File List

Here is a list of all documented files with brief descriptions:

[detail level 123456]

cell_based
src
cell
cycle
AbstractCellCycleModel.cpp
AbstractCellCycleModel.hpp
AbstractCellCycleModelOdeSolver.cpp
AbstractCellCycleModelOdeSolver.hpp
AbstractOdeBasedCellCycleModel.cpp
AbstractOdeBasedCellCycleModel.hpp
AbstractSimpleCellCycleModel.cpp
AbstractSimpleCellCycleModel.hpp
AbstractSimpleGenerationBasedCellCycleModel.cpp
AbstractSimpleGenerationBasedCellCycleModel.hpp
Alarcon2004OxygenBasedCellCycleModel.cpp
Alarcon2004OxygenBasedCellCycleModel.hpp
CellCycleModelOdeHandler.cpp
CellCycleModelOdeHandler.hpp
CellCycleModelOdeSolver.hpp
CellCycleModelOdeSolverExportWrapper.hpp
CellCyclePhases.hpp
ContactInhibitionCellCycleModel.cpp
ContactInhibitionCellCycleModel.hpp
ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.cpp
ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.hpp
FixedDurationGenerationBasedCellCycleModel.cpp
FixedDurationGenerationBasedCellCycleModel.hpp
GammaDistributedStochasticDurationCellCycleModel.cpp
GammaDistributedStochasticDurationCellCycleModel.hpp
SimpleOxygenBasedCellCycleModel.cpp
SimpleOxygenBasedCellCycleModel.hpp
StochasticDurationCellCycleModel.cpp
StochasticDurationCellCycleModel.hpp
StochasticDurationGenerationBasedCellCycleModel.cpp
StochasticDurationGenerationBasedCellCycleModel.hpp
StochasticOxygenBasedCellCycleModel.cpp
StochasticOxygenBasedCellCycleModel.hpp
TysonNovakCellCycleModel.cpp
TysonNovakCellCycleModel.hpp
properties
mutations
AbstractCellMutationState.cpp
AbstractCellMutationState.hpp
ApcOneHitCellMutationState.cpp
ApcOneHitCellMutationState.hpp
ApcTwoHitCellMutationState.cpp
ApcTwoHitCellMutationState.hpp
BetaCateninOneHitCellMutationState.cpp
BetaCateninOneHitCellMutationState.hpp
WildTypeCellMutationState.cpp
WildTypeCellMutationState.hpp
proliferative_types
AbstractCellProliferativeType.cpp
AbstractCellProliferativeType.hpp
DefaultCellProliferativeType.cpp
DefaultCellProliferativeType.hpp
DifferentiatedCellProliferativeType.cpp
DifferentiatedCellProliferativeType.hpp
StemCellProliferativeType.cpp
StemCellProliferativeType.hpp
TransitCellProliferativeType.cpp
TransitCellProliferativeType.hpp
AbstractCellProperty.cpp
AbstractCellProperty.hpp
ApoptoticCellProperty.cpp
ApoptoticCellProperty.hpp
CellAncestor.cpp
CellAncestor.hpp
CellData.cpp
CellData.hpp
CellId.cpp
CellId.hpp
CellLabel.cpp
CellLabel.hpp
CellPropertyCollection.cpp
CellPropertyCollection.hpp
CellPropertyRegistry.cpp
CellPropertyRegistry.hpp
CellVecData.cpp
CellVecData.hpp
srn
AbstractOdeSrnModel.cpp
AbstractOdeSrnModel.hpp
AbstractSrnModel.cpp
AbstractSrnModel.hpp
DeltaNotchSrnModel.cpp
DeltaNotchSrnModel.hpp
Goldbeter1991SrnModel.cpp
Goldbeter1991SrnModel.hpp
NullSrnModel.cpp
NullSrnModel.hpp
Cell.cpp
Cell.hpp
CellsGenerator.hpp
ParallelCellsGenerator.hpp
common
OdeLinearSystemSolver.cpp
OdeLinearSystemSolver.hpp
SimulationTime.cpp
SimulationTime.hpp
fortests
AbstractCellBasedTestSuite.hpp
AbstractCellBasedWithTimingsTestSuite.hpp
CheckReadyToDivideAndPhaseIsUpdated.hpp
mesh
PottsElement.cpp
PottsElement.hpp
PottsMesh.cpp
PottsMesh.hpp
PottsMeshGenerator.cpp
PottsMeshGenerator.hpp
PottsMeshReader.cpp
PottsMeshReader.hpp
PottsMeshWriter.cpp
PottsMeshWriter.hpp
odes
Alarcon2004OxygenBasedCellCycleOdeSystem.cpp
Alarcon2004OxygenBasedCellCycleOdeSystem.hpp
CellwiseOdeSystemInformation.hpp
DeltaNotchOdeSystem.cpp
DeltaNotchOdeSystem.hpp
Goldbeter1991OdeSystem.cpp
Goldbeter1991OdeSystem.hpp
TysonNovak2001OdeSystem.cpp
TysonNovak2001OdeSystem.hpp
population
boundary_conditions
AbstractCellPopulationBoundaryCondition.cpp
AbstractCellPopulationBoundaryCondition.hpp
PlaneBoundaryCondition.cpp
PlaneBoundaryCondition.hpp
SphereGeometryBoundaryCondition.cpp
SphereGeometryBoundaryCondition.hpp
division_rules
AbstractCaBasedDivisionRule.cpp
AbstractCaBasedDivisionRule.hpp
AbstractVertexBasedDivisionRule.cpp
AbstractVertexBasedDivisionRule.hpp
DiagonalVertexBasedDivisionRule.cpp
DiagonalVertexBasedDivisionRule.hpp
ExclusionCaBasedDivisionRule.cpp
ExclusionCaBasedDivisionRule.hpp
RandomDirectionVertexBasedDivisionRule.cpp
RandomDirectionVertexBasedDivisionRule.hpp
ShortAxisVertexBasedDivisionRule.cpp
ShortAxisVertexBasedDivisionRule.hpp
forces
AbstractForce.cpp
AbstractForce.hpp
AbstractTwoBodyInteractionForce.cpp
AbstractTwoBodyInteractionForce.hpp
BuskeAdhesiveForce.cpp
BuskeAdhesiveForce.hpp
BuskeCompressionForce.cpp
BuskeCompressionForce.hpp
BuskeElasticForce.cpp
BuskeElasticForce.hpp
ChemotacticForce.cpp
ChemotacticForce.hpp
DifferentialAdhesionGeneralisedLinearSpringForce.cpp
DifferentialAdhesionGeneralisedLinearSpringForce.hpp
DiffusionForce.cpp
DiffusionForce.hpp
DiscreteSystemForceCalculator.cpp
DiscreteSystemForceCalculator.hpp
FarhadifarForce.cpp
FarhadifarForce.hpp
GeneralisedLinearSpringForce.cpp
GeneralisedLinearSpringForce.hpp
NagaiHondaDifferentialAdhesionForce.cpp
NagaiHondaDifferentialAdhesionForce.hpp
NagaiHondaForce.cpp
NagaiHondaForce.hpp
RepulsionForce.cpp
RepulsionForce.hpp
WelikyOsterForce.cpp
WelikyOsterForce.hpp
killers
AbstractCellKiller.cpp
AbstractCellKiller.hpp
ApoptoticCellKiller.cpp
ApoptoticCellKiller.hpp
IsolatedLabelledCellKiller.cpp
IsolatedLabelledCellKiller.hpp
PlaneBasedCellKiller.cpp
PlaneBasedCellKiller.hpp
RandomCellKiller.cpp
RandomCellKiller.hpp
T2SwapCellKiller.cpp
T2SwapCellKiller.hpp
TargetedCellKiller.cpp
TargetedCellKiller.hpp
pdes
AveragedSourcePde.cpp
AveragedSourcePde.hpp
CellBasedPdeHandler.cpp
CellBasedPdeHandler.hpp
CellBasedPdeHandlerOnCuboid.cpp
CellBasedPdeHandlerOnCuboid.hpp
CellBasedPdeSolver.cpp
CellBasedPdeSolver.hpp
CellwiseSourcePde.cpp
CellwiseSourcePde.hpp
PdeAndBoundaryConditions.cpp
PdeAndBoundaryConditions.hpp
SimpleUniformSourcePde.cpp
SimpleUniformSourcePde.hpp
VolumeDependentAveragedSourcePde.cpp
VolumeDependentAveragedSourcePde.hpp
update_rules
AbstractCaSwitchingUpdateRule.cpp
AbstractCaSwitchingUpdateRule.hpp
AbstractCaUpdateRule.cpp
AbstractCaUpdateRule.hpp
AbstractPottsUpdateRule.cpp
AbstractPottsUpdateRule.hpp
AdhesionPottsUpdateRule.cpp
AdhesionPottsUpdateRule.hpp
ChemotaxisPottsUpdateRule.cpp
ChemotaxisPottsUpdateRule.hpp
DifferentialAdhesionPottsUpdateRule.cpp
DifferentialAdhesionPottsUpdateRule.hpp
DiffusionCaUpdateRule.cpp
DiffusionCaUpdateRule.hpp
RandomCaSwitchingUpdateRule.cpp
RandomCaSwitchingUpdateRule.hpp
SurfaceAreaConstraintPottsUpdateRule.cpp
SurfaceAreaConstraintPottsUpdateRule.hpp
VolumeConstraintPottsUpdateRule.cpp
VolumeConstraintPottsUpdateRule.hpp
AbstractCellPopulation.cpp
AbstractCellPopulation.hpp
AbstractCentreBasedCellPopulation.cpp
AbstractCentreBasedCellPopulation.hpp
AbstractOffLatticeCellPopulation.cpp
AbstractOffLatticeCellPopulation.hpp
AbstractOnLatticeCellPopulation.cpp
AbstractOnLatticeCellPopulation.hpp
CaBasedCellPopulation.cpp
CaBasedCellPopulation.hpp
CellwiseDataGradient.cpp
CellwiseDataGradient.hpp
MeshBasedCellPopulation.cpp
MeshBasedCellPopulation.hpp
MeshBasedCellPopulationWithGhostNodes.cpp
MeshBasedCellPopulationWithGhostNodes.hpp
NodeBasedCellPopulation.cpp
NodeBasedCellPopulation.hpp
NodeBasedCellPopulationWithBuskeUpdate.cpp
NodeBasedCellPopulationWithBuskeUpdate.hpp
NodeBasedCellPopulationWithParticles.cpp
NodeBasedCellPopulationWithParticles.hpp
PottsBasedCellPopulation.cpp
PottsBasedCellPopulation.hpp
VertexBasedCellPopulation.cpp
VertexBasedCellPopulation.hpp
simulation
modifiers
AbstractCellBasedSimulationModifier.cpp
AbstractCellBasedSimulationModifier.hpp
AbstractTargetAreaModifier.cpp
AbstractTargetAreaModifier.hpp
DeltaNotchTrackingModifier.cpp
DeltaNotchTrackingModifier.hpp
FarhadifarTypeModifier.cpp
FarhadifarTypeModifier.hpp
SimpleTargetAreaModifier.cpp
SimpleTargetAreaModifier.hpp
VolumeTrackingModifier.cpp
VolumeTrackingModifier.hpp
AbstractCellBasedSimulation.cpp
AbstractCellBasedSimulation.hpp
CellBasedSimulationArchiver.hpp
OffLatticeSimulation.cpp
OffLatticeSimulation.hpp
OnLatticeSimulation.cpp
OnLatticeSimulation.hpp
writers
cell_writers
AbstractCellWriter.cpp
AbstractCellWriter.hpp
CellAgesWriter.cpp
CellAgesWriter.hpp
CellAncestorWriter.cpp
CellAncestorWriter.hpp
CellCycleModelProteinConcentrationsWriter.cpp
CellCycleModelProteinConcentrationsWriter.hpp
CellDeltaNotchWriter.cpp
CellDeltaNotchWriter.hpp
CellIdWriter.cpp
CellIdWriter.hpp
CellLabelWriter.cpp
CellLabelWriter.hpp
CellLocationIndexWriter.cpp
CellLocationIndexWriter.hpp
CellMutationStatesWriter.cpp
CellMutationStatesWriter.hpp
CellProliferativePhasesWriter.cpp
CellProliferativePhasesWriter.hpp
CellProliferativeTypesWriter.cpp
CellProliferativeTypesWriter.hpp
CellRadiusWriter.cpp
CellRadiusWriter.hpp
CellRosetteRankWriter.cpp
CellRosetteRankWriter.hpp
CellVolumesWriter.cpp
CellVolumesWriter.hpp
population_count_writers
AbstractCellPopulationCountWriter.cpp
AbstractCellPopulationCountWriter.hpp
CellMutationStatesCountWriter.cpp
CellMutationStatesCountWriter.hpp
CellProliferativePhasesCountWriter.cpp
CellProliferativePhasesCountWriter.hpp
CellProliferativeTypesCountWriter.cpp
CellProliferativeTypesCountWriter.hpp
population_writers
AbstractCellPopulationWriter.cpp
AbstractCellPopulationWriter.hpp
BoundaryNodeWriter.cpp
BoundaryNodeWriter.hpp
CellPopulationAdjacencyMatrixWriter.cpp
CellPopulationAdjacencyMatrixWriter.hpp
CellPopulationAreaWriter.cpp
CellPopulationAreaWriter.hpp
CellPopulationElementWriter.cpp
CellPopulationElementWriter.hpp
HeterotypicBoundaryLengthWriter.cpp
HeterotypicBoundaryLengthWriter.hpp
NodeLocationWriter.cpp
NodeLocationWriter.hpp
NodeVelocityWriter.cpp
NodeVelocityWriter.hpp
VertexT1SwapLocationsWriter.cpp
VertexT1SwapLocationsWriter.hpp
VertexT2SwapLocationsWriter.cpp
VertexT2SwapLocationsWriter.hpp
VertexT3SwapLocationsWriter.cpp
VertexT3SwapLocationsWriter.hpp
VoronoiDataWriter.cpp
VoronoiDataWriter.hpp
AbstractCellBasedWriter.cpp
AbstractCellBasedWriter.hpp
continuum_mechanics
src
common
NonlinearElasticityTools.cpp
NonlinearElasticityTools.hpp
problem
material_laws
AbstractCompressibleMaterialLaw.hpp
AbstractIncompressibleMaterialLaw.hpp
AbstractIsotropicCompressibleMaterialLaw.cpp
AbstractIsotropicCompressibleMaterialLaw.hpp
AbstractIsotropicIncompressibleMaterialLaw.cpp
AbstractIsotropicIncompressibleMaterialLaw.hpp
AbstractMaterialLaw.cpp
AbstractMaterialLaw.hpp
CompressibleExponentialLaw.cpp
CompressibleExponentialLaw.hpp
CompressibleMooneyRivlinMaterialLaw.hpp
ExponentialMaterialLaw.cpp
ExponentialMaterialLaw.hpp
MooneyRivlinMaterialLaw.cpp
MooneyRivlinMaterialLaw.hpp
NashHunterPoleZeroLaw.cpp
NashHunterPoleZeroLaw.hpp
PoleZeroMaterialLaw.cpp
PoleZeroMaterialLaw.hpp
PolynomialMaterialLaw3d.cpp
PolynomialMaterialLaw3d.hpp
SchmidCostaExponentialLaw2d.cpp
SchmidCostaExponentialLaw2d.hpp
CompressibilityType.hpp
ContinuumMechanicsProblemDefinition.cpp
ContinuumMechanicsProblemDefinition.hpp
SolidMechanicsProblemDefinition.cpp
SolidMechanicsProblemDefinition.hpp
StokesFlowProblemDefinition.hpp
solver
AbstractContinuumMechanicsAssembler.hpp
AbstractContinuumMechanicsSolver.hpp
AbstractNonlinearElasticitySolver.hpp
CompressibleNonlinearElasticitySolver.cpp
CompressibleNonlinearElasticitySolver.hpp
ContinuumMechanicsNeumannBcsAssembler.hpp
IncompressibleNonlinearElasticitySolver.cpp
IncompressibleNonlinearElasticitySolver.hpp
StokesFlowAssembler.hpp
StokesFlowPreconditionerAssembler.hpp
StokesFlowSolver.hpp
VtkNonlinearElasticitySolutionWriter.cpp
VtkNonlinearElasticitySolutionWriter.hpp
crypt
src
boundary_conditions
CryptSimulationBoundaryCondition.cpp
CryptSimulationBoundaryCondition.hpp
cell
cycle
AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp
AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp
AbstractWntOdeBasedCellCycleModel.cpp
AbstractWntOdeBasedCellCycleModel.hpp
SimpleWntCellCycleModel.cpp
SimpleWntCellCycleModel.hpp
SingleOdeWntCellCycleModel.cpp
SingleOdeWntCellCycleModel.hpp
StochasticWntCellCycleModel.cpp
StochasticWntCellCycleModel.hpp
VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.cpp
VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.hpp
VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.cpp
VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.hpp
WntCellCycleModel.cpp
WntCellCycleModel.hpp
WntConcentration.cpp
WntConcentration.hpp
CryptCellsGenerator.hpp
forces
CryptProjectionForce.cpp
CryptProjectionForce.hpp
LinearSpringWithVariableSpringConstantsForce.cpp
LinearSpringWithVariableSpringConstantsForce.hpp
VertexCryptBoundaryForce.cpp
VertexCryptBoundaryForce.hpp
killers
RadialSloughingCellKiller.cpp
RadialSloughingCellKiller.hpp
SloughingCellKiller.cpp
SloughingCellKiller.hpp
odes
Mirams2010WntOdeSystem.cpp
Mirams2010WntOdeSystem.hpp
VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp
VanLeeuwen2009WntSwatCellCycleOdeSystem.hpp
WntCellCycleOdeSystem.cpp
WntCellCycleOdeSystem.hpp
simulation
CryptSimulation1d.cpp
CryptSimulation1d.hpp
CryptSimulation2d.cpp
CryptSimulation2d.hpp
statistics
AbstractCryptStatistics.cpp
AbstractCryptStatistics.hpp
CryptProjectionStatistics.cpp
CryptProjectionStatistics.hpp
CryptStatistics.cpp
CryptStatistics.hpp
writers
CellBetaCateninWriter.cpp
CellBetaCateninWriter.hpp
global
src
checkpointing
ArchiveLocationInfo.cpp
ArchiveLocationInfo.hpp
ArchiveOpener.cpp
ArchiveOpener.hpp
ChasteSerialization.hpp
ChasteSerializationVersion.hpp
CheckpointArchiveTypes.hpp
CheckpointArchiveTypesIfNeeded.hpp
ClassIsAbstract.hpp
Identifiable.cpp
Identifiable.hpp
ProcessSpecificArchive.cpp
ProcessSpecificArchive.hpp
SerializableSingleton.hpp
SerializationExportWrapper.hpp
SerializationExportWrapperForCpp.hpp
fortests
AbstractFileComparison.hpp
CommandLineArgumentsMocker.cpp
CommandLineArgumentsMocker.hpp
FakePetscSetup.hpp
FileComparison.hpp
NumericFileComparison.hpp
PetscSetupAndFinalize.hpp
PetscSetupUtils.cpp
PetscSetupUtils.hpp
parallel
DistributedVector.cpp
DistributedVector.hpp
DistributedVectorException.cpp
DistributedVectorException.hpp
DistributedVectorFactory.cpp
DistributedVectorFactory.hpp
PetscException.cpp
PetscException.hpp
PetscTools.cpp
PetscTools.hpp
ReplicatableVector.cpp
ReplicatableVector.hpp
timing
CellBasedEventHandler.cpp
CellBasedEventHandler.hpp
GenericEventHandler.hpp
HeartEventHandler.cpp
HeartEventHandler.hpp
MechanicsEventHandler.cpp
MechanicsEventHandler.hpp
Timer.cpp
Timer.hpp
Boost156NormalDistribution.hpp
BoostFilesystem.hpp
ChasteBuildRoot.hpp
ChasteSyscalls.hpp
Citations.cpp
Citations.hpp
CommandLineArguments.cpp
CommandLineArguments.hpp
Debug.cpp
Debug.hpp
DoxygenMainPage.hpp
Exception.cpp
Exception.hpp
ExecutableSupport.cpp
ExecutableSupport.hpp
FileFinder.cpp
FileFinder.hpp
GetCurrentWorkingDirectory.cpp
GetCurrentWorkingDirectory.hpp
IsNan.hpp
LogFile.cpp
LogFile.hpp
MathsCustomFunctions.cpp
MathsCustomFunctions.hpp
ObjectCommunicator.hpp
OutputDirectoryFifoQueue.cpp
OutputDirectoryFifoQueue.hpp
OutputFileHandler.cpp
OutputFileHandler.hpp
PosixPathFixer.cpp
PosixPathFixer.hpp
ProgressReporter.cpp
ProgressReporter.hpp
RandomNumberGenerator.cpp
RandomNumberGenerator.hpp
SmartPointers.hpp
TimeStepper.cpp
TimeStepper.hpp
VectorHelperFunctions.hpp
Version.hpp
Warnings.cpp
Warnings.hpp
heart
src
convergence
AbstractConvergenceTester.cpp
AbstractConvergenceTester.hpp
OdeConvergenceTester.hpp
OdePdeConvergenceTester.hpp
PdeConvergenceTester.hpp
SpaceConvergenceTester.hpp
fortests
CheckMonoLr91Vars.hpp
LuoRudySpiralWaveCellFactory.hpp
RunAndCheckIonicModels.hpp
SimpleBathProblemSetup.hpp
io
FibreConverter.cpp
FibreConverter.hpp
FibreReader.cpp
FibreReader.hpp
FibreWriter.cpp
FibreWriter.hpp
HeartFileFinder.cpp
HeartFileFinder.hpp
XmlTools.cpp
XmlTools.hpp
odes
contractionmodels
AbstractAlgebraicContractionModel.hpp
AbstractContractionModel.hpp
AbstractOdeBasedContractionModel.hpp
ConstantActiveTension.hpp
ContractionModelName.hpp
FakeBathContractionModel.cpp
FakeBathContractionModel.hpp
Kerchoffs2003ContractionModel.cpp
Kerchoffs2003ContractionModel.hpp
Nash2004ContractionModel.cpp
Nash2004ContractionModel.hpp
NhsContractionModel.cpp
NhsContractionModel.hpp
NhsModelWithBackwardSolver.cpp
NhsModelWithBackwardSolver.hpp
NonPhysiologicalContractionModel.cpp
NonPhysiologicalContractionModel.hpp
ionicmodels
noncardiac
CorriasBuistICCModified.cpp
CorriasBuistICCModified.hpp
CorriasBuistSMCModified.cpp
CorriasBuistSMCModified.hpp
FakeBathCell.cpp
FakeBathCell.hpp
FitzHughNagumo1961OdeSystem.cpp
FitzHughNagumo1961OdeSystem.hpp
NobleVargheseKohlNoble1998WithSac.cpp
NobleVargheseKohlNoble1998WithSac.hpp
modifiers
AbstractModifier.hpp
DummyModifier.cpp
DummyModifier.hpp
FactorModifier.cpp
FactorModifier.hpp
FixedModifier.cpp
FixedModifier.hpp
TimeModifier.cpp
TimeModifier.hpp
single_cell
AbstractSteadyStateRunner.cpp
AbstractSteadyStateRunner.hpp
SteadyStateRunner.cpp
SteadyStateRunner.hpp
AbstractBackwardEulerCardiacCell.hpp
AbstractCardiacCell.cpp
AbstractCardiacCell.hpp
AbstractCardiacCellInterface.cpp
AbstractCardiacCellInterface.hpp
AbstractCardiacCellWithModifiers.cpp
AbstractCardiacCellWithModifiers.hpp
AbstractCvodeCell.cpp
AbstractCvodeCell.hpp
AbstractCvodeCellWithDataClamp.cpp
AbstractCvodeCellWithDataClamp.hpp
AbstractDynamicallyLoadableEntity.cpp
AbstractDynamicallyLoadableEntity.hpp
AbstractGeneralizedRushLarsenCardiacCell.cpp
AbstractGeneralizedRushLarsenCardiacCell.hpp
AbstractLookupTableCollection.cpp
AbstractLookupTableCollection.hpp
AbstractRushLarsenCardiacCell.cpp
AbstractRushLarsenCardiacCell.hpp
CardiacNewtonSolver.hpp
CellMLLoader.cpp
CellMLLoader.hpp
CellMLToSharedLibraryConverter.cpp
CellMLToSharedLibraryConverter.hpp
DynamicCellModelLoader.cpp
DynamicCellModelLoader.hpp
DynamicModelLoaderRegistry.cpp
DynamicModelLoaderRegistry.hpp
postprocessing
CellProperties.cpp
CellProperties.hpp
Hdf5ToCmguiConverter.cpp
Hdf5ToCmguiConverter.hpp
PostProcessingWriter.cpp
PostProcessingWriter.hpp
PropagationPropertiesCalculator.cpp
PropagationPropertiesCalculator.hpp
PseudoEcgCalculator.cpp
PseudoEcgCalculator.hpp
VoltageInterpolaterOntoMechanicsMesh.cpp
VoltageInterpolaterOntoMechanicsMesh.hpp
problem
cell_factories
AbstractCardiacCellFactory.cpp
AbstractCardiacCellFactory.hpp
AbstractContractionCellFactory.hpp
AbstractPurkinjeCellFactory.cpp
AbstractPurkinjeCellFactory.hpp
GeneralPlaneStimulusCellFactory.hpp
HeartConfigRelatedCellFactory.cpp
HeartConfigRelatedCellFactory.hpp
LabelBasedContractionCellFactory.hpp
PlaneStimulusCellFactory.hpp
ZeroStimulusCellFactory.hpp
conductivity_tensors
AbstractConductivityTensors.cpp
AbstractConductivityTensors.hpp
AxisymmetricConductivityTensors.cpp
AxisymmetricConductivityTensors.hpp
OrthotropicConductivityTensors.cpp
OrthotropicConductivityTensors.hpp
AbstractCardiacProblem.cpp
AbstractCardiacProblem.hpp
AbstractOutputModifier.hpp
ActivationOutputModifier.cpp
ActivationOutputModifier.hpp
BidomainProblem.cpp
BidomainProblem.hpp
BidomainWithBathProblem.cpp
BidomainWithBathProblem.hpp
CardiacElectroMechanicsProblem.cpp
CardiacElectroMechanicsProblem.hpp
CardiacElectroMechProbRegularGeom.hpp
CardiacSimulation.cpp
CardiacSimulation.hpp
CardiacSimulationArchiver.cpp
CardiacSimulationArchiver.hpp
Electrodes.cpp
Electrodes.hpp
ElectroMechanicsProblemDefinition.cpp
ElectroMechanicsProblemDefinition.hpp
ExtendedBidomainProblem.cpp
ExtendedBidomainProblem.hpp
HeartConfig.cpp
HeartConfig.hpp
HeartConfigDefaults.hpp
HeartGeometryInformation.cpp
HeartGeometryInformation.hpp
HeartRegionCodes.cpp
HeartRegionCodes.hpp
MonodomainProblem.cpp
MonodomainProblem.hpp
PapillaryFibreCalculator.hpp
SingleTraceOutputModifier.cpp
SingleTraceOutputModifier.hpp
SolverType.hpp
StreeterFibreGenerator.cpp
StreeterFibreGenerator.hpp
solver
electrics
bidomain
AbstractBidomainSolver.cpp
AbstractBidomainSolver.hpp
BidomainAssembler.cpp
BidomainAssembler.hpp
BidomainCorrectionTermAssembler.cpp
BidomainCorrectionTermAssembler.hpp
BidomainMassMatrixAssembler.cpp
BidomainMassMatrixAssembler.hpp
BidomainNeumannSurfaceTermAssembler.hpp
BidomainSolver.cpp
BidomainSolver.hpp
BidomainWithBathAssembler.cpp
BidomainWithBathAssembler.hpp
extended_bidomain
AbstractExtendedBidomainSolver.cpp
AbstractExtendedBidomainSolver.hpp
ExtendedBidomainAssembler.cpp
ExtendedBidomainAssembler.hpp
ExtendedBidomainMassMatrixAssembler.cpp
ExtendedBidomainMassMatrixAssembler.hpp
ExtendedBidomainNeumannSurfaceTermAssembler.hpp
ExtendedBidomainSolver.cpp
ExtendedBidomainSolver.hpp
monodomain
MonodomainAssembler.cpp
MonodomainAssembler.hpp
MonodomainCorrectionTermAssembler.cpp
MonodomainCorrectionTermAssembler.hpp
MonodomainSolver.cpp
MonodomainSolver.hpp
MonodomainStiffnessMatrixAssembler.hpp
OperatorSplittingMonodomainSolver.cpp
OperatorSplittingMonodomainSolver.hpp
AbstractCardiacFeVolumeIntegralAssembler.hpp
AbstractCorrectionTermAssembler.cpp
AbstractCorrectionTermAssembler.hpp
mechanics
AbstractCardiacMechanicsSolver.cpp
AbstractCardiacMechanicsSolver.hpp
AbstractCardiacMechanicsSolverInterface.hpp
ExplicitCardiacMechanicsSolver.cpp
ExplicitCardiacMechanicsSolver.hpp
ImplicitCardiacMechanicsSolver.cpp
ImplicitCardiacMechanicsSolver.hpp
stimulus
tissue_electrodes
AbstractStimulusFactory.cpp
AbstractStimulusFactory.hpp
ElectrodesStimulusFactory.cpp
ElectrodesStimulusFactory.hpp
ZeroNetChargeElectrodes.cpp
ZeroNetChargeElectrodes.hpp
AbstractStimulusFunction.cpp
AbstractStimulusFunction.hpp
MultiStimulus.cpp
MultiStimulus.hpp
PurkinjeVentricularJunctionStimulus.cpp
PurkinjeVentricularJunctionStimulus.hpp
RegularStimulus.cpp
RegularStimulus.hpp
RegularStimulusZeroNetCharge.cpp
RegularStimulusZeroNetCharge.hpp
S1S2Stimulus.cpp
S1S2Stimulus.hpp
SimpleStimulus.cpp
SimpleStimulus.hpp
SteadyStateRestitutionStimulus.cpp
SteadyStateRestitutionStimulus.hpp
StimulusBoundaryCondition.cpp
StimulusBoundaryCondition.hpp
ZeroStimulus.cpp
ZeroStimulus.hpp
tissue
AbstractCardiacTissue.cpp
AbstractCardiacTissue.hpp
AbstractConductivityModifier.hpp
BidomainTissue.cpp
BidomainTissue.hpp
ExtendedBidomainTissue.cpp
ExtendedBidomainTissue.hpp
MonodomainTissue.cpp
MonodomainTissue.hpp
io
src
common
AbstractHdf5Access.cpp
AbstractHdf5Access.hpp
ColumnDataConstants.hpp
fortests
CompareHdf5ResultsFiles.cpp
CompareHdf5ResultsFiles.hpp
reader
AbstractDataReader.hpp
ColumnDataReader.cpp
ColumnDataReader.hpp
Hdf5DataReader.cpp
Hdf5DataReader.hpp
writer
AbstractDataWriter.hpp
ColumnDataWriter.cpp
ColumnDataWriter.hpp
DataWriterVariable.hpp
Hdf5DataWriter.cpp
Hdf5DataWriter.hpp
ParallelColumnDataWriter.cpp
ParallelColumnDataWriter.hpp
SimpleDataWriter.cpp
SimpleDataWriter.hpp
linalg
src
AbstractNonlinearSolver.hpp
FourthOrderTensor.hpp
LinearSystem.cpp
LinearSystem.hpp
PCBlockDiagonal.cpp
PCBlockDiagonal.hpp
PCLDUFactorisation.cpp
PCLDUFactorisation.hpp
PCTwoLevelsBlockDiagonal.cpp
PCTwoLevelsBlockDiagonal.hpp
PetscMatTools.cpp
PetscMatTools.hpp
PetscVecTools.cpp
PetscVecTools.hpp
SimpleNewtonNonlinearSolver.cpp
SimpleNewtonNonlinearSolver.hpp
SimplePetscNonlinearSolver.cpp
SimplePetscNonlinearSolver.hpp
UblasCustomFunctions.cpp
UblasCustomFunctions.hpp
UblasIncludes.hpp
UblasMatrixInclude.hpp
UblasVectorInclude.hpp
mesh
src
3rdparty
tetgen1.4.2
predicates.cpp
predicates.hpp
tetgen.cpp
triangle
triangle.cpp
common
AbstractChasteRegion.hpp
AbstractElement.cpp
AbstractElement.hpp
AbstractMesh.cpp
AbstractMesh.hpp
AbstractTetrahedralElement.cpp
AbstractTetrahedralElement.hpp
AbstractTetrahedralMesh.cpp
AbstractTetrahedralMesh.hpp
BoundaryElement.cpp
BoundaryElement.hpp
ChastePoint.cpp
ChastePoint.hpp
DistributedQuadraticMesh.cpp
DistributedQuadraticMesh.hpp
DistributedTetrahedralMesh.cpp
DistributedTetrahedralMesh.hpp
DistributedTetrahedralMeshPartitionType.hpp
Element.cpp
Element.hpp
ElementAttributes.cpp
ElementAttributes.hpp
MixedDimensionMesh.cpp
MixedDimensionMesh.hpp
MutableElement.cpp
MutableElement.hpp
MutableMesh.cpp
MutableMesh.hpp
Node.cpp
Node.hpp
NodeAttributes.cpp
NodeAttributes.hpp
NodeMap.cpp
NodeMap.hpp
NodePartitioner.cpp
NodePartitioner.hpp
NodesOnlyMesh.cpp
NodesOnlyMesh.hpp
NonCachedTetrahedralMesh.cpp
NonCachedTetrahedralMesh.hpp
QuadraticMesh.cpp
QuadraticMesh.hpp
QuadraticMeshHelper.cpp
QuadraticMeshHelper.hpp
TetrahedralMesh.cpp
TetrahedralMesh.hpp
mutable
Cylindrical2dMesh.cpp
Cylindrical2dMesh.hpp
Cylindrical2dNodesOnlyMesh.cpp
Cylindrical2dNodesOnlyMesh.hpp
CylindricalHoneycombMeshGenerator.cpp
CylindricalHoneycombMeshGenerator.hpp
HoneycombMeshGenerator.cpp
HoneycombMeshGenerator.hpp
reader
AbstractCachedMeshReader.cpp
AbstractCachedMeshReader.hpp
AbstractMeshReader.cpp
AbstractMeshReader.hpp
FemlabMeshReader.cpp
FemlabMeshReader.hpp
GenericMeshReader.hpp
GmshMeshReader.cpp
GmshMeshReader.hpp
MemfemMeshReader.cpp
MemfemMeshReader.hpp
TrianglesMeshReader.cpp
TrianglesMeshReader.hpp
VtkMeshReader.cpp
VtkMeshReader.hpp
utilities
AbstractPerElementWriter.hpp
Box.cpp
Box.hpp
BoxCollection.cpp
BoxCollection.hpp
ChasteCuboid.cpp
ChasteCuboid.hpp
ChasteEllipsoid.cpp
ChasteEllipsoid.hpp
ChasteNodesList.cpp
ChasteNodesList.hpp
CuboidMeshConstructor.cpp
CuboidMeshConstructor.hpp
DistanceMapCalculator.cpp
DistanceMapCalculator.hpp
DistributedBoxCollection.cpp
DistributedBoxCollection.hpp
vertex
Cylindrical2dVertexMesh.cpp
Cylindrical2dVertexMesh.hpp
CylindricalHoneycombVertexMeshGenerator.cpp
CylindricalHoneycombVertexMeshGenerator.hpp
HoneycombVertexMeshGenerator.cpp
HoneycombVertexMeshGenerator.hpp
MutableVertexMesh.cpp
MutableVertexMesh.hpp
Toroidal2dVertexMesh.cpp
Toroidal2dVertexMesh.hpp
ToroidalHoneycombVertexMeshGenerator.cpp
ToroidalHoneycombVertexMeshGenerator.hpp
VertexElement.cpp
VertexElement.hpp
VertexElementMap.cpp
VertexElementMap.hpp
VertexMesh.cpp
VertexMesh.hpp
VertexMeshReader.cpp
VertexMeshReader.hpp
VertexMeshWriter.cpp
VertexMeshWriter.hpp
VoronoiVertexMeshGenerator.cpp
VoronoiVertexMeshGenerator.hpp
writer
AbstractMeshWriter.cpp
AbstractMeshWriter.hpp
AbstractTetrahedralMeshWriter.cpp
AbstractTetrahedralMeshWriter.hpp
CmguiDeformedSolutionsWriter.cpp
CmguiDeformedSolutionsWriter.hpp
CmguiMeshWriter.cpp
CmguiMeshWriter.hpp
MeshalyzerMeshWriter.cpp
MeshalyzerMeshWriter.hpp
TrianglesMeshWriter.cpp
TrianglesMeshWriter.hpp
VtkMeshWriter.cpp
VtkMeshWriter.hpp
XdmfMeshWriter.cpp
XdmfMeshWriter.hpp
ode
src
common
AbstractCvodeSystem.cpp
AbstractCvodeSystem.hpp
AbstractOdeSystem.cpp
AbstractOdeSystem.hpp
AbstractOdeSystemForCoupledPdeSystem.hpp
AbstractOdeSystemInformation.cpp
AbstractOdeSystemInformation.hpp
AbstractOdeSystemWithAnalyticJacobian.hpp
AbstractParameterisedSystem.cpp
AbstractParameterisedSystem.hpp
AbstractUntemplatedParameterisedSystem.cpp
AbstractUntemplatedParameterisedSystem.hpp
CombinedOdeSystem.cpp
CombinedOdeSystem.hpp
CombinedOdeSystemInformation.cpp
CombinedOdeSystemInformation.hpp
OdeSolution.cpp
OdeSolution.hpp
OdeSystemInformation.hpp
fortests
OdeSystemForCoupledHeatEquation.hpp
OdeSystemForCoupledHeatEquationWithSource.hpp
solver
AbstractIvpOdeSolver.cpp
AbstractIvpOdeSolver.hpp
AbstractOneStepIvpOdeSolver.cpp
AbstractOneStepIvpOdeSolver.hpp
BackwardEulerIvpOdeSolver.cpp
BackwardEulerIvpOdeSolver.hpp
CvodeAdaptor.cpp
CvodeAdaptor.hpp
EulerIvpOdeSolver.cpp
EulerIvpOdeSolver.hpp
GRL1IvpOdeSolver.cpp
GRL1IvpOdeSolver.hpp
GRL2IvpOdeSolver.cpp
GRL2IvpOdeSolver.hpp
HeunIvpOdeSolver.cpp
HeunIvpOdeSolver.hpp
MockEulerIvpOdeSolver.cpp
MockEulerIvpOdeSolver.hpp
RungeKutta2IvpOdeSolver.cpp
RungeKutta2IvpOdeSolver.hpp
RungeKutta4IvpOdeSolver.cpp
RungeKutta4IvpOdeSolver.hpp
RungeKuttaFehlbergIvpOdeSolver.cpp
RungeKuttaFehlbergIvpOdeSolver.hpp
pde
src
common
AbstractBoundaryCondition.hpp
AbstractBoundaryConditionsContainer.cpp
AbstractBoundaryConditionsContainer.hpp
AbstractBoundaryConditionsContainerImplementation.hpp
AbstractFunctionalCalculator.hpp
AbstractTimeAdaptivityController.hpp
BoundaryConditionsContainer.cpp
BoundaryConditionsContainer.hpp
BoundaryConditionsContainerImplementation.hpp
ConstBoundaryCondition.cpp
ConstBoundaryCondition.hpp
FineCoarseMeshPair.cpp
FineCoarseMeshPair.hpp
FunctionalBoundaryCondition.cpp
FunctionalBoundaryCondition.hpp
PdeSimulationTime.cpp
PdeSimulationTime.hpp
QuadraturePointsGroup.cpp
QuadraturePointsGroup.hpp
postprocessing
AbstractHdf5Converter.cpp
AbstractHdf5Converter.hpp
Hdf5ToMeshalyzerConverter.cpp
Hdf5ToMeshalyzerConverter.hpp
Hdf5ToTxtConverter.cpp
Hdf5ToTxtConverter.hpp
Hdf5ToVtkConverter.cpp
Hdf5ToVtkConverter.hpp
Hdf5ToXdmfConverter.cpp
Hdf5ToXdmfConverter.hpp
problem
AbstractLinearEllipticPde.hpp
AbstractLinearParabolicPde.hpp
AbstractLinearParabolicPdeSystemForCoupledOdeSystem.hpp
AbstractNonlinearEllipticPde.hpp
solver
AbstractAssemblerSolverHybrid.hpp
AbstractDynamicLinearPdeSolver.hpp
AbstractFeAssemblerCommon.hpp
AbstractFeAssemblerInterface.hpp
AbstractFeCableIntegralAssembler.hpp
AbstractFeSurfaceIntegralAssembler.hpp
AbstractFeVolumeIntegralAssembler.hpp
AbstractLinearPdeSolver.hpp
AbstractNonlinearAssemblerSolverHybrid.hpp
AbstractStaticLinearPdeSolver.hpp
GaussianQuadratureRule.cpp
GaussianQuadratureRule.hpp
LinearBasisFunction.cpp
LinearBasisFunction.hpp
LinearParabolicPdeSystemWithCoupledOdeSystemSolver.hpp
MassMatrixAssembler.hpp
NaturalNeumannSurfaceTermAssembler.hpp
QuadraticBasisFunction.cpp
QuadraticBasisFunction.hpp
SimpleLinearEllipticSolver.cpp
SimpleLinearEllipticSolver.hpp
SimpleLinearParabolicSolver.cpp
SimpleLinearParabolicSolver.hpp
SimpleNonlinearEllipticSolver.cpp
SimpleNonlinearEllipticSolver.hpp
StiffnessMatrixAssembler.hpp