HeartConfig Class Reference

#include <HeartConfig.hpp>

Collaboration diagram for HeartConfig:

List of all members.

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)

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< ChasteCuboid< 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< ChasteCuboid< DIM > > &rStimulatedAreas) const

template<unsigned DIM>

void GetCellHeterogeneities (std::vector< 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 ()

bool AreCellularHeterogeneitiesSpecifiedByCuboids ()

double GetEpiLayerFraction ()

double GetEndoLayerFraction ()

double GetMidLayerFraction ()

unsigned GetEpiLayerIndex ()

unsigned GetEndoLayerIndex ()

unsigned GetMidLayerIndex ()

template<unsigned DIM>

void GetConductivityHeterogeneities (std::vector< 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 () const

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

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 IsOutputVisualizerPresent () const

bool GetVisualizeWithMeshalyzer () const

bool GetVisualizeWithCmgui () const

bool GetVisualizeWithVtk () const

bool IsElectrodesPresent () const

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 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 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 EnsureOutputVisualizerExists (void)

void SetVisualizeWithMeshalyzer (bool useMeshalyzer=true)

void SetVisualizeWithCmgui (bool useCmgui=true)

void SetVisualizeWithVtk (bool useVtk=true)

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

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

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 ()

std::string EscapeSpaces (const std::string &rPath)

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

bool mUseFixedSchemaLocation

double mEpiFraction

double mEndoFraction

double mMidFraction

unsigned mIndexMid

unsigned mIndexEpi

unsigned mIndexEndo

bool mUserAskedForCellularTransmuralHeterogeneities

bool mUserAskedForCuboidsForCellularHeterogeneities

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 76 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 164 of file HeartConfig.hpp.

Constructor & Destructor Documentation

HeartConfig::~HeartConfig ( )

Destructor

Definition at line 316 of file HeartConfig.cpp.

Member Function Documentation

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 2449 of file HeartConfig.cpp.

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

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

template<class Archive>

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

Archive the object.

Parameters:

	archive
	version

Definition at line 96 of file HeartConfig.hpp.

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

template<class Archive>

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

Un-archive the object.

Parameters:

	archive
	version

Definition at line 113 of file HeartConfig.hpp.

References ArchiveLocationInfo::GetArchiveDirectory(), Instance(), mpUserParameters, SetCheckpointSimulation(), SetDefaultsFile(), SetParametersFile(), and 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 574 of file HeartConfig.cpp.

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

Referenced by load().

void HeartConfig::SetDefaultSchemaLocations ( ) [private]

Set default schema locations in the Chaste source tree.

Definition at line 404 of file HeartConfig.cpp.

References ChasteBuildInfo::GetRootDir(), and mSchemaLocations.

std::string HeartConfig::EscapeSpaces ( const std::string & rPath ) [private]

Helper method for URL-escaping spaces in file paths, to avoid confusing Xerces regarding schema locations. Note that this is a very specific fix: it doesn't do general URL-escaping.

Parameters:

rPath

the path to escape

Definition at line 461 of file HeartConfig.cpp.

Referenced by ReadFile().

HeartConfig * HeartConfig::Instance ( ) [static]

Call this method to access the global parameters holder.

Returns:: a single instance of the class

Definition at line 283 of file HeartConfig.cpp.

References mpInstance.

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 456 of file HeartConfig.cpp.

References mUseFixedSchemaLocation.

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

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 450 of file HeartConfig.cpp.

References mSchemaLocations, and SetUseFixedSchemaLocation().

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 320 of file HeartConfig.cpp.

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

Referenced by load().

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 566 of file HeartConfig.cpp.

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

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

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 333 of file HeartConfig.cpp.

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

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter().

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 382 of file HeartConfig.cpp.

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

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

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 478 of file HeartConfig.cpp.

References XmlTransforms::CheckForIluPreconditioner(), EscapeSpaces(), EXCEPTION, GetVersionFromNamespace(), mpDefaultParameters, mpUserParameters, mSchemaLocations, mUseFixedSchemaLocation, XmlTools::ReadFileToDomDocument(), 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 682 of file HeartConfig.cpp.

References mpInstance.

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

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 416 of file HeartConfig.cpp.

References EXCEPTION.

Referenced by ReadFile().

bool HeartConfig::IsSimulationDefined ( ) const

Returns whether the configuration file defines a new simulation.

Returns:: is a new simulation?

Definition at line 690 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 695 of file HeartConfig.cpp.

References mpUserParameters.

Referenced by CheckSimulationIsDefined().

unsigned HeartConfig::GetSpaceDimension ( ) const

Returns:: space dimension 1, 2 or 3.

Definition at line 731 of file HeartConfig.cpp.

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

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

double HeartConfig::GetSimulationDuration ( ) const

Returns:: duration of the simulation (ms)

Definition at line 745 of file HeartConfig.cpp.

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

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

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 759 of file HeartConfig.cpp.

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

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

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 773 of file HeartConfig.cpp.

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

template<unsigned DIM>

void HeartConfig::GetIonicModelRegions	(	std::vector< ChasteCuboid< 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 783 of file HeartConfig.cpp.

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

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

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)

Todo:: will this break if the user parameters don't include an IonicModels element?

Definition at line 2156 of file HeartConfig.cpp.

References mpUserParameters.

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 847 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::GetCreateMesh ( ) const

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

Definition at line 864 of file HeartConfig.cpp.

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

Referenced by GetInterNodeSpace().

bool HeartConfig::GetCreateSlab ( ) const

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

Definition at line 875 of file HeartConfig.cpp.

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

Referenced by GetSlabDimensions().

bool HeartConfig::GetCreateSheet ( ) const

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

Definition at line 886 of file HeartConfig.cpp.

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

Referenced by GetSheetDimensions().

bool HeartConfig::GetCreateFibre ( ) const

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

Definition at line 897 of file HeartConfig.cpp.

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

Referenced by GetFibreLength().

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 909 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().

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

Todo:: IsMeshProvided and GetLoadMesh are subtly different but very similar. Can one of them go?

Parameters:

slabDimensions

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

Definition at line 918 of file HeartConfig.cpp.

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

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

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

Parameters:

sheetDimensions

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

Definition at line 936 of file HeartConfig.cpp.

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

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

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

Parameters:

fibreLength

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

Definition at line 953 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::GetInterNodeSpace ( ) const

Returns:: internode space of cuboid mesh (cm)

Definition at line 970 of file HeartConfig.cpp.

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

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

std::string HeartConfig::GetMeshName ( ) const

Returns:: path/basename of mesh files

Definition at line 1000 of file HeartConfig.cpp.

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

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

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 1010 of file HeartConfig.cpp.

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

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

template<unsigned DIM>

void HeartConfig::GetStimuli	(	std::vector< boost::shared_ptr< AbstractStimulusFunction > > &	rStimuliApplied,
		std::vector< ChasteCuboid< 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 1021 of file HeartConfig.cpp.

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

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

template<unsigned DIM>

void HeartConfig::GetCellHeterogeneities	(	std::vector< 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 1112 of file HeartConfig.cpp.

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

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

bool HeartConfig::GetConductivityHeterogeneitiesProvided ( ) const

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

Definition at line 1278 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::AreCellularTransmuralHeterogeneitiesRequested ( )

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

Definition at line 1238 of file HeartConfig.cpp.

References mUserAskedForCellularTransmuralHeterogeneities.

bool HeartConfig::AreCellularHeterogeneitiesSpecifiedByCuboids ( )

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

Definition at line 1243 of file HeartConfig.cpp.

References mUserAskedForCuboidsForCellularHeterogeneities.

double HeartConfig::GetEpiLayerFraction ( )

Returns:: the fraction of epicardial layer

Definition at line 1248 of file HeartConfig.cpp.

References mEpiFraction.

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

double HeartConfig::GetEndoLayerFraction ( )

Returns:: the fraction of endocardial layer

Definition at line 1253 of file HeartConfig.cpp.

References mEndoFraction.

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

double HeartConfig::GetMidLayerFraction ( )

Returns:: the fraction of endocardial layer

Definition at line 1258 of file HeartConfig.cpp.

References mMidFraction.

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 1263 of file HeartConfig.cpp.

References mIndexEpi.

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 1268 of file HeartConfig.cpp.

References mIndexEndo.

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

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 1273 of file HeartConfig.cpp.

References mIndexMid.

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

template<unsigned DIM>

void HeartConfig::GetConductivityHeterogeneities	(	std::vector< 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 1295 of file HeartConfig.cpp.

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

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

std::string HeartConfig::GetOutputDirectory ( ) const

Returns:: output directory path name

Definition at line 1369 of file HeartConfig.cpp.

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

Referenced by CardiacSimulation::CreateAndRun(), Hdf5ToCmguiConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToCmguiConverter(), Hdf5ToMeshalyzerConverter< ELEMENT_DIM, SPACE_DIM >::Hdf5ToMeshalyzerConverter(), 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 1377 of file HeartConfig.cpp.

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

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

bool HeartConfig::GetOutputVariablesProvided ( ) const

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

Definition at line 1385 of file HeartConfig.cpp.

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

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 1402 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::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 1421 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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 1436 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 1462 of file HeartConfig.cpp.

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

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

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 1480 of file HeartConfig.cpp.

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

Referenced by CardiacSimulation::CreateResumeXmlFile().

HeartFileFinder HeartConfig::GetArchivedSimulationDir ( ) const

Get directory where the archived simulation to resume is defined

Definition at line 1499 of file HeartConfig.cpp.

References CheckResumeSimulationIsDefined(), 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 1507 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

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

2D version

Parameters:

intraConductivities

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

Definition at line 1525 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

1D version

Parameters:

intraConductivities

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

Definition at line 1540 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 1551 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

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

2D version

Parameters:

extraConductivities

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

Definition at line 1569 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

1D version

Parameters:

extraConductivities

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

Definition at line 1584 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

double HeartConfig::GetBathConductivity ( ) const

Returns:: conductivity for perfusing bath (mS/cm)

Definition at line 1595 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetSurfaceAreaToVolumeRatio ( ) const

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

Definition at line 1603 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by MonodomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), MonodomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), AbstractCardiacCellInterface::GetIntracellularAreaStimulus(), MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

double HeartConfig::GetCapacitance ( ) const

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

Definition at line 1611 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by MonodomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), MonodomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), BidomainAssembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), CML_noble_varghese_kohl_noble_1998_basic_with_sac::GetIIonic(), MatrixBasedMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem(), and MatrixBasedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetupLinearSystem().

double HeartConfig::GetOdeTimeStep ( ) const

Returns:: ODE time-step (ms)

Definition at line 1619 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetPdeTimeStep ( ) const

Returns:: PDE time-step (ms)

Definition at line 1626 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetPrintingTimeStep ( ) const

Returns:: priting time-step (ms)

Definition at line 1633 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), CheckTimeSteps(), AbstractCvodeCell::Compute(), SetOdeTimeStep(), and SetPdeTimeStep().

bool HeartConfig::GetUseAbsoluteTolerance ( ) const

Returns:: true if we are using KSP absolute tolerance

Definition at line 1640 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetAbsoluteTolerance ( ) const

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

Definition at line 1647 of file HeartConfig.cpp.

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

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

bool HeartConfig::GetUseRelativeTolerance ( ) const

Returns:: true if we are using KSP relative tolerance

Definition at line 1658 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetRelativeTolerance ( ) const

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

Definition at line 1665 of file HeartConfig.cpp.

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

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

const char * HeartConfig::GetKSPSolver ( ) const

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

Definition at line 1676 of file HeartConfig.cpp.

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

const char * HeartConfig::GetKSPPreconditioner ( ) const

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

Definition at line 1694 of file HeartConfig.cpp.

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

bool HeartConfig::IsAdaptivityParametersPresent ( ) const

Returns:: true if there is an adaptivity section

Definition at line 1725 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetTargetErrorForAdaptivity ( ) const

Returns:: value of target error used in adaptivity

Definition at line 1742 of file HeartConfig.cpp.

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

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

double HeartConfig::GetSigmaForAdaptivity ( ) const

Returns:: value of sigma used in adaptivity

Definition at line 1756 of file HeartConfig.cpp.

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

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

double HeartConfig::GetMaxEdgeLengthForAdaptivity ( ) const

Returns:: maximum edge length in mesh after an adapt

Definition at line 1770 of file HeartConfig.cpp.

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

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

double HeartConfig::GetMinEdgeLengthForAdaptivity ( ) const

Returns:: minimum edge length in mesh after an adapt

Definition at line 1784 of file HeartConfig.cpp.

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

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

double HeartConfig::GetGradationForAdaptivity ( ) const

Returns:: value of gradation used in adaptivity

Definition at line 1798 of file HeartConfig.cpp.

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

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

unsigned HeartConfig::GetMaxNodesForAdaptivity ( ) const

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

Definition at line 1812 of file HeartConfig.cpp.

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

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

unsigned HeartConfig::GetNumberOfAdaptiveSweeps ( ) const

Returns:: number of adaptive sweeps through mesh during adaptivity

Definition at line 1826 of file HeartConfig.cpp.

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

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

bool HeartConfig::IsPostProcessingSectionPresent ( ) const

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

Definition at line 1844 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

void HeartConfig::EnsurePostProcessingSectionPresent ( )

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

Definition at line 1861 of file HeartConfig.cpp.

References mpUserParameters.

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

bool HeartConfig::IsPostProcessingRequested ( ) const

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

Definition at line 1866 of file HeartConfig.cpp.

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

bool HeartConfig::IsApdMapsRequested ( ) const

Returns:: true if APD maps have been requested

Definition at line 1880 of file HeartConfig.cpp.

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

Referenced by GetApdMaps(), and IsPostProcessingRequested().

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 1891 of file HeartConfig.cpp.

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

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

bool HeartConfig::IsUpstrokeTimeMapsRequested ( ) const

Returns:: true if upstroke time maps have been requested

Definition at line 1911 of file HeartConfig.cpp.

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

Referenced by GetUpstrokeTimeMaps(), and IsPostProcessingRequested().

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 1921 of file HeartConfig.cpp.

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

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

bool HeartConfig::IsMaxUpstrokeVelocityMapRequested ( ) const

Returns:: true maximum upstroke velocity maps have been requested

Definition at line 1939 of file HeartConfig.cpp.

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

Referenced by GetMaxUpstrokeVelocityMaps(), and IsPostProcessingRequested().

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 1951 of file HeartConfig.cpp.

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

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

bool HeartConfig::IsConductionVelocityMapsRequested ( ) const

Returns:: true if conduction velocity maps have been requested

Definition at line 1969 of file HeartConfig.cpp.

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

Referenced by GetConductionVelocityMaps(), and IsPostProcessingRequested().

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 1980 of file HeartConfig.cpp.

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

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

bool HeartConfig::IsOutputVisualizerPresent ( ) const

Whether there is an OutputVisualizer element present.

Definition at line 2002 of file HeartConfig.cpp.

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

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

bool HeartConfig::GetVisualizeWithMeshalyzer ( ) const

Whether to convert the output from HDF5 to meshalyzer readable format

Definition at line 2021 of file HeartConfig.cpp.

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

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

bool HeartConfig::GetVisualizeWithCmgui ( ) const

Whether to convert the output from HDF5 to Cmgui readable format

Definition at line 2035 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 2049 of file HeartConfig.cpp.

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

bool HeartConfig::IsElectrodesPresent ( ) const

Returns:: true if there is an electrodes section

Definition at line 2064 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by GetElectrodeParameters(), and SetElectrodeParameters().

void HeartConfig::SetSpaceDimension ( unsigned spaceDimension )

Set the configuration dimension

Parameters:

spaceDimension

1, 2 or 3.

Definition at line 2084 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetSimulationDuration ( double simulationDuration )

Set the configuration simulation duration

Parameters:

simulationDuration

duration of the simulation (ms)

Definition at line 2089 of file HeartConfig.cpp.

References mpUserParameters.

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

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 2095 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 2100 of file HeartConfig.cpp.

References mpUserParameters.

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 2108 of file HeartConfig.cpp.

References 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 2120 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 2132 of file HeartConfig.cpp.

References 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 2144 of file HeartConfig.cpp.

References 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 2182 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 2230 of file HeartConfig.cpp.

References mpUserParameters.

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

Parameters:

rOutputDirectory

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

Definition at line 2278 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 2283 of file HeartConfig.cpp.

References mpUserParameters.

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

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

Warning: when specifying output variables, you cannot convert the HDF5 output to Meshalyzer, Cmgui or VTK formats, since the converter will get confused by the presence of extra data. This method thus also turns off visualizer output if the provided vector is non-empty.

Todo:: #1596 is this no longer needed?

Definition at line 2288 of file HeartConfig.cpp.

References mpUserParameters, SetVisualizeWithCmgui(), SetVisualizeWithMeshalyzer(), and SetVisualizeWithVtk().

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 2317 of file HeartConfig.cpp.

References mpUserParameters.

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

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 2323 of file HeartConfig.cpp.

References CheckTimeSteps(), and mpUserParameters.

Referenced by load(), and UpdateParametersFromResumeSimulation().

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

3D version

Parameters:

rIntraConductivities

DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2346 of file HeartConfig.cpp.

References mpUserParameters.

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

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

2D version

Parameters:

rIntraConductivities

DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2357 of file HeartConfig.cpp.

References mpUserParameters.

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

1D version

Parameters:

rIntraConductivities

DIM-vector of intracellular conductivities (mS/cm)

Definition at line 2367 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 2376 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 2387 of file HeartConfig.cpp.

References mpUserParameters.

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

1D version

Parameters:

rExtraConductivities

DIM-vector of extracellular conductivities (mS/cm)

Definition at line 2397 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetBathConductivity ( double bathConductivity )

Set bath conductivity

Parameters:

bathConductivity

conductivity for perfusing bath (mS/cm)

Todo:: Is this used anywhere?

Definition at line 2406 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetSurfaceAreaToVolumeRatio ( double ratio )

Set surface area to volume ratio Am (for PDE)

Parameters:

ratio

(1/cm)

Definition at line 2412 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetCapacitance ( double capacitance )

Set surface capacitance Cm (for PDE)

Parameters:

capacitance

(uF/cm^2)

Definition at line 2418 of file HeartConfig.cpp.

References mpUserParameters.

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 2426 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 2434 of file HeartConfig.cpp.

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

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 2439 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 2444 of file HeartConfig.cpp.

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

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 2494 of file HeartConfig.cpp.

References 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 2502 of file HeartConfig.cpp.

References 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 2510 of file HeartConfig.cpp.

References EXCEPTION, and mpUserParameters.

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

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 2532 of file HeartConfig.cpp.

References EXCEPTION, and mpUserParameters.

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

Todo:: I think you can just do the 'if' clause regardless.

Definition at line 2584 of file HeartConfig.cpp.

References EXCEPTION, IsAdaptivityParametersPresent(), and mpUserParameters.

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

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 2620 of file HeartConfig.cpp.

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

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 2631 of file HeartConfig.cpp.

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

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 2642 of file HeartConfig.cpp.

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

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 2653 of file HeartConfig.cpp.

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

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 2664 of file HeartConfig.cpp.

References GetMaxEdgeLengthForAdaptivity(), 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 2675 of file HeartConfig.cpp.

References GetGradationForAdaptivity(), GetMaxEdgeLengthForAdaptivity(), GetMinEdgeLengthForAdaptivity(), 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 2686 of file HeartConfig.cpp.

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

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 2697 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

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

Set the parameters of the upstroke time map requested

Parameters:

rUpstrokeTimeMaps

is the list of thresholds (? ///

Todo:: improve the description of threshold) with respect to which the upstroke time maps are calculated.

Definition at line 2715 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

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

Set the parameters of the maximal upstroke velocity map requested

Parameters:

rMaxUpstrokeVelocityMaps

is the list of thresholds (? ///

Todo:: improve the description of threshold) with respect to which the upstroke velocity maps are calculated.

Definition at line 2733 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

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 2754 of file HeartConfig.cpp.

References EnsurePostProcessingSectionPresent(), and mpUserParameters.

void HeartConfig::EnsureOutputVisualizerExists ( void )

Create the OutputVisualizer element if it doesn't exist

Definition at line 2774 of file HeartConfig.cpp.

References mpUserParameters.

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

void HeartConfig::SetVisualizeWithMeshalyzer ( bool useMeshalyzer = true )

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

Parameters:

useMeshalyzer

Definition at line 2779 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

Referenced by SetOutputVariables(), and UpdateParametersFromResumeSimulation().

void HeartConfig::SetVisualizeWithCmgui ( bool useCmgui = true )

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

Parameters:

useCmgui

Definition at line 2787 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

Referenced by SetOutputVariables(), and UpdateParametersFromResumeSimulation().

void HeartConfig::SetVisualizeWithVtk ( bool useVtk = true )

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

Parameters:

useVtk

Definition at line 2795 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

Referenced by SetOutputVariables(), and UpdateParametersFromResumeSimulation().

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 2803 of file HeartConfig.cpp.

References IsElectrodesPresent(), and mpUserParameters.

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 2842 of file HeartConfig.cpp.

References EXCEPTION, IsElectrodesPresent(), and mpUserParameters.

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

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 702 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(), GetExtracellularConductivities(), GetFibreLength(), GetGradationForAdaptivity(), GetInterNodeSpace(), GetIntracellularConductivities(), GetIonicModelRegions(), GetKSPPreconditioner(), GetKSPSolver(), GetLoadMesh(), GetMaxCheckpointsOnDisk(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMaxUpstrokeVelocityMaps(), GetMeshName(), GetMinEdgeLengthForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetOdeTimeStep(), GetOutputDirectory(), GetOutputFilenamePrefix(), GetOutputUsingOriginalNodeOrdering(), GetOutputVariables(), GetOutputVariablesProvided(), GetPdeTimeStep(), GetPrintingTimeStep(), GetRelativeTolerance(), GetSheetDimensions(), GetSigmaForAdaptivity(), GetSimulationDuration(), GetSlabDimensions(), GetSpaceDimension(), GetStimuli(), GetSurfaceAreaToVolumeRatio(), GetTargetErrorForAdaptivity(), GetUpstrokeTimeMaps(), GetUseAbsoluteTolerance(), GetUseRelativeTolerance(), GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithVtk(), IsAdaptivityParametersPresent(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), IsElectrodesPresent(), IsMaxUpstrokeVelocityMapRequested(), IsMeshProvided(), IsOutputVisualizerPresent(), IsPostProcessingSectionPresent(), and IsUpstrokeTimeMapsRequested().

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 and exception if not.

Parameters:

callingMethod

string describing the get method performing the check.

Definition at line 715 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::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 and exception if not.

Parameters:

callingMethod

string describing the get method performing the check.

Definition at line 723 of file HeartConfig.cpp.

References EXCEPTION, and IsSimulationDefined().

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

Friends And Related Function Documentation

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

Needed for serialization.

Definition at line 88 of file HeartConfig.hpp.

Member Data Documentation

SchemaLocationsMap HeartConfig::mSchemaLocations [private]

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

Definition at line 170 of file HeartConfig.hpp.

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

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 1061 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(), GetElectrodeParameters(), GetExtracellularConductivities(), GetFibreLength(), GetGradationForAdaptivity(), GetInterNodeSpace(), GetIntracellularConductivities(), GetIonicModelRegions(), GetKSPPreconditioner(), GetKSPSolver(), GetLoadMesh(), GetMaxCheckpointsOnDisk(), GetMaxEdgeLengthForAdaptivity(), GetMaxNodesForAdaptivity(), GetMaxUpstrokeVelocityMaps(), GetMeshName(), GetMinEdgeLengthForAdaptivity(), GetNumberOfAdaptiveSweeps(), GetOdeTimeStep(), GetOutputDirectory(), GetOutputFilenamePrefix(), GetOutputUsingOriginalNodeOrdering(), GetOutputVariables(), GetOutputVariablesProvided(), GetPdeTimeStep(), GetPrintingTimeStep(), GetRelativeTolerance(), GetSheetDimensions(), GetSigmaForAdaptivity(), GetSimulationDuration(), GetSlabDimensions(), GetSpaceDimension(), GetStimuli(), GetSurfaceAreaToVolumeRatio(), GetTargetErrorForAdaptivity(), GetUpstrokeTimeMaps(), GetUseAbsoluteTolerance(), GetUseRelativeTolerance(), GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithVtk(), IsAdaptivityParametersPresent(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), IsElectrodesPresent(), IsMaxUpstrokeVelocityMapRequested(), IsMeshProvided(), IsOutputVisualizerPresent(), IsPostProcessingSectionPresent(), IsSimulationDefined(), IsSimulationResumed(), IsUpstrokeTimeMapsRequested(), load(), ReadFile(), SetAdaptivityParameters(), SetApdMaps(), SetBathConductivity(), SetCapacitance(), SetCheckpointSimulation(), SetConductionVelocityMaps(), SetConductivityHeterogeneities(), SetConductivityHeterogeneitiesEllipsoid(), SetDefaultIonicModel(), SetDefaultsFile(), SetDomain(), SetElectrodeParameters(), SetExtracellularConductivities(), SetFibreLength(), SetIntracellularConductivities(), SetIonicModelRegions(), SetKSPPreconditioner(), SetKSPSolver(), SetMaxUpstrokeVelocityMaps(), SetMeshFileName(), SetOdePdeAndPrintingTimeSteps(), SetOutputDirectory(), SetOutputFilenamePrefix(), SetOutputUsingOriginalNodeOrdering(), SetOutputVariables(), SetParametersFile(), SetSheetDimensions(), SetSimulationDuration(), SetSlabDimensions(), SetSpaceDimension(), SetSurfaceAreaToVolumeRatio(), SetUpstrokeTimeMaps(), SetUseAbsoluteTolerance(), SetUseRelativeTolerance(), SetVisualizeWithCmgui(), SetVisualizeWithMeshalyzer(), SetVisualizeWithVtk(), UpdateParametersFromResumeSimulation(), and Write().

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 1065 of file HeartConfig.hpp.

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

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

The single instance of the class

Definition at line 1068 of file HeartConfig.hpp.

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

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 1074 of file HeartConfig.hpp.

Referenced by ReadFile(), and SetUseFixedSchemaLocation().

double HeartConfig::mEpiFraction [private]

Fraction of epicardial layer

Definition at line 1079 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), and GetEpiLayerFraction().

double HeartConfig::mEndoFraction [private]

Fraction of endocardial layer

Definition at line 1084 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), and GetEndoLayerFraction().

double HeartConfig::mMidFraction [private]

Fraction of midmyocardial layer

Definition at line 1089 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), and GetMidLayerFraction().

unsigned HeartConfig::mIndexMid [private]

Order index in which the midmyocardial heterogeneities are supplied

Definition at line 1094 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), and GetMidLayerIndex().

unsigned HeartConfig::mIndexEpi [private]

Order index in which the epicardial heterogeneities are supplied

Definition at line 1099 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), and GetEpiLayerIndex().

unsigned HeartConfig::mIndexEndo [private]

Order index in which the endocardial heterogeneities are supplied

Definition at line 1104 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), and GetEndoLayerIndex().

bool HeartConfig::mUserAskedForCellularTransmuralHeterogeneities [private]

Flag to check whether the user asked for cellular transmural heterogeneities

Definition at line 1109 of file HeartConfig.hpp.

Referenced by AreCellularTransmuralHeterogeneitiesRequested(), and GetCellHeterogeneities().

bool HeartConfig::mUserAskedForCuboidsForCellularHeterogeneities [private]

Flag to check whether the user asked for cellular heterogeneities with cuboids

Definition at line 1114 of file HeartConfig.hpp.

Referenced by AreCellularHeterogeneitiesSpecifiedByCuboids(), and GetCellHeterogeneities().

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

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


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)
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< ChasteCuboid< 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< ChasteCuboid< DIM > > &rStimulatedAreas) const
template<unsigned DIM>
void	GetCellHeterogeneities (std::vector< 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 ()
bool	AreCellularHeterogeneitiesSpecifiedByCuboids ()
double	GetEpiLayerFraction ()
double	GetEndoLayerFraction ()
double	GetMidLayerFraction ()
unsigned	GetEpiLayerIndex ()
unsigned	GetEndoLayerIndex ()
unsigned	GetMidLayerIndex ()
template<unsigned DIM>
void	GetConductivityHeterogeneities (std::vector< 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 () const
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
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	IsOutputVisualizerPresent () const
bool	GetVisualizeWithMeshalyzer () const
bool	GetVisualizeWithCmgui () const
bool	GetVisualizeWithVtk () const
bool	IsElectrodesPresent () const
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	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	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	EnsureOutputVisualizerExists (void)
void	SetVisualizeWithMeshalyzer (bool useMeshalyzer=true)
void	SetVisualizeWithCmgui (bool useCmgui=true)
void	SetVisualizeWithVtk (bool useVtk=true)
void	SetElectrodeParameters (bool groundSecondElectrode, unsigned index, double magnitude, double startTime, double duration)
void	GetElectrodeParameters (bool &rGroundSecondElectrode, unsigned &rIndex, double &rMagnitude, double &rStartTime, double &rDuration)
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 ()
std::string	EscapeSpaces (const std::string &rPath)
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
bool	mUseFixedSchemaLocation
double	mEpiFraction
double	mEndoFraction
double	mMidFraction
unsigned	mIndexMid
unsigned	mIndexEpi
unsigned	mIndexEndo
bool	mUserAskedForCellularTransmuralHeterogeneities
bool	mUserAskedForCuboidsForCellularHeterogeneities
Static Private Attributes
static std::auto_ptr< HeartConfig >	mpInstance
Friends
class	boost::serialization::access
class	TestHeartConfig