HeartConfig Class Reference

#include <HeartConfig.hpp>

Collaboration diagram for HeartConfig:

Public Types
typedef std::map< std::string, std::string >	SchemaLocationsMap
Public Member Functions
void	SetUseFixedSchemaLocation (bool useFixedSchemaLocation)
void	SetFixedSchemaLocations (const SchemaLocationsMap &rSchemaLocations)
void	SetDefaultsFile (const std::string &rFileName)
void	SetParametersFile (const std::string &rFileName)
void	Write (bool useArchiveLocationInfo=false, std::string subfolderName="output")
void	CopySchema (const std::string &rToDirectory)
boost::shared_ptr < cp::chaste_parameters_type >	ReadFile (const std::string &rFileName)
	~HeartConfig ()
unsigned	GetVersionFromNamespace (const std::string &rNamespaceUri)
FileFinder	GetParametersFilePath ()
bool	IsSimulationDefined () const
bool	IsSimulationResumed () const
unsigned	GetSpaceDimension () const
double	GetSimulationDuration () const
cp::domain_type	GetDomain () const
cp::ionic_model_selection_type	GetDefaultIonicModel () const
template<unsigned DIM>
void	GetIonicModelRegions (std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &rDefinedRegions, std::vector< cp::ionic_model_selection_type > &rIonicModels) const
void	SetIonicModelRegions (std::vector< ChasteCuboid< 3 > > &rDefinedRegions, std::vector< cp::ionic_model_selection_type > &rIonicModels) const
bool	IsMeshProvided () const
bool	GetCreateMesh () const
bool	GetCreateSlab () const
bool	GetCreateSheet () const
bool	GetCreateFibre () const
bool	GetLoadMesh () const
void	GetSlabDimensions (c_vector< double, 3 > &slabDimensions) const
void	GetSheetDimensions (c_vector< double, 2 > &sheetDimensions) const
void	GetFibreLength (c_vector< double, 1 > &fibreLength) const
double	GetInterNodeSpace () const
std::string	GetMeshName () const
cp::media_type	GetConductivityMedia () const
template<unsigned DIM>
void	GetStimuli (std::vector< boost::shared_ptr< AbstractStimulusFunction > > &rStimuliApplied, std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &rStimulatedAreas) const
template<unsigned DIM>
void	GetCellHeterogeneities (std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &rCellHeterogeneityRegions, std::vector< double > &rScaleFactorGks, std::vector< double > &rScaleFactorIto, std::vector< double > &rScaleFactorGkr, std::vector< std::map< std::string, double > > *pParameterSettings)
bool	GetConductivityHeterogeneitiesProvided () const
bool	AreCellularTransmuralHeterogeneitiesRequested ()
double	GetEpiLayerFraction ()
double	GetEndoLayerFraction ()
double	GetMidLayerFraction ()
unsigned	GetEpiLayerIndex ()
unsigned	GetEndoLayerIndex ()
unsigned	GetMidLayerIndex ()
template<unsigned DIM>
void	GetConductivityHeterogeneities (std::vector< boost::shared_ptr< AbstractChasteRegion< DIM > > > &conductivitiesHeterogeneityAreas, std::vector< c_vector< double, 3 > > &intraConductivities, std::vector< c_vector< double, 3 > > &extraConductivities) const
std::string	GetOutputDirectory () const
std::string	GetOutputFilenamePrefix () const
bool	GetOutputVariablesProvided () const
void	GetOutputVariables (std::vector< std::string > &rOutputVariables) const
bool	GetOutputUsingOriginalNodeOrdering ()
bool	GetCheckpointSimulation () const
double	GetCheckpointTimestep () const
unsigned	GetMaxCheckpointsOnDisk () const
HeartFileFinder	GetArchivedSimulationDir () const
void	GetIntracellularConductivities (c_vector< double, 3 > &intraConductivities) const
void	GetIntracellularConductivities (c_vector< double, 2 > &intraConductivities) const
void	GetIntracellularConductivities (c_vector< double, 1 > &intraConductivities) const
void	GetExtracellularConductivities (c_vector< double, 3 > &extraConductivities) const
void	GetExtracellularConductivities (c_vector< double, 2 > &extraConductivities) const
void	GetExtracellularConductivities (c_vector< double, 1 > &extraConductivities) const
double	GetBathConductivity (unsigned bathRegion=UINT_MAX) const
const std::set< unsigned > &	rGetTissueIdentifiers ()
const std::set< unsigned > &	rGetBathIdentifiers ()
double	GetSurfaceAreaToVolumeRatio () const
double	GetCapacitance () const
double	GetOdeTimeStep () const
double	GetPdeTimeStep () const
double	GetPrintingTimeStep () const
bool	GetUseAbsoluteTolerance () const
double	GetAbsoluteTolerance () const
bool	GetUseRelativeTolerance () const
double	GetRelativeTolerance () const
const char *	GetKSPSolver () const
const char *	GetKSPPreconditioner () const
DistributedTetrahedralMeshPartitionType::type	GetMeshPartitioning () const
bool	IsAdaptivityParametersPresent () const
double	GetTargetErrorForAdaptivity () const
double	GetSigmaForAdaptivity () const
double	GetMaxEdgeLengthForAdaptivity () const
double	GetMinEdgeLengthForAdaptivity () const
double	GetGradationForAdaptivity () const
unsigned	GetMaxNodesForAdaptivity () const
unsigned	GetNumberOfAdaptiveSweeps () const
bool	IsPostProcessingSectionPresent () const
void	EnsurePostProcessingSectionPresent ()
bool	IsPostProcessingRequested () const
bool	IsApdMapsRequested () const
void	GetApdMaps (std::vector< std::pair< double, double > > &rApdMaps) const
bool	IsUpstrokeTimeMapsRequested () const
void	GetUpstrokeTimeMaps (std::vector< double > &rUpstrokeTimeMaps) const
bool	IsMaxUpstrokeVelocityMapRequested () const
void	GetMaxUpstrokeVelocityMaps (std::vector< double > &rUpstrokeVelocityMaps) const
bool	IsConductionVelocityMapsRequested () const
void	GetConductionVelocityMaps (std::vector< unsigned > &rConductionVelocityMaps) const
bool	IsAnyNodalTimeTraceRequested () const
void	GetNodalTimeTraceRequested (std::vector< unsigned > &rRequestedNodes) const
bool	IsPseudoEcgCalculationRequested () const
template<unsigned SPACE_DIM>
void	GetPseudoEcgElectrodePositions (std::vector< ChastePoint< SPACE_DIM > > &rPseudoEcgElectrodePositions) const
bool	GetUseStateVariableInterpolation () const
bool	IsOutputVisualizerPresent () const
bool	GetVisualizeWithMeshalyzer () const
bool	GetVisualizeWithCmgui () const
bool	GetVisualizeWithVtk () const
bool	GetVisualizeWithParallelVtk () const
unsigned	GetVisualizerOutputPrecision ()
bool	IsElectrodesPresent () const
void	GetElectrodeParameters (bool &rGroundSecondElectrode, unsigned &rIndex, double &rMagnitude, double &rStartTime, double &rDuration)
bool	GetUseMassLumping ()
bool	GetUseMassLumpingForPrecond ()
bool	GetUseReactionDiffusionOperatorSplitting ()
bool	GetUseFixedNumberIterationsLinearSolver ()
unsigned	GetEvaluateNumItsEveryNSolves ()
void	SetSpaceDimension (unsigned spaceDimension)
void	SetSimulationDuration (double simulationDuration)
void	SetDomain (const cp::domain_type &rDomain)
void	SetDefaultIonicModel (const cp::ionic_models_available_type &rIonicModel)
void	SetSlabDimensions (double x, double y, double z, double inter_node_space)
void	SetSheetDimensions (double x, double y, double inter_node_space)
void	SetFibreLength (double x, double inter_node_space)
void	SetMeshFileName (std::string meshPrefix, cp::media_type fibreDefinition=cp::media_type::NoFibreOrientation)
void	SetConductivityHeterogeneities (std::vector< ChasteCuboid< 3 > > &rConductivityAreas, std::vector< c_vector< double, 3 > > &rIntraConductivities, std::vector< c_vector< double, 3 > > &rExtraConductivities)
void	SetConductivityHeterogeneitiesEllipsoid (std::vector< ChasteEllipsoid< 3 > > &conductivityAreas, std::vector< c_vector< double, 3 > > &intraConductivities, std::vector< c_vector< double, 3 > > &extraConductivities)
void	SetOutputDirectory (const std::string &rOutputDirectory)
void	SetOutputFilenamePrefix (const std::string &rOutputFilenamePrefix)
void	SetOutputVariables (const std::vector< std::string > &rOutputVariables)
void	SetOutputUsingOriginalNodeOrdering (bool useOriginal)
void	SetCheckpointSimulation (bool checkpointSimulation, double checkpointTimestep=-1.0, unsigned maxCheckpointsOnDisk=UINT_MAX)
void	SetIntracellularConductivities (const c_vector< double, 3 > &rIntraConductivities)
void	SetIntracellularConductivities (const c_vector< double, 2 > &rIntraConductivities)
void	SetIntracellularConductivities (const c_vector< double, 1 > &rIntraConductivities)
void	SetExtracellularConductivities (const c_vector< double, 3 > &rExtraConductivities)
void	SetExtracellularConductivities (const c_vector< double, 2 > &rExtraConductivities)
void	SetExtracellularConductivities (const c_vector< double, 1 > &rExtraConductivities)
void	SetBathConductivity (double bathConductivity)
void	SetBathMultipleConductivities (std::map< unsigned, double > bathConductivities)
void	SetTissueAndBathIdentifiers (const std::set< unsigned > &tissueIds, const std::set< unsigned > &bathIds)
void	SetSurfaceAreaToVolumeRatio (double ratio)
void	SetCapacitance (double capacitance)
void	SetOdePdeAndPrintingTimeSteps (double odeTimeStep, double pdeTimeStep, double printingTimeStep)
void	SetOdeTimeStep (double odeTimeStep)
void	SetPdeTimeStep (double pdeTimeStep)
void	SetPrintingTimeStep (double printingTimeStep)
void	SetUseRelativeTolerance (double relativeTolerance)
void	SetUseAbsoluteTolerance (double absoluteTolerance)
void	SetKSPSolver (const char *kspSolver)
void	SetKSPPreconditioner (const char *kspPreconditioner)
void	SetMeshPartitioning (const char *meshPartioningMethod)
void	SetAdaptivityParameters (double targetError, double sigma, double maxEdgeLength, double minEdgeLength, double gradation, unsigned maxNodes, unsigned numSweeps)
void	SetTargetErrorForAdaptivity (double targetError)
void	SetSigmaForAdaptivity (double sigma)
void	SetMaxEdgeLengthForAdaptivity (double maxEdgeLength)
void	SetMinEdgeLengthForAdaptivity (double minEdgeLength)
void	SetGradationForAdaptivity (double gradation)
void	SetMaxNodesForAdaptivity (unsigned maxNodes)
void	SetNumberOfAdaptiveSweeps (unsigned numSweeps)
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 ()
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	UpdateParametersFromResumeSimulation (boost::shared_ptr< cp::chaste_parameters_type > pResumeParameters)
void	SetDefaultSchemaLocations ()
	HeartConfig ()
template<class TYPE >
TYPE *	DecideLocation (TYPE params_ptr, TYPE defaults_ptr, const std::string &rNameParameter) const
void	CheckSimulationIsDefined (std::string callingMethod="") const
void	CheckResumeSimulationIsDefined (std::string callingMethod="") const
Private Attributes
SchemaLocationsMap	mSchemaLocations
boost::shared_ptr < cp::chaste_parameters_type >	mpUserParameters
boost::shared_ptr < cp::chaste_parameters_type >	mpDefaultParameters
FileFinder	mParametersFilePath
bool	mUseFixedSchemaLocation
double	mEpiFraction
double	mEndoFraction
double	mMidFraction
unsigned	mIndexMid
unsigned	mIndexEpi
unsigned	mIndexEndo
bool	mUserAskedForCellularTransmuralHeterogeneities
bool	mUseMassLumping
bool	mUseMassLumpingForPrecond
bool	mUseReactionDiffusionOperatorSplitting
std::map< unsigned, double >	mBathConductivities
std::set< unsigned >	mTissueIdentifiers
std::set< unsigned >	mBathIdentifiers
bool	mUseFixedNumberIterations
unsigned	mEvaluateNumItsEveryNSolves
Static Private Attributes
static std::auto_ptr< HeartConfig >	mpInstance
Friends
class	boost::serialization::access
class	TestHeartConfig

Detailed Description

A singleton class containing configuration parameters for heart simulations.

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

chaste_parameters_type is a convenience class created by CodeSynthesis XSD

Definition at line 74 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 162 of file HeartConfig.hpp.

Constructor & Destructor Documentation

HeartConfig::~HeartConfig ( )

Destructor

Definition at line 206 of file HeartConfig.cpp.

HeartConfig::HeartConfig ( ) [private]

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

Definition at line 173 of file HeartConfig.cpp.

References CreateDefaultParameters(), mBathIdentifiers, mEndoFraction, mEpiFraction, mIndexEndo, mIndexEpi, mIndexMid, mMidFraction, mpDefaultParameters, mpInstance, mpUserParameters, 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 1225 of file HeartConfig.cpp.

References mUserAskedForCellularTransmuralHeterogeneities.

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

CheckSimulationIsDefined is a convience 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 598 of file HeartConfig.cpp.

References EXCEPTION, and IsSimulationDefined().

Referenced by GetArchivedSimulationDir(), GetCheckpointSimulation(), GetCheckpointTimestep(), and GetMaxCheckpointsOnDisk().

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

CheckSimulationIsDefined is a convience 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 590 of file HeartConfig.cpp.

References EXCEPTION, and IsSimulationResumed().

Referenced by GetCellHeterogeneities(), GetCheckpointSimulation(), GetCheckpointTimestep(), GetConductivityHeterogeneities(), GetConductivityHeterogeneitiesProvided(), GetConductivityMedia(), GetCreateFibre(), GetCreateMesh(), GetCreateSheet(), GetCreateSlab(), GetDefaultIonicModel(), GetFibreLength(), GetInterNodeSpace(), GetIonicModelRegions(), GetLoadMesh(), GetMaxCheckpointsOnDisk(), GetMeshName(), GetOutputDirectory(), GetOutputFilenamePrefix(), GetOutputVariables(), GetOutputVariablesProvided(), GetSheetDimensions(), GetSlabDimensions(), GetStimuli(), 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 2608 of file HeartConfig.cpp.

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

Referenced by SetCheckpointSimulation(), SetDefaultsFile(), 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.

Parameters:

rToDirectory

directory to copy to

Definition at line 278 of file HeartConfig.cpp.

References ABORT_IF_NON0, PetscTools::AmMaster(), RelativeTo::ChasteSourceRoot, RelativeTo::CWD, FileFinder::Exists(), FileFinder::GetAbsolutePath(), and FileFinder::SetPath().

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

template<class TYPE >

TYPE * HeartConfig::DecideLocation	(	TYPE *	params_ptr,
		TYPE *	defaults_ptr,
		const std::string &	rNameParameter
	)			const `[inline, private]`

DecideLocation is a convenience method used to get the correct parameter value from the defaults/parameters files. It checks if the first value is present and (if not) moves onto the second

Parameters:

	params_ptr	Pointer to quantity within the parameters file (checked first, since it will override a default)
	defaults_ptr	Pointer to quantity within the defaults file (used if there was no override)
	rNameParameter	Name of quatity within params_ptr/defaults_ptr (so we can throw a meaningful exception if it's not found)

Definition at line 576 of file HeartConfig.cpp.

References EXCEPTION.

Referenced by GetAbsoluteTolerance(), GetApdMaps(), GetBathConductivity(), GetCapacitance(), GetCellHeterogeneities(), GetCheckpointSimulation(), GetCheckpointTimestep(), GetConductionVelocityMaps(), GetConductivityHeterogeneities(), GetConductivityHeterogeneitiesProvided(), GetConductivityMedia(), GetCreateFibre(), GetCreateMesh(), GetCreateSheet(), GetCreateSlab(), GetDefaultIonicModel(), GetDomain(), GetDrugDose(), GetExtracellularConductivities(), GetFibreLength(), GetGradationForAdaptivity(), GetIc50Values(), GetInterNodeSpace(), GetIntracellularConductivities(), GetIonicModelRegions(), GetKSPPreconditioner(), GetKSPSolver(), GetLoadMesh(), GetMaxCheckpointsOnDisk(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMaxUpstrokeVelocityMaps(), GetMeshName(), GetMeshPartitioning(), GetMinEdgeLengthForAdaptivity(), GetNodalTimeTraceRequested(), GetNumberOfAdaptiveSweeps(), GetOdeTimeStep(), GetOutputDirectory(), GetOutputFilenamePrefix(), GetOutputUsingOriginalNodeOrdering(), GetOutputVariables(), GetOutputVariablesProvided(), GetPdeTimeStep(), GetPrintingTimeStep(), GetPseudoEcgElectrodePositions(), GetRelativeTolerance(), GetSheetDimensions(), GetSigmaForAdaptivity(), GetSimulationDuration(), GetSlabDimensions(), GetSpaceDimension(), GetStimuli(), GetSurfaceAreaToVolumeRatio(), GetTargetErrorForAdaptivity(), GetUpstrokeTimeMaps(), GetUseAbsoluteTolerance(), GetUseRelativeTolerance(), GetUseStateVariableInterpolation(), GetVisualizerOutputPrecision(), GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithParallelVtk(), GetVisualizeWithVtk(), HasDrugDose(), IsAdaptivityParametersPresent(), IsAnyNodalTimeTraceRequested(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), IsElectrodesPresent(), IsMaxUpstrokeVelocityMapRequested(), IsMeshProvided(), IsOutputVisualizerPresent(), IsPostProcessingSectionPresent(), IsPseudoEcgCalculationRequested(), and IsUpstrokeTimeMapsRequested().

void HeartConfig::EnsureOutputVisualizerExists ( void )

Create the OutputVisualizer element if it doesn't exist

Definition at line 2999 of file HeartConfig.cpp.

References mpUserParameters.

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 1906 of file HeartConfig.cpp.

References mpUserParameters.

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 1670 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, GetUseAbsoluteTolerance(), mpDefaultParameters, and mpUserParameters.

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

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

Parameters:

rApdMaps

each entry is a request for a map with

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

Definition at line 1938 of file HeartConfig.cpp.

References DecideLocation(), IsApdMapsRequested(), mpDefaultParameters, and mpUserParameters.

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

HeartFileFinder HeartConfig::GetArchivedSimulationDir ( ) const

Get directory where the archived simulation to resume is defined

Definition at line 1483 of file HeartConfig.cpp.

References CheckResumeSimulationIsDefined(), and mpUserParameters.

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 1579 of file HeartConfig.cpp.

References DecideLocation(), HeartRegionCode::IsRegionBath(), mBathConductivities, mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetCapacitance ( ) const

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

Definition at line 1634 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

template<unsigned DIM>

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

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

Todo:

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

Parameters:

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

Todo:: There is no set method

Definition at line 1081 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, mEndoFraction, mEpiFraction, mIndexEndo, mIndexEpi, mIndexMid, mMidFraction, mpDefaultParameters, mpUserParameters, and mUserAskedForCellularTransmuralHeterogeneities.

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

bool HeartConfig::GetCheckpointSimulation ( ) const

Get whether simulation should be checkpointed or not

Returns:: archive simulation

Todo:: #1160 What code covers this? Should be removed ideally.

Definition at line 1420 of file HeartConfig.cpp.

References CheckResumeSimulationIsDefined(), CheckSimulationIsDefined(), DecideLocation(), IsSimulationDefined(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetCheckpointTimestep ( ) const

Get checkpointing timestep

Returns:: checkpointing timestep

Todo:: #1160 What code covers this? Should be removed ideally.

Definition at line 1446 of file HeartConfig.cpp.

References CheckResumeSimulationIsDefined(), CheckSimulationIsDefined(), DecideLocation(), IsSimulationDefined(), mpDefaultParameters, and mpUserParameters.

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 2027 of file HeartConfig.cpp.

References DecideLocation(), IsConductionVelocityMapsRequested(), mpDefaultParameters, and mpUserParameters.

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

template<unsigned DIM>

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

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

Todo:

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

Parameters:

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

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

Definition at line 1277 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, GetExtracellularConductivities(), GetIntracellularConductivities(), mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::GetConductivityHeterogeneitiesProvided ( ) const

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

Definition at line 1260 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

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 927 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), GetLoadMesh(), mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::GetCreateFibre ( ) const

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

Definition at line 815 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by GetFibreLength().

bool HeartConfig::GetCreateMesh ( ) const

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

Definition at line 782 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by GetInterNodeSpace().

bool HeartConfig::GetCreateSheet ( ) const

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

Definition at line 804 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by GetSheetDimensions().

bool HeartConfig::GetCreateSlab ( ) const

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

Definition at line 793 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by 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 648 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

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 634 of file HeartConfig.cpp.

References DecideLocation(), IsSimulationDefined(), mpDefaultParameters, and mpUserParameters.

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 3162 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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 3083 of file HeartConfig.cpp.

References EXCEPTION, IsElectrodesPresent(), and mpUserParameters.

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

double HeartConfig::GetEndoLayerFraction ( )

Returns:: the fraction of endocardial layer

Definition at line 1235 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 1250 of file HeartConfig.cpp.

References mIndexEndo.

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

double HeartConfig::GetEpiLayerFraction ( )

Returns:: the fraction of epicardial layer

Definition at line 1230 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 1245 of file HeartConfig.cpp.

References mIndexEpi.

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

unsigned HeartConfig::GetEvaluateNumItsEveryNSolves ( )

Get 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 3278 of file HeartConfig.cpp.

References mEvaluateNumItsEveryNSolves.

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

1D version

Parameters:

extraConductivities

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

Definition at line 1568 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

2D version

Parameters:

extraConductivities

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

Definition at line 1553 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

3D version

Parameters:

extraConductivities

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

Definition at line 1535 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

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

Parameters:

fibreLength

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

Definition at line 871 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, GetCreateFibre(), GetSpaceDimension(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetGradationForAdaptivity ( ) const

Returns:: value of gradation used in adaptivity

Definition at line 1843 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, IsAdaptivityParametersPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by AdaptiveTetrahedralMesh::CalculateErrorMetric(), AdaptiveBidomainProblem::GetGradation(), SetMaxEdgeLengthForAdaptivity(), SetMaxNodesForAdaptivity(), SetMinEdgeLengthForAdaptivity(), SetNumberOfAdaptiveSweeps(), SetSigmaForAdaptivity(), and SetTargetErrorForAdaptivity().

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 3182 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetInterNodeSpace ( ) const

Returns:: internode space of cuboid mesh (cm)

Definition at line 887 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), GetCreateMesh(), GetSpaceDimension(), mpDefaultParameters, mpUserParameters, and NEVER_REACHED.

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

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

1D version

Parameters:

intraConductivities

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

Definition at line 1524 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

2D version

Parameters:

intraConductivities

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

Definition at line 1509 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

3D version

Parameters:

intraConductivities

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

Definition at line 1491 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

template<unsigned DIM>

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

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

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

Parameters:

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

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

Definition at line 658 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, mpDefaultParameters, mpUserParameters, 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 1719 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, mpDefaultParameters, and mpUserParameters.

const char * HeartConfig::GetKSPSolver ( ) const

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

Definition at line 1699 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, mpDefaultParameters, and mpUserParameters.

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 827 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

unsigned HeartConfig::GetMaxCheckpointsOnDisk ( ) const

Get number of checkpoints to keep on disk

Returns:: checkpointing timestep

Todo:: #1160 What code covers this? Should be removed ideally.

Definition at line 1464 of file HeartConfig.cpp.

References CheckResumeSimulationIsDefined(), CheckSimulationIsDefined(), DecideLocation(), IsSimulationDefined(), mpDefaultParameters, and mpUserParameters.

Referenced by CardiacSimulation::CreateResumeXmlFile().

double HeartConfig::GetMaxEdgeLengthForAdaptivity ( ) const

Returns:: maximum edge length in mesh after an adapt

Definition at line 1815 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, IsAdaptivityParametersPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by AdaptiveTetrahedralMesh::CalculateErrorMetric(), AdaptiveBidomainProblem::GetMaxEdgeLength(), SetGradationForAdaptivity(), SetMaxNodesForAdaptivity(), SetMinEdgeLengthForAdaptivity(), SetNumberOfAdaptiveSweeps(), SetSigmaForAdaptivity(), and SetTargetErrorForAdaptivity().

unsigned HeartConfig::GetMaxNodesForAdaptivity ( ) const

Returns:: maximum number of nodes in mesh after an adapt

Definition at line 1857 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, IsAdaptivityParametersPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by AdaptiveTetrahedralMesh::CalculateErrorMetric(), AdaptiveBidomainProblem::GetMaxMeshNodes(), SetGradationForAdaptivity(), SetMaxEdgeLengthForAdaptivity(), SetMinEdgeLengthForAdaptivity(), SetNumberOfAdaptiveSweeps(), SetSigmaForAdaptivity(), and SetTargetErrorForAdaptivity().

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 1998 of file HeartConfig.cpp.

References DecideLocation(), IsMaxUpstrokeVelocityMapRequested(), mpDefaultParameters, and mpUserParameters.

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

std::string HeartConfig::GetMeshName ( ) const

Returns:: path/basename of mesh files

Definition at line 917 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), GetLoadMesh(), mpDefaultParameters, and mpUserParameters.

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

DistributedTetrahedralMeshPartitionType::type HeartConfig::GetMeshPartitioning ( ) const

Returns:: the mesh partitioning method to use

Definition at line 1750 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetMidLayerFraction ( )

Returns:: the fraction of endocardial layer

Definition at line 1240 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 1255 of file HeartConfig.cpp.

References mIndexMid.

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

double HeartConfig::GetMinEdgeLengthForAdaptivity ( ) const

Returns:: minimum edge length in mesh after an adapt

Definition at line 1829 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, IsAdaptivityParametersPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by AdaptiveTetrahedralMesh::CalculateErrorMetric(), AdaptiveBidomainProblem::GetMinEdgeLength(), SetGradationForAdaptivity(), SetMaxEdgeLengthForAdaptivity(), SetMaxNodesForAdaptivity(), SetNumberOfAdaptiveSweeps(), SetSigmaForAdaptivity(), and SetTargetErrorForAdaptivity().

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 2056 of file HeartConfig.cpp.

References DecideLocation(), IsAnyNodalTimeTraceRequested(), mpDefaultParameters, and mpUserParameters.

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

unsigned HeartConfig::GetNumberOfAdaptiveSweeps ( ) const

Returns:: number of adaptive sweeps through mesh during adaptivity

Definition at line 1871 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, IsAdaptivityParametersPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by AdaptiveBidomainProblem::GetNumAdaptSweeps(), SetGradationForAdaptivity(), SetMaxEdgeLengthForAdaptivity(), SetMaxNodesForAdaptivity(), SetMinEdgeLengthForAdaptivity(), SetSigmaForAdaptivity(), and SetTargetErrorForAdaptivity().

double HeartConfig::GetOdeTimeStep ( ) const

Returns:: ODE time-step (ms)

Definition at line 1642 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

std::string HeartConfig::GetOutputDirectory ( ) const

Returns:: output directory path name

Definition at line 1353 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by CardiacSimulation::CreateAndRun(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), CardiacElectroMechanicsProblem< 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 1361 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseWriter(), AdaptiveBidomainProblem::Solve(), 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 DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

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

Get 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 1386 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

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 1369 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

FileFinder HeartConfig::GetParametersFilePath ( )

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

Definition at line 442 of file HeartConfig.cpp.

References mParametersFilePath.

double HeartConfig::GetPdeTimeStep ( ) const

Returns:: PDE time-step (ms)

Definition at line 1649 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetPrintingTimeStep ( ) const

Returns:: priting time-step (ms)

Definition at line 1656 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

template<unsigned SPACE_DIM>

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

Parameters:

rPseudoEcgElectrodePositions

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

Definition at line 2087 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetRelativeTolerance ( ) const

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

Definition at line 1688 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, GetUseRelativeTolerance(), mpDefaultParameters, and mpUserParameters.

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

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

Parameters:

sheetDimensions

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

Definition at line 854 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, GetCreateSheet(), GetSpaceDimension(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetSigmaForAdaptivity ( ) const

Returns:: value of sigma used in adaptivity

Definition at line 1801 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, IsAdaptivityParametersPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by AdaptiveTetrahedralMesh::CalculateErrorMetric(), AdaptiveBidomainProblem::GetSigma(), SetGradationForAdaptivity(), SetMaxEdgeLengthForAdaptivity(), SetMaxNodesForAdaptivity(), SetMinEdgeLengthForAdaptivity(), SetNumberOfAdaptiveSweeps(), and SetTargetErrorForAdaptivity().

double HeartConfig::GetSimulationDuration ( ) const

Returns:: duration of the simulation (ms)

Definition at line 620 of file HeartConfig.cpp.

References DecideLocation(), IsSimulationDefined(), mpDefaultParameters, and mpUserParameters.

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 836 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, GetCreateSlab(), GetSpaceDimension(), mpDefaultParameters, and mpUserParameters.

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

unsigned HeartConfig::GetSpaceDimension ( ) const

Returns:: space dimension 1, 2 or 3.

Definition at line 606 of file HeartConfig.cpp.

References DecideLocation(), IsSimulationDefined(), mpDefaultParameters, and mpUserParameters.

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

template<unsigned DIM>

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

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

Todo:

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

Parameters:

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

Todo:: There is no set method

Definition at line 938 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), EXCEPTION, mpDefaultParameters, mpUserParameters, 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 1626 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetTargetErrorForAdaptivity ( ) const

Returns:: value of target error used in adaptivity

Definition at line 1787 of file HeartConfig.cpp.

References DecideLocation(), EXCEPTION, IsAdaptivityParametersPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by AdaptiveTetrahedralMesh::CalculateErrorMetric(), AdaptiveBidomainProblem::GetTargetError(), SetGradationForAdaptivity(), SetMaxEdgeLengthForAdaptivity(), SetMaxNodesForAdaptivity(), SetMinEdgeLengthForAdaptivity(), SetNumberOfAdaptiveSweeps(), and SetSigmaForAdaptivity().

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 1968 of file HeartConfig.cpp.

References DecideLocation(), IsUpstrokeTimeMapsRequested(), mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::GetUseAbsoluteTolerance ( ) const

Returns:: true if we are using KSP absolute tolerance

Definition at line 1663 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::GetUseFixedNumberIterationsLinearSolver ( )

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

Definition at line 3273 of file HeartConfig.cpp.

References mUseFixedNumberIterations.

bool HeartConfig::GetUseMassLumping ( )

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

Definition at line 3242 of file HeartConfig.cpp.

References mUseMassLumping.

bool HeartConfig::GetUseMassLumpingForPrecond ( )

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

Definition at line 3252 of file HeartConfig.cpp.

References mUseMassLumpingForPrecond.

bool HeartConfig::GetUseReactionDiffusionOperatorSplitting ( )

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

Definition at line 3262 of file HeartConfig.cpp.

References mUseReactionDiffusionOperatorSplitting.

bool HeartConfig::GetUseRelativeTolerance ( ) const

Returns:: true if we are using KSP relative tolerance

Definition at line 1681 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::GetUseStateVariableInterpolation ( ) const

Returns:: true if state variable interpolation is used

Definition at line 3116 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

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

Get 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 319 of file HeartConfig.cpp.

References EXCEPTION.

Referenced by ReadFile().

unsigned HeartConfig::GetVisualizerOutputPrecision ( )

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

Definition at line 2182 of file HeartConfig.cpp.

References DecideLocation(), IsOutputVisualizerPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Write(), and Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Write().

bool HeartConfig::GetVisualizeWithCmgui ( ) const

Whether to convert the output from HDF5 to Cmgui readable format

Definition at line 2140 of file HeartConfig.cpp.

References DecideLocation(), IsOutputVisualizerPresent(), mpDefaultParameters, and mpUserParameters.

bool HeartConfig::GetVisualizeWithMeshalyzer ( ) const

Whether to convert the output from HDF5 to meshalyzer readable format

Definition at line 2126 of file HeartConfig.cpp.

References DecideLocation(), IsOutputVisualizerPresent(), mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::GetVisualizeWithParallelVtk ( ) const

Whether to convert the output from HDF5 to parallel Vtk readable format

Definition at line 2154 of file HeartConfig.cpp.

References DecideLocation(), IsOutputVisualizerPresent(), mpDefaultParameters, and mpUserParameters.

bool HeartConfig::GetVisualizeWithVtk ( ) const

Whether to convert the output from HDF5 to Vtk readable format

Definition at line 2168 of file HeartConfig.cpp.

References DecideLocation(), IsOutputVisualizerPresent(), mpDefaultParameters, and mpUserParameters.

bool HeartConfig::HasDrugDose ( ) const

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

Definition at line 3145 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

HeartConfig * HeartConfig::Instance ( ) [static]

Call this method to access the global parameters holder.

Returns:: a single instance of the class

Definition at line 164 of file HeartConfig.cpp.

References mpInstance.

bool HeartConfig::IsAdaptivityParametersPresent ( ) const

Returns:: true if there is an adaptivity section

Definition at line 1770 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by GetGradationForAdaptivity(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMinEdgeLengthForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetSigmaForAdaptivity(), GetTargetErrorForAdaptivity(), and SetAdaptivityParameters().

bool HeartConfig::IsAnyNodalTimeTraceRequested ( ) const

Returns:: true if any nodal time trace is requested

Definition at line 2045 of file HeartConfig.cpp.

References DecideLocation(), IsPostProcessingSectionPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by GetNodalTimeTraceRequested(), and IsPostProcessingRequested().

bool HeartConfig::IsApdMapsRequested ( ) const

Returns:: true if APD maps have been requested

Definition at line 1927 of file HeartConfig.cpp.

References DecideLocation(), IsPostProcessingSectionPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by GetApdMaps(), and IsPostProcessingRequested().

bool HeartConfig::IsConductionVelocityMapsRequested ( ) const

Returns:: true if conduction velocity maps have been requested

Definition at line 2016 of file HeartConfig.cpp.

References DecideLocation(), IsPostProcessingSectionPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by GetConductionVelocityMaps(), and IsPostProcessingRequested().

bool HeartConfig::IsElectrodesPresent ( ) const

Returns:: true if there is an electrodes section

Definition at line 2197 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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 1986 of file HeartConfig.cpp.

References DecideLocation(), IsPostProcessingSectionPresent(), mpDefaultParameters, and mpUserParameters.

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 765 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::IsOutputVisualizerPresent ( ) const

Whether there is an OutputVisualizer element present.

Definition at line 2107 of file HeartConfig.cpp.

References CheckSimulationIsDefined(), DecideLocation(), mpDefaultParameters, and mpUserParameters.

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 1911 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 1889 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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 2075 of file HeartConfig.cpp.

References DecideLocation(), IsPostProcessingSectionPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by IsPostProcessingRequested().

bool HeartConfig::IsSimulationDefined ( ) const

Returns whether the configuration file defines a new simulation.

Returns:: is a new simulation?

Definition at line 564 of file HeartConfig.cpp.

References mpUserParameters.

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

bool HeartConfig::IsSimulationResumed ( ) const

Returns whether the configuration file resumes an archived simulation.

Returns:: is a resumed simulation?

Definition at line 569 of file HeartConfig.cpp.

References mpUserParameters.

Referenced by CheckSimulationIsDefined().

bool HeartConfig::IsUpstrokeTimeMapsRequested ( ) const

Returns:: true if upstroke time maps have been requested

Definition at line 1958 of file HeartConfig.cpp.

References DecideLocation(), IsPostProcessingSectionPresent(), mpDefaultParameters, and mpUserParameters.

Referenced by GetUpstrokeTimeMaps(), and IsPostProcessingRequested().

template<class Archive >

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

Un-archive the object.

Parameters:

	archive
	version

Definition at line 111 of file HeartConfig.hpp.

References ArchiveLocationInfo::GetArchiveDirectory(), Instance(), mpUserParameters, SetCheckpointSimulation(), SetDefaultsFile(), SetParametersFile(), and UpdateParametersFromResumeSimulation().

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

Definition at line 364 of file HeartConfig.cpp.

References XmlTransforms::CheckForIluPreconditioner(), XmlTools::EscapeSpaces(), EXCEPTION, GetVersionFromNamespace(), mpDefaultParameters, mpUserParameters, mSchemaLocations, mUseFixedSchemaLocation, XmlTools::ReadXmlFile(), XmlTools::SetNamespace(), XmlTransforms::TransformArchiveDirectory(), and XmlTransforms::TransformIonicModelDefinitions().

Referenced by SetDefaultsFile(), and SetParametersFile().

void HeartConfig::Reset ( ) [static]

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

Definition at line 556 of file HeartConfig.cpp.

References mpInstance.

Referenced by CardiacSimulation::ReadParametersFromFile(), and CardiacElectroMechanicsProblem< 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 1621 of file HeartConfig.cpp.

References mBathIdentifiers.

Referenced by 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 1616 of file HeartConfig.cpp.

References mTissueIdentifiers.

Referenced by HeartRegionCode::GetValidTissueId().

template<class Archive >

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

Archive the object.

Parameters:

	archive
	version

Definition at line 94 of file HeartConfig.hpp.

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

void HeartConfig::SetAdaptivityParameters	(	double	targetError,
		double	sigma,
		double	maxEdgeLength,
		double	minEdgeLength,
		double	gradation,
		unsigned	maxNodes,
		unsigned	numSweeps
	)

Set the parameters to be used during mesh adaptation.

Parameters:

	targetError	is the target error passed to the adaptivity library
	sigma	is the value of sigma passed to the adaptivity library
	maxEdgeLength	is the maximum edge length permitted in the adapted mesh
	minEdgeLength	is the minimum edge length permitted in the adapted mesh
	gradation	is the value of gradation passed to the adaptivity library
	maxNodes	is the maximum number of nodes permitted in the adapted mesh
	numSweeps	is the number of adaptive sweeps through the mesh performed by the adaptivity library

Definition at line 2775 of file HeartConfig.cpp.

References EXCEPTION, IsAdaptivityParametersPresent(), and mpUserParameters.

Referenced by SetGradationForAdaptivity(), SetMaxEdgeLengthForAdaptivity(), SetMaxNodesForAdaptivity(), SetMinEdgeLengthForAdaptivity(), SetNumberOfAdaptiveSweeps(), SetSigmaForAdaptivity(), and SetTargetErrorForAdaptivity().

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 2886 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

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 2532 of file HeartConfig.cpp.

References mpUserParameters.

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 2538 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 2577 of file HeartConfig.cpp.

References mpUserParameters.

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 2448 of file HeartConfig.cpp.

References CheckTimeSteps(), and mpUserParameters.

Referenced by load(), 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 2943 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

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 2316 of file HeartConfig.cpp.

References mpUserParameters.

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

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

Parameters:

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

Definition at line 2364 of file HeartConfig.cpp.

References mpUserParameters.

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 2233 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetDefaultSchemaLocations ( ) [private]

Set default schema locations in the Chaste source tree.

Definition at line 304 of file HeartConfig.cpp.

References ChasteBuildInfo::GetRootDir(), and mSchemaLocations.

Referenced by HeartConfig().

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

Allows users to override the built-in defaults.

Parameters:

rFileName

The name of the defaults file

Definition at line 210 of file HeartConfig.cpp.

References CheckTimeSteps(), mpDefaultParameters, mpUserParameters, and ReadFile().

Referenced by load().

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 2228 of file HeartConfig.cpp.

References mpUserParameters.

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 3169 of file HeartConfig.cpp.

References mpUserParameters.

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 3044 of file HeartConfig.cpp.

References IsElectrodesPresent(), and mpUserParameters.

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

1D version

Parameters:

rExtraConductivities

DIM-vector of extracellular conductivities (mS/cm)

Definition at line 2523 of file HeartConfig.cpp.

References mpUserParameters.

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

2D version

Parameters:

rExtraConductivities

DIM-vector of extracellular conductivities (mS/cm)

Definition at line 2513 of file HeartConfig.cpp.

References mpUserParameters.

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

3D version

Parameters:

rExtraConductivities

DIM-vector of extracellular conductivities (mS/cm)

Definition at line 2502 of file HeartConfig.cpp.

References mpUserParameters.

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 2265 of file HeartConfig.cpp.

References mpUserParameters.

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 353 of file HeartConfig.cpp.

References mSchemaLocations, and SetUseFixedSchemaLocation().

void HeartConfig::SetGradationForAdaptivity ( double gradation )

Set the gradation to be used during mesh adaptation.

Parameters:

gradation

is the gradation passed to the adaptivity library

Definition at line 2853 of file HeartConfig.cpp.

References GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMinEdgeLengthForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetSigmaForAdaptivity(), GetTargetErrorForAdaptivity(), and SetAdaptivityParameters().

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 3203 of file HeartConfig.cpp.

References mpUserParameters, and SetDrugDose().

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

1D version

Parameters:

rIntraConductivities

DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2493 of file HeartConfig.cpp.

References mpUserParameters.

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

2D version

Parameters:

rIntraConductivities

DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2483 of file HeartConfig.cpp.

References mpUserParameters.

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

3D version

Parameters:

rIntraConductivities

DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2472 of file HeartConfig.cpp.

References mpUserParameters.

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 2289 of file HeartConfig.cpp.

References mpUserParameters.

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 2696 of file HeartConfig.cpp.

References EXCEPTION, and mpUserParameters.

void HeartConfig::SetKSPSolver ( const char * kspSolver )

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

Parameters:

kspSolver

a string from {"gmres", "cg", "symmlq"}

Definition at line 2669 of file HeartConfig.cpp.

References EXCEPTION, and mpUserParameters.

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

void HeartConfig::SetMaxEdgeLengthForAdaptivity ( double maxEdgeLength )

Set the maximum edge length to be used during mesh adaptation.

Parameters:

maxEdgeLength

is the maximum edge length permitted in the adapted mesh

Definition at line 2831 of file HeartConfig.cpp.

References GetGradationForAdaptivity(), GetMaxNodesForAdaptivity(), GetMinEdgeLengthForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetSigmaForAdaptivity(), GetTargetErrorForAdaptivity(), and SetAdaptivityParameters().

void HeartConfig::SetMaxNodesForAdaptivity ( unsigned maxNodes )

Set the maximum number of nodes to be used during mesh adaptation.

Parameters:

maxNodes

is the maximum number of nodes permitted in the adapted mesh

Definition at line 2864 of file HeartConfig.cpp.

References GetGradationForAdaptivity(), GetMaxEdgeLengthForAdaptivity(), GetMinEdgeLengthForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetSigmaForAdaptivity(), GetTargetErrorForAdaptivity(), and SetAdaptivityParameters().

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 2922 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

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 2277 of file HeartConfig.cpp.

References mpUserParameters.

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 2748 of file HeartConfig.cpp.

References EXCEPTION, and mpUserParameters.

void HeartConfig::SetMinEdgeLengthForAdaptivity ( double minEdgeLength )

Set the minimum edge length to be used during mesh adaptation.

Parameters:

minEdgeLength

is the minimum edge length permitted in the adapted mesh

Definition at line 2842 of file HeartConfig.cpp.

References GetGradationForAdaptivity(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetSigmaForAdaptivity(), GetTargetErrorForAdaptivity(), and SetAdaptivityParameters().

void HeartConfig::SetNumberOfAdaptiveSweeps ( unsigned numSweeps )

Set the number of adaptive sweeps to be used during mesh adaptation.

Parameters:

numSweeps

is the number of adaptive sweeps through the mesh performed by the adaptivity library

Definition at line 2875 of file HeartConfig.cpp.

References GetGradationForAdaptivity(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMinEdgeLengthForAdaptivity(), GetSigmaForAdaptivity(), GetTargetErrorForAdaptivity(), and SetAdaptivityParameters().

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

Set the configuration to use ode, pde and printing times of given values Calls CheckTimeSteps to ensure compatibility

Parameters:

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

Definition at line 2585 of file HeartConfig.cpp.

References CheckTimeSteps(), and mpUserParameters.

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 of given value Calls CheckTimeSteps via SetOdePdeAndPrintingTimeSteps

Parameters:

odeTimeStep

the value to use

Definition at line 2593 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 2412 of file HeartConfig.cpp.

References mpUserParameters.

Referenced by CardiacElectroMechanicsProblem< DIM >::CardiacElectroMechanicsProblem(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), CardiacElectroMechanicsProblem< 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 2417 of file HeartConfig.cpp.

References mpUserParameters.

Referenced by CardiacElectroMechanicsProblem< 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 2442 of file HeartConfig.cpp.

References mpUserParameters.

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

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

Parameters:

rOutputVariables

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

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

Definition at line 2422 of file HeartConfig.cpp.

References mpUserParameters.

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

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

Parameters:

rFileName

The name of the parameters file

Definition at line 434 of file HeartConfig.cpp.

References RelativeTo::AbsoluteOrCwd, CheckTimeSteps(), mParametersFilePath, mpUserParameters, ReadFile(), and FileFinder::SetPath().

Referenced by load(), and 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 2598 of file HeartConfig.cpp.

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

void HeartConfig::SetPrintingTimeStep ( double printingTimeStep )

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

Parameters:

printingTimeStep

the value to use

Definition at line 2603 of file HeartConfig.cpp.

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

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

template<unsigned SPACE_DIM>

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

Set the parameters for pseudo-ECG calculation.

Parameters:

rPseudoEcgElectrodePositions

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

Definition at line 2976 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

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

Sets the requested nodes for extrapolation of the time trace. 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 2959 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

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 2253 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetSigmaForAdaptivity ( double sigma )

Set the value of sigma to be used during mesh adaptation.

Parameters:

sigma

is the value of sigma passed to the adaptivity library

Definition at line 2820 of file HeartConfig.cpp.

References GetGradationForAdaptivity(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMinEdgeLengthForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetTargetErrorForAdaptivity(), and SetAdaptivityParameters().

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 2222 of file HeartConfig.cpp.

References mpUserParameters.

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 2241 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetSpaceDimension ( unsigned spaceDimension )

Set the configuration dimension

Parameters:

spaceDimension

1, 2 or 3.

Definition at line 2217 of file HeartConfig.cpp.

References mpUserParameters.

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 2571 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetTargetErrorForAdaptivity ( double targetError )

Set the target error to be used during mesh adaptation.

Parameters:

targetError

is the target error passed to the adaptivity library

Definition at line 2809 of file HeartConfig.cpp.

References GetGradationForAdaptivity(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMinEdgeLengthForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetSigmaForAdaptivity(), and SetAdaptivityParameters().

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

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

Parameters:

	tissueIds	set of identifiers
	bathIds	set of identifiers

Definition at line 2550 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 2904 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

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 2661 of file HeartConfig.cpp.

References mpUserParameters.

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 3267 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 359 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 3237 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 3247 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 3257 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 2653 of file HeartConfig.cpp.

References mpUserParameters.

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 3131 of file HeartConfig.cpp.

References mpUserParameters.

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 3036 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

void HeartConfig::SetVisualizeWithCmgui ( bool useCmgui = true )

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

Parameters:

useCmgui

Definition at line 3012 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

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 3004 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

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 3028 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

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 3020 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

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 447 of file HeartConfig.cpp.

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

Referenced by load().

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 223 of file HeartConfig.cpp.

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

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 86 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 1342 of file HeartConfig.hpp.

Referenced by GetBathConductivity(), and SetBathMultipleConductivities().

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

Mesh region identifiers to be considered as Bath

Definition at line 1352 of file HeartConfig.hpp.

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

double HeartConfig::mEndoFraction [private]

Fraction of endocardial layer

Definition at line 1296 of file HeartConfig.hpp.

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

double HeartConfig::mEpiFraction [private]

Fraction of epicardial layer

Definition at line 1291 of file HeartConfig.hpp.

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

unsigned HeartConfig::mEvaluateNumItsEveryNSolves [private]

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

Definition at line 1364 of file HeartConfig.hpp.

Referenced by GetEvaluateNumItsEveryNSolves(), and SetUseFixedNumberIterationsLinearSolver().

unsigned HeartConfig::mIndexEndo [private]

Order index in which the endocardial heterogeneities are supplied

Definition at line 1316 of file HeartConfig.hpp.

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

unsigned HeartConfig::mIndexEpi [private]

Order index in which the epicardial heterogeneities are supplied

Definition at line 1311 of file HeartConfig.hpp.

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

unsigned HeartConfig::mIndexMid [private]

Order index in which the midmyocardial heterogeneities are supplied

Definition at line 1306 of file HeartConfig.hpp.

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

double HeartConfig::mMidFraction [private]

Fraction of midmyocardial layer

Definition at line 1301 of file HeartConfig.hpp.

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

FileFinder HeartConfig::mParametersFilePath [private]

Where the user parameters were read from.

Definition at line 1280 of file HeartConfig.hpp.

Referenced by GetParametersFilePath(), and SetParametersFile().

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

Pointer to parameters read from the default input XML file (to be read before mpUserParameters, but may be subsequently overridden).

Definition at line 1272 of file HeartConfig.hpp.

Referenced by GetAbsoluteTolerance(), GetApdMaps(), GetBathConductivity(), GetCapacitance(), GetCellHeterogeneities(), GetCheckpointSimulation(), GetCheckpointTimestep(), GetConductionVelocityMaps(), GetConductivityHeterogeneities(), GetConductivityHeterogeneitiesProvided(), GetConductivityMedia(), GetCreateFibre(), GetCreateMesh(), GetCreateSheet(), GetCreateSlab(), GetDefaultIonicModel(), GetDomain(), GetDrugDose(), GetExtracellularConductivities(), GetFibreLength(), GetGradationForAdaptivity(), GetIc50Values(), GetInterNodeSpace(), GetIntracellularConductivities(), GetIonicModelRegions(), GetKSPPreconditioner(), GetKSPSolver(), GetLoadMesh(), GetMaxCheckpointsOnDisk(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMaxUpstrokeVelocityMaps(), GetMeshName(), GetMeshPartitioning(), GetMinEdgeLengthForAdaptivity(), GetNodalTimeTraceRequested(), GetNumberOfAdaptiveSweeps(), GetOdeTimeStep(), GetOutputDirectory(), GetOutputFilenamePrefix(), GetOutputUsingOriginalNodeOrdering(), GetOutputVariables(), GetOutputVariablesProvided(), GetPdeTimeStep(), GetPrintingTimeStep(), GetPseudoEcgElectrodePositions(), GetRelativeTolerance(), GetSheetDimensions(), GetSigmaForAdaptivity(), GetSimulationDuration(), GetSlabDimensions(), GetSpaceDimension(), GetStimuli(), GetSurfaceAreaToVolumeRatio(), GetTargetErrorForAdaptivity(), GetUpstrokeTimeMaps(), GetUseAbsoluteTolerance(), GetUseRelativeTolerance(), GetUseStateVariableInterpolation(), GetVisualizerOutputPrecision(), GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithParallelVtk(), GetVisualizeWithVtk(), HasDrugDose(), HeartConfig(), IsAdaptivityParametersPresent(), IsAnyNodalTimeTraceRequested(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), IsElectrodesPresent(), IsMaxUpstrokeVelocityMapRequested(), IsMeshProvided(), IsOutputVisualizerPresent(), IsPostProcessingSectionPresent(), IsPseudoEcgCalculationRequested(), IsUpstrokeTimeMapsRequested(), ReadFile(), SetDefaultsFile(), and Write().

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

The single instance of the class

Definition at line 1275 of file HeartConfig.hpp.

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

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

Pointer to parameters read from the user's input XML file (override those given by mpDefaultParameters).

Definition at line 1267 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(), GetGradationForAdaptivity(), GetIc50Values(), GetInterNodeSpace(), GetIntracellularConductivities(), GetIonicModelRegions(), GetKSPPreconditioner(), GetKSPSolver(), GetLoadMesh(), GetMaxCheckpointsOnDisk(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMaxUpstrokeVelocityMaps(), GetMeshName(), GetMeshPartitioning(), GetMinEdgeLengthForAdaptivity(), GetNodalTimeTraceRequested(), GetNumberOfAdaptiveSweeps(), GetOdeTimeStep(), GetOutputDirectory(), GetOutputFilenamePrefix(), GetOutputUsingOriginalNodeOrdering(), GetOutputVariables(), GetOutputVariablesProvided(), GetPdeTimeStep(), GetPrintingTimeStep(), GetPseudoEcgElectrodePositions(), GetRelativeTolerance(), GetSheetDimensions(), GetSigmaForAdaptivity(), GetSimulationDuration(), GetSlabDimensions(), GetSpaceDimension(), GetStimuli(), GetSurfaceAreaToVolumeRatio(), GetTargetErrorForAdaptivity(), GetUpstrokeTimeMaps(), GetUseAbsoluteTolerance(), GetUseRelativeTolerance(), GetUseStateVariableInterpolation(), GetVisualizerOutputPrecision(), GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithParallelVtk(), GetVisualizeWithVtk(), HasDrugDose(), HeartConfig(), IsAdaptivityParametersPresent(), IsAnyNodalTimeTraceRequested(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), IsElectrodesPresent(), IsMaxUpstrokeVelocityMapRequested(), IsMeshProvided(), IsOutputVisualizerPresent(), IsPostProcessingSectionPresent(), IsPseudoEcgCalculationRequested(), IsSimulationDefined(), IsSimulationResumed(), IsUpstrokeTimeMapsRequested(), load(), ReadFile(), SetAdaptivityParameters(), SetApdMaps(), SetBathConductivity(), SetCapacitance(), SetCheckpointSimulation(), SetConductionVelocityMaps(), SetConductivityHeterogeneities(), SetConductivityHeterogeneitiesEllipsoid(), SetDefaultIonicModel(), SetDefaultsFile(), SetDomain(), SetDrugDose(), SetElectrodeParameters(), SetExtracellularConductivities(), SetFibreLength(), SetIc50Value(), SetIntracellularConductivities(), SetIonicModelRegions(), SetKSPPreconditioner(), SetKSPSolver(), SetMaxUpstrokeVelocityMaps(), SetMeshFileName(), SetMeshPartitioning(), SetOdePdeAndPrintingTimeSteps(), SetOutputDirectory(), SetOutputFilenamePrefix(), SetOutputUsingOriginalNodeOrdering(), SetOutputVariables(), SetParametersFile(), SetPseudoEcgElectrodePositions(), 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 168 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 1347 of file HeartConfig.hpp.

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

bool HeartConfig::mUseFixedNumberIterations [private]

Whether to use a fixed number of iterations for the linear solver

Definition at line 1357 of file HeartConfig.hpp.

Referenced by GetUseFixedNumberIterationsLinearSolver(), and SetUseFixedNumberIterationsLinearSolver().

bool HeartConfig::mUseFixedSchemaLocation [private]

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 1286 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 1326 of file HeartConfig.hpp.

Referenced by GetUseMassLumping(), and SetUseMassLumping().

bool HeartConfig::mUseMassLumpingForPrecond [private]

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

Definition at line 1331 of file HeartConfig.hpp.

Referenced by GetUseMassLumpingForPrecond(), and SetUseMassLumpingForPrecond().

bool HeartConfig::mUserAskedForCellularTransmuralHeterogeneities [private]

Flag to check whether the user asked for cellular transmural heterogeneities