurkinjeConductivity(), SetPurkinjeSurfaceAreaToVolumeRatio(), SetRequestedNodalTimeTraces(), SetSheetDimensions(), SetSimulationDuration(), SetSlabDimensions(), SetSpaceDimension(), SetSurfaceAreaToVolumeRatio(), SetUpstrokeTimeMaps(), SetUseAbsoluteTolerance(), SetUseRelativeTolerance(), SetUseStateVariableInterpolation(), SetVisualizerOutputPrecision(), SetVisualizeWithCmgui(), SetVisualizeWithMeshalyzer(), SetVisualizeWithParallelVtk(), SetVisualizeWithVtk(), UpdateParametersFromResumeSimulation(), and Write().

SchemaLocationsMap HeartConfig::mSchemaLocations [private]

Fixed location of schema files for the different Chaste parameters namespaces.

Definition at line 146 of file HeartConfig.hpp.

Referenced by ReadFile(), SetDefaultSchemaLocations(), and SetFixedSchemaLocations().

std::set<unsigned> HeartConfig::mTissueIdentifiers [private]

Mesh region identifiers to be considered as cardiac tissue

Definition at line 1304 of file HeartConfig.hpp.

Referenced by HeartConfig(), rGetTissueIdentifiers(), and SetTissueAndBathIdentifiers().

bool HeartConfig::mUseFixedNumberIterations [private]

Returns:: whether to use a fixed number of iterations for the linear solver

Definition at line 1314 of file HeartConfig.hpp.

Referenced by GetUseFixedNumberIterationsLinearSolver(), and SetUseFixedNumberIterationsLinearSolver().

bool HeartConfig::mUseFixedSchemaLocation [private]

Returns:: whether to read the schema location from the XML file (false) or use the schema located at heart/src/io/ChasteParameters.xsd in the Chaste source tree (true).

Definition at line 1243 of file HeartConfig.hpp.

Referenced by HeartConfig(), ReadFile(), and SetUseFixedSchemaLocation().

bool HeartConfig::mUseMassLumping [private]

Flag telling whether to use mass lumping or not.

Definition at line 1283 of file HeartConfig.hpp.

Referenced by GetUseMassLumping(), and SetUseMassLumping().

bool HeartConfig::mUseMassLumpingForPrecond [private]

Flag telling whether to use mass lumping in the preconditioner or not.

Definition at line 1288 of file HeartConfig.hpp.

Referenced by GetUseMassLumpingForPrecond(), and SetUseMassLumpingForPrecond().

bool HeartConfig::mUserAskedForCellularTransmuralHeterogeneities [private]

Flag to check whether the user asked for cellular transmural heterogeneities