HeartConfig Class Reference

#include <HeartConfig.hpp>

Collaboration diagram for HeartConfig:

Public Types
typedef std::map< std::string, std::string >	SchemaLocationsMap
Public Member Functions
void	SetUseFixedSchemaLocation (bool useFixedSchemaLocation)
void	SetFixedSchemaLocations (const SchemaLocationsMap &rSchemaLocations)
void	SetDefaultsFile (const std::string &rFileName)
void	SetParametersFile (const std::string &rFileName)
void	Write (bool useArchiveLocationInfo=false, std::string subfolderName="output")
boost::shared_ptr < cp::chaste_parameters_type >	ReadFile (const std::string &rFileName)
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< SimpleStimulus > > &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)
bool	GetConductivityHeterogeneitiesProvided () const
bool	AreCellularTransmuralHeterogeneitiesRequested ()
bool	AreCellularlHeterogeneitiesSpecifiedByCuboids ()
double	GetEpiLayerFraction ()
double	GetEndoLayerFraction ()
double	GetMidLayerFraction ()
unsigned	GetEpiLayerIndex ()
unsigned	GetEndoLayerIndex ()
unsigned	GetMidLayerIndex ()
template<unsigned DIM>
void	GetConductivityHeterogeneities (std::vector< ChasteCuboid< 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 > &outputVariables) const
bool	GetCheckpointSimulation () const
double	GetCheckpointTimestep () const
unsigned	GetMaxCheckpointsOnDisk () const
std::string	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
bool	IsPostProcessingRequested () const
bool	IsApdMapsRequested () const
void	GetApdMaps (std::vector< std::pair< double, double > > &apdMaps) const
bool	IsUpstrokeTimeMapsRequested () const
void	GetUpstrokeTimeMaps (std::vector< double > &upstrokeTimeMaps) const
bool	IsMaxUpstrokeVelocityMapRequested () const
void	GetMaxUpstrokeVelocityMaps (std::vector< double > &upstrokeVelocityMaps) const
bool	IsConductionVelocityMapsRequested () const
void	GetConductionVelocityMaps (std::vector< unsigned > &conductionVelocityMaps) const
bool	IsOutputVisualizerPresent () const
bool	GetVisualizeWithMeshalyzer () const
bool	GetVisualizeWithCmgui () const
bool	GetVisualizeWithVtk () 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 > > &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	SetCheckpointSimulation (bool checkpointSimulation, double checkpointTimestep=-1.0, unsigned maxCheckpointsOnDisk=UINT_MAX)
void	SetIntracellularConductivities (const c_vector< double, 3 > &intraConductivities)
void	SetIntracellularConductivities (const c_vector< double, 2 > &intraConductivities)
void	SetIntracellularConductivities (const c_vector< double, 1 > &intraConductivities)
void	SetExtracellularConductivities (const c_vector< double, 3 > &extraConductivities)
void	SetExtracellularConductivities (const c_vector< double, 2 > &extraConductivities)
void	SetExtracellularConductivities (const c_vector< double, 1 > &extraConductivities)
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 > > &apdMaps)
void	SetUpstrokeTimeMaps (std::vector< double > &upstrokeTimeMaps)
void	SetMaxUpstrokeVelocityMaps (std::vector< double > &maxUpstrokeVelocityMaps)
void	SetConductionVelocityMaps (std::vector< unsigned > &conductionVelocityMaps)
void	EnsureOutputVisualizerExists (void)
void	SetVisualizeWithMeshalyzer (bool useMeshalyzer=true)
void	SetVisualizeWithCmgui (bool useCmgui=true)
void	SetVisualizeWithVtk (bool useVtk=true)
	~HeartConfig ()
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)
xsd::cxx::xml::dom::auto_ptr < xercesc::DOMDocument >	ReadFileToDomDocument (const std::string &rFileName,::xml_schema::error_handler &rErrorHandler, const ::xml_schema::properties &rProps)
void	SetDefaultSchemaLocations ()
std::string	EscapeSpaces (const std::string &rPath)
xercesc::DOMElement *	AddNamespace (xercesc::DOMDocument pDocument, xercesc::DOMElement pElement, const std::string &rNamespace)
xercesc::DOMElement *	AddNamespace (xercesc::DOMDocument pDocument, xercesc::DOMElement pElement, const XMLCh *pNamespace)
void	TransformIonicModelDefinitions (xercesc::DOMDocument pDocument, xercesc::DOMElement pRootElement)
void	WrapContentInElement (xercesc::DOMDocument pDocument, xercesc::DOMElement pElement, const XMLCh *pNewElementLocalName)
template<class TYPE >
TYPE *	DecideLocation (TYPE params_ptr, TYPE defaults_ptr, const std::string &nameParameter) 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 68 of file HeartConfig.hpp.

Member Typedef Documentation

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

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

Definition at line 184 of file HeartConfig.hpp.

Constructor & Destructor Documentation

HeartConfig::~HeartConfig ( )

Destructor

Definition at line 134 of file HeartConfig.cpp.

Member Function Documentation

xercesc::DOMElement * HeartConfig::AddNamespace	(	xercesc::DOMDocument *	pDocument,
		xercesc::DOMElement *	pElement,
		const XMLCh *	pNamespace
	)			`[private]`

Fake having a namespace in older configuration files, by adding a namespace to each element in a tree.

Based on http://wiki.codesynthesis.com/Tree/FAQ#How_do_I_parse_an_XML_document_that_is_missing_namespace_information.3F

Parameters:

	pDocument	the DOM document containing the tree to be transformed
	pElement	the root of the tree to be transformed
	pNamespace	the namespace to put elements in

Definition at line 2491 of file HeartConfig.cpp.

References AddNamespace().

xercesc::DOMElement * HeartConfig::AddNamespace	(	xercesc::DOMDocument *	pDocument,
		xercesc::DOMElement *	pElement,
		const std::string &	rNamespace
	)			`[private]`

Fake having a namespace in older configuration files, by adding a namespace to each element in a tree.

Based on http://wiki.codesynthesis.com/Tree/FAQ#How_do_I_parse_an_XML_document_that_is_missing_namespace_information.3F

Parameters:

	pDocument	the DOM document containing the tree to be transformed
	pElement	the root of the tree to be transformed
	rNamespace	the namespace to put elements in

Definition at line 2513 of file HeartConfig.cpp.

Referenced by AddNamespace(), and ReadFile().

bool HeartConfig::AreCellularlHeterogeneitiesSpecifiedByCuboids ( )

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

Definition at line 860 of file HeartConfig.cpp.

References mUserAskedForCuboidsForCellularHeterogeneities.

bool HeartConfig::AreCellularTransmuralHeterogeneitiesRequested ( )

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

Definition at line 855 of file HeartConfig.cpp.

References mUserAskedForCellularTransmuralHeterogeneities.

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

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

Throws and exception if not.

Parameters:

callingMethod

string describing the get method performing the check.

Definition at line 364 of file HeartConfig.cpp.

References IsSimulationDefined().

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

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

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

Throws and exception if not.

Parameters:

callingMethod

string describing the get method performing the check.

Definition at line 356 of file HeartConfig.cpp.

References IsSimulationResumed().

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

void HeartConfig::CheckTimeSteps ( ) const [private]

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

Definition at line 1994 of file HeartConfig.cpp.

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

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

template<class TYPE >

TYPE * HeartConfig::DecideLocation	(	TYPE *	params_ptr,
		TYPE *	defaults_ptr,
		const std::string &	nameParameter
	)			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)
	nameParameter	Name of quatity within params_ptr/defaults_ptr (so we can throw a meaningful exception if it's not found)

Definition at line 343 of file HeartConfig.cpp.

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(), GetOutputVariables(), GetOutputVariablesProvided(), GetPdeTimeStep(), GetPrintingTimeStep(), GetRelativeTolerance(), GetSheetDimensions(), GetSigmaForAdaptivity(), GetSimulationDuration(), GetSlabDimensions(), GetSpaceDimension(), GetStimuli(), GetSurfaceAreaToVolumeRatio(), GetTargetErrorForAdaptivity(), GetUpstrokeTimeMaps(), GetUseAbsoluteTolerance(), GetUseRelativeTolerance(), GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithVtk(), IsAdaptivityParametersPresent(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), IsMaxUpstrokeVelocityMapRequested(), IsMeshProvided(), IsOutputVisualizerPresent(), IsPostProcessingSectionPresent(), and IsUpstrokeTimeMapsRequested().

void HeartConfig::EnsureOutputVisualizerExists ( void )

Create the OutputVisualizer element if it doesn't exist

Definition at line 2321 of file HeartConfig.cpp.

References IsOutputVisualizerPresent(), and mpUserParameters.

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

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 214 of file HeartConfig.cpp.

Referenced by ReadFile(), and Write().

double HeartConfig::GetAbsoluteTolerance ( ) const

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

Definition at line 1268 of file HeartConfig.cpp.

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

Referenced by AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::DisplayRun(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

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

Parameters:

apdMaps

each entry is a request for a map with

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

Definition at line 1507 of file HeartConfig.cpp.

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

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

std::string HeartConfig::GetArchivedSimulationDir ( ) const

Get directory where the archived simulation to resume is defined

Definition at line 1120 of file HeartConfig.cpp.

References CheckResumeSimulationIsDefined(), and mpUserParameters.

double HeartConfig::GetBathConductivity ( ) const

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

Definition at line 1216 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetCapacitance ( ) const

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

Definition at line 1232 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), MonodomainMatrixBasedAssembler< ELEMENT_DIM, SPACE_DIM >::ConstructVectorForMatrixBasedRhsAssembly(), BidomainWithBathMatrixBasedAssembler< ELEMENT_DIM, SPACE_DIM >::ConstructVectorForMatrixBasedRhsAssembly(), and BidomainMatrixBasedAssembler< ELEMENT_DIM, SPACE_DIM >::ConstructVectorForMatrixBasedRhsAssembly().

template<unsigned DIM>

void HeartConfig::GetCellHeterogeneities	(	std::vector< AbstractChasteRegion< DIM > * > &	rCellHeterogeneityRegions,
		std::vector< double > &	rScaleFactorGks,
		std::vector< double > &	rScaleFactorIto,
		std::vector< double > &	rScaleFactorGkr
	)			`[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

Todo:: There is no set method

Definition at line 722 of file HeartConfig.cpp.

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

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

bool HeartConfig::GetCheckpointSimulation ( ) const

Get whether simulation should be checkpointed or not

Returns:: archive simulation

Definition at line 1057 of file HeartConfig.cpp.

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

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

double HeartConfig::GetCheckpointTimestep ( ) const

Get checkpointing timestep

Returns:: checkpointing timestep

Definition at line 1083 of file HeartConfig.cpp.

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

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

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

Parameters:

conductionVelocityMaps

each entry is a request for a map with

an index to treat as ths source for wave propagation

Definition at line 1596 of file HeartConfig.cpp.

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

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

template<unsigned DIM>

void HeartConfig::GetConductivityHeterogeneities	(	std::vector< ChasteCuboid< 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 912 of file HeartConfig.cpp.

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

Referenced by BidomainPde< SPACE_DIM >::CreateExtracellularConductivityTensors(), and AbstractCardiacPde< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor().

bool HeartConfig::GetConductivityHeterogeneitiesProvided ( ) const

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

Definition at line 895 of file HeartConfig.cpp.

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

Referenced by BidomainPde< SPACE_DIM >::CreateExtracellularConductivityTensors(), and AbstractCardiacPde< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor().

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 650 of file HeartConfig.cpp.

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

Referenced by BidomainPde< SPACE_DIM >::CreateExtracellularConductivityTensors(), and AbstractCardiacPde< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor().

bool HeartConfig::GetCreateFibre ( ) const

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

Definition at line 538 of file HeartConfig.cpp.

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

Referenced by GetFibreLength().

bool HeartConfig::GetCreateMesh ( ) const

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

Definition at line 505 of file HeartConfig.cpp.

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

Referenced by GetInterNodeSpace().

bool HeartConfig::GetCreateSheet ( ) const

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

Definition at line 527 of file HeartConfig.cpp.

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

Referenced by GetSheetDimensions().

bool HeartConfig::GetCreateSlab ( ) const

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

Definition at line 516 of file HeartConfig.cpp.

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

Referenced by GetSlabDimensions().

cp::ionic_model_selection_type HeartConfig::GetDefaultIonicModel ( ) const

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

Returns:: type of model

Definition at line 414 of file HeartConfig.cpp.

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

cp::domain_type HeartConfig::GetDomain ( ) const

domain_type is an xsd convenience class type

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

Definition at line 400 of file HeartConfig.cpp.

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

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

double HeartConfig::GetEndoLayerFraction ( )

Returns:: the fraction of endocardial layer

Definition at line 870 of file HeartConfig.cpp.

References mEndoFraction.

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

unsigned HeartConfig::GetEndoLayerIndex ( )

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

Definition at line 885 of file HeartConfig.cpp.

References mIndexEndo.

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

double HeartConfig::GetEpiLayerFraction ( )

Returns:: the fraction of epicardial layer

Definition at line 865 of file HeartConfig.cpp.

References mEpiFraction.

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

unsigned HeartConfig::GetEpiLayerIndex ( )

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

Definition at line 880 of file HeartConfig.cpp.

References mIndexEpi.

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

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

1D version

Parameters:

extraConductivities

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

Definition at line 1205 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

2D version

Parameters:

extraConductivities

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

Definition at line 1190 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 1172 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

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

Parameters:

fibreLength

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

Definition at line 594 of file HeartConfig.cpp.

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

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

double HeartConfig::GetGradationForAdaptivity ( ) const

Returns:: value of gradation used in adaptivity

Definition at line 1419 of file HeartConfig.cpp.

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

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

double HeartConfig::GetInterNodeSpace ( ) const

Returns:: internode space of cuboid mesh (cm)

Definition at line 611 of file HeartConfig.cpp.

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

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

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

1D version

Parameters:

intraConductivities

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

Definition at line 1161 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

2D version

Parameters:

intraConductivities

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

Definition at line 1146 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

3D version

Parameters:

intraConductivities

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

Definition at line 1128 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

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). 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 424 of file HeartConfig.cpp.

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

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

const char * HeartConfig::GetKSPPreconditioner ( ) const

Returns:: name of -pc_type from {"ilu", "jacobi", "bjacobi", "hypre", "none"}

Definition at line 1315 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

const char * HeartConfig::GetKSPSolver ( ) const

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

Definition at line 1297 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

bool HeartConfig::GetLoadMesh ( ) const

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

Definition at line 550 of file HeartConfig.cpp.

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

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

unsigned HeartConfig::GetMaxCheckpointsOnDisk ( ) const

Get number of checkpoints to keep on disk

Returns:: checkpointing timestep

Definition at line 1101 of file HeartConfig.cpp.

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

Referenced by CardiacSimulation::CreateResumeXmlFile().

double HeartConfig::GetMaxEdgeLengthForAdaptivity ( ) const

Returns:: maximum edge length in mesh after an adapt

Definition at line 1391 of file HeartConfig.cpp.

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

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

unsigned HeartConfig::GetMaxNodesForAdaptivity ( ) const

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

Definition at line 1433 of file HeartConfig.cpp.

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

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

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

Parameters:

upstrokeVelocityMaps

each entry is a request for a map with

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

Definition at line 1567 of file HeartConfig.cpp.

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

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

std::string HeartConfig::GetMeshName ( ) const

Returns:: path/basename of mesh files

Definition at line 640 of file HeartConfig.cpp.

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

Referenced by BidomainPde< SPACE_DIM >::CreateExtracellularConductivityTensors(), AbstractCardiacPde< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), and HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas().

double HeartConfig::GetMidLayerFraction ( )

Returns:: the fraction of endocardial layer

Definition at line 875 of file HeartConfig.cpp.

References mMidFraction.

unsigned HeartConfig::GetMidLayerIndex ( )

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

Definition at line 890 of file HeartConfig.cpp.

References mIndexMid.

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

double HeartConfig::GetMinEdgeLengthForAdaptivity ( ) const

Returns:: minimum edge length in mesh after an adapt

Definition at line 1405 of file HeartConfig.cpp.

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

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

unsigned HeartConfig::GetNumberOfAdaptiveSweeps ( ) const

Returns:: number of adaptive sweeps through mesh during adaptivity

Definition at line 1447 of file HeartConfig.cpp.

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

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

double HeartConfig::GetOdeTimeStep ( ) const

Returns:: ODE time-step (ms)

Definition at line 1240 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

std::string HeartConfig::GetOutputDirectory ( ) const

Returns:: output directory path name

Definition at line 1005 of file HeartConfig.cpp.

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

Referenced by 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(), 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 1013 of file HeartConfig.cpp.

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

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

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

Get the extra output variables from the xml file

Parameters:

outputVariables

reference to std::vector to contain the output variables requested

Definition at line 1038 of file HeartConfig.cpp.

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

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

bool HeartConfig::GetOutputVariablesProvided ( ) const

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

Definition at line 1021 of file HeartConfig.cpp.

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

double HeartConfig::GetPdeTimeStep ( ) const

Returns:: PDE time-step (ms)

Definition at line 1247 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 1254 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

double HeartConfig::GetRelativeTolerance ( ) const

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

Definition at line 1286 of file HeartConfig.cpp.

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

Referenced by AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::DisplayRun(), and BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve().

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

Parameters:

sheetDimensions

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

Definition at line 577 of file HeartConfig.cpp.

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

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

double HeartConfig::GetSigmaForAdaptivity ( ) const

Returns:: value of sigma used in adaptivity

Definition at line 1377 of file HeartConfig.cpp.

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

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

double HeartConfig::GetSimulationDuration ( ) const

Returns:: duration of the simulation (ms)

Definition at line 386 of file HeartConfig.cpp.

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

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

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 559 of file HeartConfig.cpp.

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

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

unsigned HeartConfig::GetSpaceDimension ( ) const

Returns:: space dimension 1, 2 or 3.

Definition at line 372 of file HeartConfig.cpp.

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

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

template<unsigned DIM>

void HeartConfig::GetStimuli	(	std::vector< boost::shared_ptr< SimpleStimulus > > &	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 661 of file HeartConfig.cpp.

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

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

double HeartConfig::GetSurfaceAreaToVolumeRatio ( ) const

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

Definition at line 1224 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

Referenced by MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeMatrixTerm(), MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::ComputeVectorTerm(), MonodomainMatrixBasedAssembler< ELEMENT_DIM, SPACE_DIM >::ConstructVectorForMatrixBasedRhsAssembly(), BidomainWithBathMatrixBasedAssembler< ELEMENT_DIM, SPACE_DIM >::ConstructVectorForMatrixBasedRhsAssembly(), and BidomainMatrixBasedAssembler< ELEMENT_DIM, SPACE_DIM >::ConstructVectorForMatrixBasedRhsAssembly().

double HeartConfig::GetTargetErrorForAdaptivity ( ) const

Returns:: value of target error used in adaptivity

Definition at line 1363 of file HeartConfig.cpp.

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

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

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

Parameters:

upstrokeTimeMaps

each entry is a request for a map with

a threshold (in mV)

Definition at line 1537 of file HeartConfig.cpp.

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

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

bool HeartConfig::GetUseAbsoluteTolerance ( ) const

Returns:: true if we are using KSP absolute tolerance

Definition at line 1261 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::GetUseRelativeTolerance ( ) const

Returns:: true if we are using KSP relative tolerance

Definition at line 1279 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::GetVisualizeWithCmgui ( ) const

Whether to convert the output from HDF5 to Cmgui readable format

Definition at line 1651 of file HeartConfig.cpp.

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

bool HeartConfig::GetVisualizeWithMeshalyzer ( ) const

Whether to convert the output from HDF5 to meshalyzer readable format

Definition at line 1637 of file HeartConfig.cpp.

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

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

bool HeartConfig::GetVisualizeWithVtk ( ) const

Whether to convert the output from HDF5 to Vtk readable format

Definition at line 1665 of file HeartConfig.cpp.

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

HeartConfig * HeartConfig::Instance ( ) [static]

Call this method to access the global parameters holder.

Returns:: a single instance of the class

Definition at line 100 of file HeartConfig.cpp.

References mpInstance.

bool HeartConfig::IsAdaptivityParametersPresent ( ) const

Returns:: true if there is an adaptivity section

Definition at line 1346 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::IsApdMapsRequested ( ) const

Returns:: true if APD maps have been requested

Definition at line 1496 of file HeartConfig.cpp.

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

Referenced by GetApdMaps(), and IsPostProcessingRequested().

bool HeartConfig::IsConductionVelocityMapsRequested ( ) const

Returns:: true if conduction velocity maps have been requested

Definition at line 1585 of file HeartConfig.cpp.

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

Referenced by GetConductionVelocityMaps(), and IsPostProcessingRequested().

bool HeartConfig::IsMaxUpstrokeVelocityMapRequested ( ) const

Returns:: true maximum upstroke velocity maps have been requested

Definition at line 1555 of file HeartConfig.cpp.

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

Referenced by GetMaxUpstrokeVelocityMaps(), and IsPostProcessingRequested().

bool HeartConfig::IsMeshProvided ( ) const

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

Definition at line 488 of file HeartConfig.cpp.

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

Referenced by BidomainPde< SPACE_DIM >::CreateExtracellularConductivityTensors(), and AbstractCardiacPde< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor().

bool HeartConfig::IsOutputVisualizerPresent ( ) const

Whether there is an OutputVisualizer element present.

Definition at line 1618 of file HeartConfig.cpp.

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

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

bool HeartConfig::IsPostProcessingRequested ( ) const

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

Definition at line 1482 of file HeartConfig.cpp.

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

bool HeartConfig::IsPostProcessingSectionPresent ( ) const

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

Definition at line 1465 of file HeartConfig.cpp.

References DecideLocation(), mpDefaultParameters, and mpUserParameters.

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

bool HeartConfig::IsSimulationDefined ( ) const

Returns whether the configuration file defines a new simulation.

Returns:: is a new simulation?

Definition at line 331 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 336 of file HeartConfig.cpp.

References mpUserParameters.

Referenced by CheckSimulationIsDefined().

bool HeartConfig::IsUpstrokeTimeMapsRequested ( ) const

Returns:: true if upstroke time maps have been requested

Definition at line 1527 of file HeartConfig.cpp.

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

Referenced by GetUpstrokeTimeMaps(), and IsPostProcessingRequested().

template<class Archive >

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

Un-archive the object.

Parameters:

	archive
	version

Definition at line 105 of file HeartConfig.hpp.

References ArchiveLocationInfo::GetArchiveDirectory(), GetDomain(), GetSpaceDimension(), Instance(), mpUserParameters, SetCheckpointSimulation(), SetDefaultsFile(), SetParametersFile(), SetSimulationDuration(), SetVisualizeWithCmgui(), SetVisualizeWithMeshalyzer(), and SetVisualizeWithVtk().

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 231 of file HeartConfig.cpp.

References AddNamespace(), EscapeSpaces(), mpDefaultParameters, mpUserParameters, mSchemaLocations, mUseFixedSchemaLocation, ReadFileToDomDocument(), and TransformIonicModelDefinitions().

Referenced by SetDefaultsFile(), and SetParametersFile().

xsd::cxx::xml::dom::auto_ptr< xercesc::DOMDocument > HeartConfig::ReadFileToDomDocument	(	const std::string &	rFileName,
		::xml_schema::error_handler &	rErrorHandler,
		const ::xml_schema::properties &	rProps
	)			`[private]`

Read an XML file into a DOM document. Useful for figuring out what version of the parameters file we're dealing with, so we can construct the right version of the object model.

Based on http://wiki.codesynthesis.com/Tree/FAQ#How_do_I_parse_an_XML_document_to_a_Xerces-C.2B.2B_DOM_document.3F

Requires the Xerces runtime to have been initialised.

Parameters:

	rFileName	the file to read
	rErrorHandler	handler for any parsing errors
	rProps	properties that specify fixed schema locations, if wanted

Definition at line 2379 of file HeartConfig.cpp.

Referenced by ReadFile().

void HeartConfig::Reset ( ) [static]

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

Definition at line 323 of file HeartConfig.cpp.

References mpInstance.

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

template<class Archive >

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

Archive the object.

Parameters:

	archive
	version

Definition at line 88 of file HeartConfig.hpp.

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

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

Set the parameters to be used during mesh adaptation.

Parameters:

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

Definition at line 2136 of file HeartConfig.cpp.

References IsAdaptivityParametersPresent(), and mpUserParameters.

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

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

Set the parameters of the apd map requested

Parameters:

apdMaps

each entry is a request for a map with

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

Definition at line 2248 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 1951 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 1963 of file HeartConfig.cpp.

References mpUserParameters.

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

Set whether the simulation should be checkpointed or not.

Parameters:

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

Definition at line 1868 of file HeartConfig.cpp.

References CheckTimeSteps(), and mpUserParameters.

Referenced by load().

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

Set the parameters of the conduction velocity map requested

Parameters:

conductionVelocityMaps

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

Definition at line 2302 of file HeartConfig.cpp.

References mpUserParameters.

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

Set a number of heterogeneous regions (Axis-aligned boxes) 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 1781 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). ionic_models_available_type is generated automatically from the XML Schema.

Parameters:

rIonicModel

type of model

Definition at line 1699 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetDefaultSchemaLocations ( ) [private]

Set default schema locations in the Chaste source tree.

Definition at line 192 of file HeartConfig.cpp.

References ChasteBuildInfo::GetRootDir(), and mSchemaLocations.

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

Parameters:

rFileName

The name of the default file - set by default to "ChasteDefaults.xml" on construction

Definition at line 138 of file HeartConfig.cpp.

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

Referenced by load().

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

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

Parameters:

rDomain

type of simulation bi- mono-domain

Definition at line 1694 of file HeartConfig.cpp.

References mpUserParameters.

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

1D version

Parameters:

extraConductivities

DIM-vector of extracellular conductivities (mS/cm)

Definition at line 1942 of file HeartConfig.cpp.

References mpUserParameters.

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

2D version

Parameters:

extraConductivities

DIM-vector of extracellular conductivities (mS/cm)

Definition at line 1932 of file HeartConfig.cpp.

References mpUserParameters.

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

3D version

Parameters:

extraConductivities

DIM-vector of extracellular conductivities (mS/cm)

Definition at line 1921 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 1731 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetFixedSchemaLocations ( const SchemaLocationsMap & rSchemaLocations )

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

Parameters:

rSchemaLocations

map from namespace URI to schema URI

Definition at line 203 of file HeartConfig.cpp.

References mSchemaLocations, and SetUseFixedSchemaLocation().

void HeartConfig::SetGradationForAdaptivity ( double gradation )

Set the gradation to be used during mesh adaptation.

Parameters:

gradation

is the gradation passed to the adaptivity library

Definition at line 2215 of file HeartConfig.cpp.

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

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

1D version

Parameters:

intraConductivities

DIM-vector of intracellular conductivities (mS/cm)

Definition at line 1912 of file HeartConfig.cpp.

References mpUserParameters.

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

2D version

Parameters:

intraConductivities

DIM-vector of intracellular conductivities (mS/cm)

Definition at line 1902 of file HeartConfig.cpp.

References mpUserParameters.

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

3D version

Parameters:

intraConductivities

DIM-vector of intracellular conductivities (mS/cm)

Definition at line 1891 of file HeartConfig.cpp.

References mpUserParameters.

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

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. 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 1755 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetKSPPreconditioner ( const char * kspPreconditioner )

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

Parameters:

kspPreconditioner

a string from {"ilu", "jacobi", "bjacobi", "hypre", "blockdiagonal", "none"}

Definition at line 2084 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 2062 of file HeartConfig.cpp.

References mpUserParameters.

Referenced by BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::FinaliseAssembleSystem().

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 2193 of file HeartConfig.cpp.

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

void HeartConfig::SetMaxNodesForAdaptivity ( unsigned maxNodes )

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

Parameters:

maxNodes

is the maximum number of nodes permitted in the adapted mesh

Definition at line 2226 of file HeartConfig.cpp.

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

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

Set the parameters of the maximal upstroke velocity map requested

Parameters:

maxUpstrokeVelocityMaps

is the list of thresholds (? ///

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

Definition at line 2282 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 1743 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetMinEdgeLengthForAdaptivity ( double minEdgeLength )

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

Parameters:

minEdgeLength

is the minimum edge length permitted in the adapted mesh

Definition at line 2204 of file HeartConfig.cpp.

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

void HeartConfig::SetNumberOfAdaptiveSweeps ( unsigned numSweeps )

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

Parameters:

numSweeps

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

Definition at line 2237 of file HeartConfig.cpp.

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

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

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

Parameters:

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

Definition at line 1971 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 1979 of file HeartConfig.cpp.

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

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

Parameters:

rOutputDirectory

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

Definition at line 1830 of file HeartConfig.cpp.

References mpUserParameters.

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

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 1835 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.

Definition at line 1840 of file HeartConfig.cpp.

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

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 315 of file HeartConfig.cpp.

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

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

void HeartConfig::SetPdeTimeStep ( double pdeTimeStep )

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

Parameters:

pdeTimeStep

the value to use

Definition at line 1984 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 1989 of file HeartConfig.cpp.

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

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 1719 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetSigmaForAdaptivity ( double sigma )

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

Parameters:

sigma

is the value of sigma passed to the adaptivity library

Definition at line 2182 of file HeartConfig.cpp.

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

void HeartConfig::SetSimulationDuration ( double simulationDuration )

Set the configuration simulation duration

Parameters:

simulationDuration

duration of the simulation (ms)

Definition at line 1688 of file HeartConfig.cpp.

References mpUserParameters.

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

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 1707 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetSpaceDimension ( unsigned spaceDimension )

Set the configuration dimension

Parameters:

spaceDimension

1, 2 or 3.

Definition at line 1683 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 1957 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetTargetErrorForAdaptivity ( double targetError )

Set the target error to be used during mesh adaptation.

Parameters:

targetError

is the target error passed to the adaptivity library

Definition at line 2171 of file HeartConfig.cpp.

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

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

Set the parameters of the upstroke time map requested

Parameters:

upstrokeTimeMaps

is the list of thresholds (? ///

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

Definition at line 2265 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 2055 of file HeartConfig.cpp.

References mpUserParameters.

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 209 of file HeartConfig.cpp.

References mUseFixedSchemaLocation.

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

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 2048 of file HeartConfig.cpp.

References mpUserParameters.

void HeartConfig::SetVisualizeWithCmgui ( bool useCmgui = true )

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

Parameters:

useCmgui

Definition at line 2338 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

Referenced by load(), and SetOutputVariables().

void HeartConfig::SetVisualizeWithMeshalyzer ( bool useMeshalyzer = true )

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

Parameters:

useMeshalyzer

Definition at line 2330 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

Referenced by load(), and SetOutputVariables().

void HeartConfig::SetVisualizeWithVtk ( bool useVtk = true )

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

Parameters:

useVtk

Definition at line 2346 of file HeartConfig.cpp.

References EnsureOutputVisualizerExists(), and mpUserParameters.

Referenced by load(), and SetOutputVariables().

void HeartConfig::TransformIonicModelDefinitions	(	xercesc::DOMDocument *	pDocument,
		xercesc::DOMElement *	pRootElement
	)			`[private]`

Backwards compatibility transformation method: edits the DOM tree to wrap ionic model definitions from old (release 1 or 1.1) configuration files in a 'Hardcoded' element.

Parameters:

	pDocument	the DOM document containing the tree to be transformed
	pRootElement	the root of the tree to be transformed

Definition at line 2561 of file HeartConfig.cpp.

References WrapContentInElement().

Referenced by ReadFile().

void HeartConfig::WrapContentInElement	(	xercesc::DOMDocument *	pDocument,
		xercesc::DOMElement *	pElement,
		const XMLCh *	pNewElementLocalName
	)			`[private]`

Used by TransformIonicModelDefinitions to do the actual wrapping of an element's content.

Parameters:

	pDocument	the DOM document containing the tree to be transformed
	pElement	the element whose content is to be wrapped
	pNewElementLocalName	the local name (i.e. without namespace prefix) of the wrapping element (the namespace of pElement will be used).

Definition at line 2591 of file HeartConfig.cpp.

Referenced by TransformIonicModelDefinitions().

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 151 of file HeartConfig.cpp.

References PetscTools::AmMaster(), EscapeSpaces(), ArchiveLocationInfo::GetArchiveDirectory(), GetOutputDirectory(), OutputFileHandler::GetOutputDirectoryFullPath(), ChasteBuildInfo::GetRootDir(), mpDefaultParameters, and mpUserParameters.

Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), and CardiacElectroMechanicsProblem< DIM >::Solve().

Friends And Related Function Documentation

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

Needed for serialization.

Definition at line 80 of file HeartConfig.hpp.

Member Data Documentation

double HeartConfig::mEndoFraction [private]

Fraction of endocardial layer

Definition at line 1066 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), and GetEndoLayerFraction().

double HeartConfig::mEpiFraction [private]

Fraction of epicardial layer

Definition at line 1061 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), and GetEpiLayerFraction().

unsigned HeartConfig::mIndexEndo [private]

Order index in which the endocardial heterogeneities are supplied

Definition at line 1086 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), and GetEndoLayerIndex().

unsigned HeartConfig::mIndexEpi [private]

Order index in which the epicardial heterogeneities are supplied

Definition at line 1081 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), and GetEpiLayerIndex().

unsigned HeartConfig::mIndexMid [private]

Order index in which the midmyocardial heterogeneities are supplied

Definition at line 1076 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), and GetMidLayerIndex().

double HeartConfig::mMidFraction [private]

Fraction of midmyocardial layer

Definition at line 1071 of file HeartConfig.hpp.

Referenced by GetCellHeterogeneities(), and GetMidLayerFraction().

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 1047 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(), GetOutputVariables(), GetOutputVariablesProvided(), GetPdeTimeStep(), GetPrintingTimeStep(), GetRelativeTolerance(), GetSheetDimensions(), GetSigmaForAdaptivity(), GetSimulationDuration(), GetSlabDimensions(), GetSpaceDimension(), GetStimuli(), GetSurfaceAreaToVolumeRatio(), GetTargetErrorForAdaptivity(), GetUpstrokeTimeMaps(), GetUseAbsoluteTolerance(), GetUseRelativeTolerance(), GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithVtk(), IsAdaptivityParametersPresent(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), 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 1050 of file HeartConfig.hpp.

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

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

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

Definition at line 1043 of file HeartConfig.hpp.

Referenced by EnsureOutputVisualizerExists(), GetAbsoluteTolerance(), GetApdMaps(), GetArchivedSimulationDir(), 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(), GetOutputVariables(), GetOutputVariablesProvided(), GetPdeTimeStep(), GetPrintingTimeStep(), GetRelativeTolerance(), GetSheetDimensions(), GetSigmaForAdaptivity(), GetSimulationDuration(), GetSlabDimensions(), GetSpaceDimension(), GetStimuli(), GetSurfaceAreaToVolumeRatio(), GetTargetErrorForAdaptivity(), GetUpstrokeTimeMaps(), GetUseAbsoluteTolerance(), GetUseRelativeTolerance(), GetVisualizeWithCmgui(), GetVisualizeWithMeshalyzer(), GetVisualizeWithVtk(), IsAdaptivityParametersPresent(), IsApdMapsRequested(), IsConductionVelocityMapsRequested(), IsMaxUpstrokeVelocityMapRequested(), IsMeshProvided(), IsOutputVisualizerPresent(), IsPostProcessingSectionPresent(), IsSimulationDefined(), IsSimulationResumed(), IsUpstrokeTimeMapsRequested(), load(), ReadFile(), SetAdaptivityParameters(), SetApdMaps(), SetBathConductivity(), SetCapacitance(), SetCheckpointSimulation(), SetConductionVelocityMaps(), SetConductivityHeterogeneities(), SetDefaultIonicModel(), SetDefaultsFile(), SetDomain(), SetExtracellularConductivities(), SetFibreLength(), SetIntracellularConductivities(), SetIonicModelRegions(), SetKSPPreconditioner(), SetKSPSolver(), SetMaxUpstrokeVelocityMaps(), SetMeshFileName(), SetOdePdeAndPrintingTimeSteps(), SetOutputDirectory(), SetOutputFilenamePrefix(), SetOutputVariables(), SetParametersFile(), SetSheetDimensions(), SetSimulationDuration(), SetSlabDimensions(), SetSpaceDimension(), SetSurfaceAreaToVolumeRatio(), SetUpstrokeTimeMaps(), SetUseAbsoluteTolerance(), SetUseRelativeTolerance(), SetVisualizeWithCmgui(), SetVisualizeWithMeshalyzer(), SetVisualizeWithVtk(), and Write().

SchemaLocationsMap HeartConfig::mSchemaLocations [private]

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

Definition at line 190 of file HeartConfig.hpp.

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

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 1056 of file HeartConfig.hpp.

Referenced by ReadFile(), and SetUseFixedSchemaLocation().

bool HeartConfig::mUserAskedForCellularTransmuralHeterogeneities [private]

Flag to check whether the user asked for cellular transmural heterogeneities

Definition at line 1091 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 1096 of file HeartConfig.hpp.

Referenced by AreCellularlHeterogeneitiesSpecifiedByCuboids(), and GetCellHeterogeneities().

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