#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 > &rIntraConductivities) const

void	GetIntracellularConductivities (c_vector< double, 2 > &rIntraConductivities) const

void	GetIntracellularConductivities (c_vector< double, 1 > &rIntraConductivities) const

void	GetExtracellularConductivities (c_vector< double, 3 > &rExtraConductivities) const

void	GetExtracellularConductivities (c_vector< double, 2 > &rExtraConductivities) const

void	GetExtracellularConductivities (c_vector< double, 1 > &rExtraConductivities) 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 > > &rConductivityAreas, std::vector< c_vector< double, 3 > > &rIntraConductivities, std::vector< c_vector< double, 3 > > &rExtraConductivities)

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 > &rTissueIds, const std::set< unsigned > &rBathIds)

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 boost::shared_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 81 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 184 of file HeartConfig.hpp.

Constructor & Destructor Documentation

HeartConfig::~HeartConfig ( )

Destructor

Definition at line 249 of file HeartConfig.cpp.

HeartConfig::HeartConfig ( )

private

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

Definition at line 217 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 1253 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 690 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 682 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 2360 of file HeartConfig.cpp.

References Divides(), 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 364 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 2641 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 1717 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 1605 of file HeartConfig.cpp.

References EXCEPTION, GetUseAbsoluteTolerance(), and mpParameters.

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

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 1744 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 1433 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 1524 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 1575 of file HeartConfig.cpp.

References mpParameters.

Referenced by 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(), BidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and MonodomainPurkinjeSolver< 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
	)

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 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:

do we assume the vectors are initially empty?

There is no set method

Definition at line 1117 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 1416 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 1421 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 1823 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

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

do we assume the vectors are initially empty?

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

Definition at line 1295 of file HeartConfig.cpp.

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

Referenced by BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), ExtendedBidomainTissue< 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 1288 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), and mpParameters.

Referenced by 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 972 of file HeartConfig.cpp.

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

bool HeartConfig::GetCreateFibre ( ) const

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

Definition at line 878 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 854 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 870 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 862 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 737 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 724 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 2784 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 2724 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 1263 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 1278 of file HeartConfig.cpp.

References mIndexEndo.

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

double HeartConfig::GetEpiLayerFraction ( )

Returns: the fraction of epicardial layer

Definition at line 1258 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 1273 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 2895 of file HeartConfig.cpp.

References mEvaluateNumItsEveryNSolves.

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

3D version

Parameters

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

Definition at line 1482 of file HeartConfig.cpp.

References mpParameters.

Referenced by GetConductivityHeterogeneities().

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

2D version

Parameters

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

Definition at line 1500 of file HeartConfig.cpp.

References mpParameters.

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

1D version

Parameters

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

Definition at line 1514 of file HeartConfig.cpp.

References mpParameters.

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

Parameters

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

Definition at line 924 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 2803 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 938 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, 3 > & rIntraConductivities ) const

3D version

Parameters

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

Definition at line 1440 of file HeartConfig.cpp.

References mpParameters.

Referenced by ExtendedBidomainProblem< DIM >::CreateCardiacTissue(), and GetConductivityHeterogeneities().

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

2D version

Parameters

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

Definition at line 1458 of file HeartConfig.cpp.

References mpParameters.

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

1D version

Parameters

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

Definition at line 1472 of file HeartConfig.cpp.

References mpParameters.

template<unsigned DIM>

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

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 745 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 1650 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 1631 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 886 of file HeartConfig.cpp.

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

Referenced by GetConductivityMedia(), and GetMeshName().

unsigned HeartConfig::GetMaxCheckpointsOnDisk ( ) const

Get number of checkpoints to keep on disk

Returns: checkpointing timestep

Definition at line 1427 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 1797 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 964 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 1679 of file HeartConfig.cpp.

References EXCEPTION, and mpParameters.

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

double HeartConfig::GetMidLayerFraction ( )

Returns: the fraction of endocardial layer

Definition at line 1268 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 1283 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 1849 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 1581 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 1368 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 1375 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 1405 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 1388 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 1382 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 546 of file HeartConfig.cpp.

References mParametersFilePath.

double HeartConfig::GetPdeTimeStep ( ) const

Returns: PDE time-step (ms)

Definition at line 1587 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 1593 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

Parameters

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

Definition at line 1876 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 2910 of file HeartConfig.cpp.

References mpParameters.

Referenced by MonodomainPurkinjeCableAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeCableMatrixTerm(), and MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

double HeartConfig::GetPurkinjeConductivity ( )

Returns: the default conductivity for Purkinje fibres.

Definition at line 2940 of file HeartConfig.cpp.

References mpParameters.

Referenced by MonodomainPurkinjeCableAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeCableMatrixTerm().

double HeartConfig::GetPurkinjeSurfaceAreaToVolumeRatio ( )

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

Definition at line 2925 of file HeartConfig.cpp.

References mpParameters.

Referenced by MonodomainPurkinjeCableAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeCableMatrixTerm(), AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateJunction(), and MonodomainPurkinjeSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

double HeartConfig::GetRelativeTolerance ( ) const

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

Definition at line 1621 of file HeartConfig.cpp.

References EXCEPTION, GetUseRelativeTolerance(), and mpParameters.

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

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

Parameters

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

Definition at line 909 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 711 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 893 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 698 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

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

do we assume the vectors are initially empty?

Todo:: There is no set method

Definition at line 981 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 1569 of file HeartConfig.cpp.

References mpParameters.

Referenced by AbstractCardiacCellInterface::GetIntracellularAreaStimulus(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), MonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), BidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and MonodomainPurkinjeSolver< 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 1771 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 1599 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 2890 of file HeartConfig.cpp.

References mUseFixedNumberIterations.

bool HeartConfig::GetUseMassLumping ( )

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

Definition at line 2859 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 2869 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 2879 of file HeartConfig.cpp.

References mUseReactionDiffusionOperatorSplitting.

bool HeartConfig::GetUseRelativeTolerance ( ) const

Returns: true if we are using KSP relative tolerance

Definition at line 1615 of file HeartConfig.cpp.

References mpParameters.

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

bool HeartConfig::GetUseStateVariableInterpolation ( ) const

Returns: true if state variable interpolation is used

Definition at line 2756 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(), MonodomainPurkinjeProblem< 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 409 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 1947 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 1911 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 1899 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 1923 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 1935 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 2779 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 2904 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 208 of file HeartConfig.cpp.

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 1698 of file HeartConfig.cpp.

References mpParameters.

bool HeartConfig::IsAnyNodalTimeTraceRequested ( ) const

Returns: true if any nodal time trace is requested

Definition at line 1838 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 1733 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 1812 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 1959 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 1786 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 848 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), and mpParameters.

Referenced by GetCreateFibre(), GetCreateMesh(), GetCreateSheet(), GetCreateSlab(), and GetLoadMesh().

bool HeartConfig::IsOutputVisualizerPresent ( ) const

Returns: whether there is an OutputVisualizer element present.

Definition at line 1892 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 1722 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 1712 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 1864 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 672 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 677 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 1761 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
	)

inlineprivate

Un-archive the object.

Parameters

archive
version

Definition at line 139 of file HeartConfig.hpp.

References LoadFromCheckpoint(), mBathConductivities, mBathIdentifiers, mEndoFraction, mEpiFraction, mEvaluateNumItsEveryNSolves, mIndexEndo, mIndexEpi, mIndexMid, mMidFraction, mTissueIdentifiers, mUseFixedNumberIterations, mUseMassLumping, mUseMassLumpingForPrecond, mUserAskedForCellularTransmuralHeterogeneities, and mUseReactionDiffusionOperatorSplitting.

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 319 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 454 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 664 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 1564 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 1559 of file HeartConfig.cpp.

References mTissueIdentifiers.

Referenced by HeartRegionCode::GetValidTissueId().

template<class Archive >

void HeartConfig::save	(	Archive &	archive,
		const unsigned int	version
	)		const

inlineprivate

Archive the object.

Parameters

archive
version

Definition at line 101 of file HeartConfig.hpp.

References PetscTools::AmMaster(), PetscTools::Barrier(), mBathConductivities, mBathIdentifiers, mEndoFraction, mEpiFraction, mEvaluateNumItsEveryNSolves, mIndexEndo, mIndexEpi, mIndexMid, mMidFraction, mpInstance, mTissueIdentifiers, mUseFixedNumberIterations, mUseMassLumping, mUseMassLumpingForPrecond, mUserAskedForCellularTransmuralHeterogeneities, and mUseReactionDiffusionOperatorSplitting.

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 2532 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 2285 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 2291 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 2330 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 2201 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 2586 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 2066 of file HeartConfig.cpp.

References mpParameters.

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

Set a number of heterogeneous regions (Axis-aligned ellipsoids) 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 2116 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 1983 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetDefaultSchemaLocations ( )

private

Set default schema locations in the Chaste source tree.

Definition at line 390 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 1978 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 2790 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 2685 of file HeartConfig.cpp.

References IsElectrodesPresent(), and mpParameters.

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

3D version

Parameters

rExtraConductivities DIM-vector of extracellular conductivities (mS/cm)

Definition at line 2255 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 2266 of file HeartConfig.cpp.

References mpParameters.

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

1D version

Parameters

rExtraConductivities DIM-vector of extracellular conductivities (mS/cm)

Definition at line 2276 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 2015 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 443 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 2822 of file HeartConfig.cpp.

References mpParameters, and SetDrugDose().

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

3D version

Parameters

rIntraConductivities DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2225 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 2236 of file HeartConfig.cpp.

References mpParameters.

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

1D version

Parameters

rIntraConductivities DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2246 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 2040 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 2453 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 2420 of file HeartConfig.cpp.

References EXCEPTION, GetKSPSolver(), and mpParameters.

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 2567 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 2027 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 2505 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 2337 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 2345 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 2166 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 2171 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 2195 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 ANY OUTPUT VARIABLES SET IN THE XML FILE

Definition at line 2176 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 534 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 2350 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 2355 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 )

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 2619 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 2918 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 2948 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 2933 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 2602 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 2003 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 1972 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 1991 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetSpaceDimension ( unsigned spaceDimension )

Set the configuration dimension

Parameters

spaceDimension 1, 2 or 3.

Definition at line 1967 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 2324 of file HeartConfig.cpp.

References mpParameters.

void HeartConfig::SetTissueAndBathIdentifiers	(	const std::set< unsigned > &	rTissueIds,
		const std::set< unsigned > &	rBathIds
	)

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

Parameters

rTissueIds	set of identifiers
rBathIds	set of identifiers

Definition at line 2303 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 2549 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 2412 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 2884 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 449 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 2854 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 2864 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 2874 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 2404 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 2767 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 2678 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 2654 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 2646 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 2670 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 2662 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 551 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 253 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 93 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 1343 of file HeartConfig.hpp.

Referenced by GetBathConductivity(), load(), save(), and SetBathMultipleConductivities().

std::set<unsigned> HeartConfig::mBathIdentifiers

private

Mesh region identifiers to be considered as Bath

Definition at line 1353 of file HeartConfig.hpp.

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

double HeartConfig::mEndoFraction

private

Fraction of endocardial layer

Definition at line 1297 of file HeartConfig.hpp.

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

double HeartConfig::mEpiFraction

private

Fraction of epicardial layer

Definition at line 1292 of file HeartConfig.hpp.

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

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 1365 of file HeartConfig.hpp.

Referenced by GetEvaluateNumItsEveryNSolves(), load(), save(), and SetUseFixedNumberIterationsLinearSolver().

unsigned HeartConfig::mIndexEndo

private

Order index in which the endocardial heterogeneities are supplied

Definition at line 1317 of file HeartConfig.hpp.

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

unsigned HeartConfig::mIndexEpi

private

Order index in which the epicardial heterogeneities are supplied

Definition at line 1312 of file HeartConfig.hpp.

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

unsigned HeartConfig::mIndexMid

private

Order index in which the midmyocardial heterogeneities are supplied

Definition at line 1307 of file HeartConfig.hpp.

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

double HeartConfig::mMidFraction

private

Fraction of midmyocardial layer

Definition at line 1302 of file HeartConfig.hpp.

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

FileFinder HeartConfig::mParametersFilePath

private

Where the user parameters were read from.

Definition at line 1281 of file HeartConfig.hpp.

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

boost::shared_ptr< HeartConfig > HeartConfig::mpInstance

staticprivate

The single instance of the class

Definition at line 1276 of file HeartConfig.hpp.

Referenced by HeartConfig(), 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 1273 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 190 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 1348 of file HeartConfig.hpp.

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

bool HeartConfig::mUseFixedNumberIterations

private

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

Definition at line 1358 of file HeartConfig.hpp.

Referenced by GetUseFixedNumberIterationsLinearSolver(), load(), save(), 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 1287 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 1327 of file HeartConfig.hpp.

Referenced by GetUseMassLumping(), load(), save(), and SetUseMassLumping().

bool HeartConfig::mUseMassLumpingForPrecond

private

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

Definition at line 1332 of file HeartConfig.hpp.

Referenced by GetUseMassLumpingForPrecond(), load(), save(), and SetUseMassLumpingForPrecond().

bool HeartConfig::mUserAskedForCellularTransmuralHeterogeneities

private

Flag to check whether the user asked for cellular transmural heterogeneities

Definition at line 1322 of file HeartConfig.hpp.

Referenced by AreCellularTransmuralHeterogeneitiesRequested(), GetCellHeterogeneities(), HeartConfig(), load(), and save().

bool HeartConfig::mUseReactionDiffusionOperatorSplitting

private

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

Definition at line 1338 of file HeartConfig.hpp.

Referenced by GetUseReactionDiffusionOperatorSplitting(), HeartConfig(), load(), save(), and SetUseReactionDiffusionOperatorSplitting().

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

heart/src/problem/HeartConfig.hpp
heart/src/problem/HeartConfig.cpp

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