#include <string>
#include <sstream>
#include <cfloat>
#include <climits>
#include <cstdlib>
#include <boost/preprocessor/stringize.hpp>
Go to the source code of this file.
Classes | |
class | Exception |
Defines | |
#define | EXCEPTION(message) |
#define | EXCEPT_IF_NOT(test) if (!(test)) EXCEPTION("Assertion tripped: " BOOST_PP_STRINGIZE(test)) |
#define | TERMINATE(message) Exception::Terminate(message, __FILE__, __LINE__) |
#define | NEVER_REACHED TERMINATE("Should have been impossible to reach this line of code"); exit(EXIT_FAILURE) |
#define | UNUSED_OPT(var) |
#define | EXPECT0(cmd, arg) |
#define | ABORT_IF_NON0_WITH_MSG(retcode, msg) |
#define | ABORT_IF_NON0(cmd, arg) |
#define | EXPECT_NON0(cmd, arg) |
#define | IGNORE_RET(cmd, arg) |
Variables | |
const unsigned | UNSIGNED_UNSET = UINT_MAX |
const int | INT_UNSET = INT_MAX |
const double | DOUBLE_UNSET = DBL_MAX |
Contains the Exception class, along with some macros that are widely used throughout the code.
Definition in file Exception.hpp.
#define ABORT_IF_NON0 | ( | cmd, | |||
arg | ) |
{ \ std::string _arg(arg); \ int ret = cmd(_arg.c_str()); \ ABORT_IF_NON0_WITH_MSG(ret, "Error executing command: " #cmd "(" + _arg + ")") \ }
Handy for calling functions like system which return non-zero on error. Terminate if an error occurs.
This macro should be used instead of EXPECT0 within blocks that are only executed by one process, but need to kill all processes if an error occurs.
cmd | command to call | |
arg | its argument (will be converted to std::string) |
Definition at line 248 of file Exception.hpp.
Referenced by AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), OutputFileHandler::CopyFileTo(), HeartConfig::CopySchema(), CardiacSimulation::CreateAndRun(), OutputDirectoryFifoQueue::CreateNextDir(), OutputFileHandler::MakeFoldersAndReturnFullPath(), OutputFileHandler::OutputFileHandler(), AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::save(), and AbstractCardiacTissue< SPACE_DIM >::save().
#define ABORT_IF_NON0_WITH_MSG | ( | retcode, | |||
msg | ) |
if (retcode != 0) { \ TERMINATE(msg); \ }
Handy for calling functions like system which return non-zero on error. Terminate if the return code is non-zero, printing a suitable message.
retcode | command return code | |
msg | error message to display |
Definition at line 233 of file Exception.hpp.
#define EXCEPT_IF_NOT | ( | test | ) | if (!(test)) EXCEPTION("Assertion tripped: " BOOST_PP_STRINGIZE(test)) |
Convenience macro for changing an assert into an exception - has the same calling semantics, but throws.
test | the test that must always be true. |
Definition at line 151 of file Exception.hpp.
Referenced by CellMLToSharedLibraryConverter::ConvertCellmlToSo(), FileFinder::GetLeafName(), FileFinder::GetParent(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::GetPurkinjeCell(), CommandLineArguments::GetValueCorrespondingToOption(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::rGetPurkinjeCellsDistributed(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::rGetPurkinjeIionicCacheReplicated().
#define EXCEPTION | ( | message | ) |
do { \ std::stringstream msg_stream; \ msg_stream << message; \ throw Exception(msg_stream.str(), __FILE__, __LINE__); \ } while (false)
Convenience macro for throwing an exception, in order to add file and line info.
message | the error message to use, as a streamed expression |
Definition at line 136 of file Exception.hpp.
Referenced by AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCardiacProblem(), AbstractCellPopulation< DIM >::AbstractCellPopulation(), AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), CaBasedCellPopulation< DIM >::AddCell(), VertexCryptBoundaryForce< DIM >::AddForceContribution(), LinearSpringWithVariableSpringConstantsForce< DIM >::AddForceContribution(), CryptProjectionForce::AddForceContribution(), WelikyOsterForce< DIM >::AddForceContribution(), RepulsionForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), AbstractTwoBodyInteractionForce< DIM >::AddForceContribution(), QuadraticMesh< DIM >::AddNodesToBoundaryElements(), CellPropertyCollection::AddProperty(), AbstractCardiacCell::AdjustOutOfRangeSlowValues(), RungeKuttaFehlbergIvpOdeSolver::AdjustStepSize(), Hdf5DataWriter::AdvanceAlongUnlimitedDimension(), TimeStepper::AdvanceOneTimeStep(), BidomainProblem< DIM >::AnalyseMeshForBath(), Hdf5DataWriter::ApplyPermutation(), ArchiveOpener< Archive, Stream >::ArchiveOpener(), AxisymmetricConductivityTensors< ELEMENT_DIM, SPACE_DIM >::AxisymmetricConductivityTensors(), AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), PropagationPropertiesCalculator::CalculateActionPotentialDuration(), CellProperties::CalculateActionPotentialDurations(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), BoxCollection< DIM >::CalculateContainingBox(), AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::CalculateJacobian(), AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::CalculateNormal(), CellProperties::CalculateProperties(), AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::CalculateWeightedDirection(), CardiacSimulation::CardiacSimulation(), Cell::Cell(), ChasteCuboid< SPACE_DIM >::ChasteCuboid(), ChasteEllipsoid< SPACE_DIM >::ChasteEllipsoid(), SolidMechanicsProblemDefinition< DIM >::CheckCastSuccess(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::CheckCompatibilityCondition(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::CheckCompatibilityCondition(), CellProperties::CheckExceededThreshold(), ColumnDataReader::CheckFiles(), ElectrodesStimulusFactory< DIM >::CheckForElectrodesIntersection(), XmlTransforms::CheckForIluPreconditioner(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckOutwardNormals(), HeartConfig::CheckResumeSimulationIsDefined(), CellProperties::CheckReturnedToThreshold(), HeartConfig::CheckSimulationIsDefined(), HeartConfig::CheckTimeSteps(), Hdf5DataWriter::CheckUnitsName(), ColumnDataWriter::CheckUnitsName(), Hdf5DataWriter::CheckVariableName(), ColumnDataWriter::CheckVariableName(), ColumnDataReader::ColumnDataReader(), ColumnDataWriter::ColumnDataWriter(), Hdf5DataReader::CommonConstructor(), CompressibleNonlinearElasticitySolver< DIM >::CompressibleNonlinearElasticitySolver(), FineCoarseMeshPair< DIM >::ComputeCoarseElementsForFineElementCentroids(), FineCoarseMeshPair< DIM >::ComputeCoarseElementsForFineNodes(), AbstractParameterisedSystem< VECTOR >::ComputeDerivedQuantities(), Electrodes< DIM >::ComputeElectrodesAreasAndCheckEquality(), AbstractCvodeCell::ComputeExceptVoltage(), FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseNodes(), FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseQuadPoints(), PoleZeroMaterialLaw< DIM >::ComputeStressAndStressDerivative(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRegularSlabMesh(), CellMLToSharedLibraryConverter::Convert(), CellMLToSharedLibraryConverter::ConvertCellmlToSo(), CmguiDeformedSolutionsWriter< DIM >::ConvertOutput(), OutputFileHandler::CopyFileTo(), HeartConfigRelatedCellFactory< SPACE_DIM >::CreateCellWithIntracellularStimulus(), AbstractNonlinearElasticitySolver< DIM >::CreateCmguiOutput(), CryptSimulation2d::CryptSimulation2d(), CvodeAdaptor::CvodeError(), AbstractCvodeSystem::CvodeError(), CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), HeartConfig::DecideLocation(), AbstractCellProperty::DecrementCellCount(), Hdf5DataWriter::DefineFixedDimension(), ColumnDataWriter::DefineFixedDimension(), Hdf5DataWriter::DefineFixedDimensionUsingMatrix(), Hdf5DataWriter::DefineUnlimitedDimension(), ColumnDataWriter::DefineUnlimitedDimension(), Hdf5DataWriter::DefineVariable(), ColumnDataWriter::DefineVariable(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNode(), NodesOnlyMesh< SPACE_DIM >::DeleteNode(), HeartGeometryInformation< SPACE_DIM >::DetermineLayerForEachNode(), PottsMesh< DIM >::DivideElement(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), ColumnDataWriter::DoAdvanceAlongUnlimitedDimension(), AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::DoAssemble(), AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::DoAssemble(), AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::DoAssemble(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::DumbNodePartitioning(), DynamicCellModelLoader::DynamicCellModelLoader(), ElectrodesStimulusFactory< DIM >::ElectrodesStimulusFactory(), Hdf5DataWriter::EndDefineMode(), ColumnDataWriter::EndDefineMode(), GenericEventHandler< 1, EventHandler >::EndEventImpl(), VolumeConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), SurfaceAreaConstraintPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), AdhesionPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), NhsContractionModel::EvaluateYDerivatives(), ExponentialMaterialLaw< DIM >::ExponentialMaterialLaw(), ExtendedBidomainSolver< ELEM_DIM, SPACE_DIM >::ExtendedBidomainSolver(), FibreReader< DIM >::FibreReader(), GaussianQuadratureRule< ELEMENT_DIM >::GaussianQuadratureRule(), GaussianQuadratureRule< 1 >::GaussianQuadratureRule(), CellsGenerator< CELL_CYCLE_MODEL, DIM >::GenerateBasic(), StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation(), ProcessSpecificArchive< Archive >::Get(), HeartConfig::GetAbsoluteTolerance(), ImplicitCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::GetActiveTensionAndTensionDerivs(), FibreReader< DIM >::GetAllAxi(), FibreReader< DIM >::GetAllOrtho(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetAngleBetweenNodes(), AbstractParameterisedSystem< VECTOR >::GetAnyVariable(), AbstractOdeSystemInformation::GetAnyVariableIndex(), AbstractOdeSystemInformation::GetAnyVariableUnits(), ArchiveLocationInfo::GetArchiveDirectory(), AbstractOdeSystemInformation::GetAttribute(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetCableElement(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::GetCardiacCellOrHaloCell(), VtkMeshReader< ELEMENT_DIM, SPACE_DIM >::GetCellData(), HeartConfig::GetCellHeterogeneities(), AbstractCellPopulation< DIM >::GetCellMutationStateCount(), AbstractCellPopulation< DIM >::GetCellUsingLocationIndex(), HoneycombMeshGenerator::GetCircularMesh(), HeartConfig::GetConductivityHeterogeneities(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndexWithInitialGuess(), TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndices(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndices(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetDataReader(), AbstractOdeSystemInformation::GetDerivedQuantityIndex(), AbstractOdeSystemInformation::GetDerivedQuantityUnits(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetEdgeLength(), HeartConfig::GetElectrodeParameters(), TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >::GetElementData(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetElementData(), TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >::GetFaceData(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetFaceData(), HeartConfig::GetFibreLength(), HeartConfig::GetGradationForAdaptivity(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetHeartGeometryInformation(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetIntegrand(), AbstractCardiacCell::GetIntracellularCalciumConcentration(), HeartConfig::GetIonicModelRegions(), NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetJacobianForElement(), HeartConfig::GetKSPPreconditioner(), HeartConfig::GetKSPSolver(), CellProperties::GetLastCompleteMaxUpstrokeVelocity(), CellProperties::GetLastCompletePeakPotential(), HeartConfig::GetMaxEdgeLengthForAdaptivity(), HeartConfig::GetMaxNodesForAdaptivity(), AbstractStimulusFactory< ELEMENT_DIM, SPACE_DIM >::GetMesh(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::GetMesh(), CylindricalHoneycombVertexMeshGenerator::GetMesh(), CylindricalHoneycombMeshGenerator::GetMesh(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetMeshFileBaseName(), ArchiveLocationInfo::GetMeshFilename(), HeartConfig::GetMeshPartitioning(), HeartConfig::GetMinEdgeLengthForAdaptivity(), AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::GetMixedDimensionMesh(), AbstractCardiacCellWithModifiers< CARDIAC_CELL >::GetModifier(), PottsBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeNotAlsoInElement(), VertexElementMap::GetNewIndex(), NodeMap::GetNewIndex(), DiffusionCaUpdateRule< DIM >::GetNewLocationOfCell(), AdvectionCaUpdateRule< DIM >::GetNewLocationOfCell(), NhsContractionModel::GetNextActiveTension(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextCableElementData(), VertexMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextElementData(), VtkMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextElementData(), AbstractCachedMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextElementData(), PottsMeshReader< SPACE_DIM >::GetNextElementData(), VertexMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextElementDataWithFaces(), VtkMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextFaceData(), AbstractCachedMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextFaceData(), FibreReader< DIM >::GetNextFibreSheetAndNormalMatrix(), FibreReader< DIM >::GetNextFibreVector(), TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextItemFromStream(), VertexMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextLineFromStream(), TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextLineFromStream(), PottsMeshReader< SPACE_DIM >::GetNextLineFromStream(), VertexMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextNode(), VtkMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextNode(), AbstractCachedMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextNode(), PottsMeshReader< SPACE_DIM >::GetNextNode(), Warnings::GetNextWarningMessage(), TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode(), HeartGeometryInformation< SPACE_DIM >::GetNodesAtSurface(), NonlinearElasticityTools< DIM >::GetNodesByComponentValue(), HeartConfig::GetNumberOfAdaptiveSweeps(), CommandLineArguments::GetNumberOfArgumentsForOption(), AbstractCardiacCell::GetNumSlowValues(), AbstractParameterisedSystem< VECTOR >::GetParameter(), AbstractOdeSystemInformation::GetParameterIndex(), AbstractOdeSystemInformation::GetParameterUnits(), VtkMeshReader< ELEMENT_DIM, SPACE_DIM >::GetPointData(), CellPropertyCollection::GetProperty(), AbstractCachedMeshReader< ELEMENT_DIM, SPACE_DIM >::GetRawDataFromFile(), HeartConfig::GetRelativeTolerance(), HeartConfig::GetSheetDimensions(), HeartConfig::GetSigmaForAdaptivity(), HeartConfig::GetSlabDimensions(), AbstractCardiacCell::GetSlowValues(), AbstractParameterisedSystem< VECTOR >::GetStateVariable(), AbstractOdeSystemInformation::GetStateVariableIndex(), AbstractOdeSystemInformation::GetStateVariableUnits(), HeartConfig::GetStimuli(), AbstractLookupTableCollection::GetTableIndex(), HeartConfig::GetTargetErrorForAdaptivity(), CellProperties::GetTimeAtLastCompleteMaxUpstrokeVelocity(), Cell::GetTimeUntilDeath(), FibreReader< DIM >::GetTokensAtNextLine(), ColumnDataReader::GetUnlimitedDimensionValues(), CommandLineArguments::GetUnsignedCorrespondingToOption(), CellwiseData< DIM >::GetValue(), ColumnDataReader::GetValues(), OdeSolution::GetVariableAtIndex(), Hdf5DataWriter::GetVariableByName(), Hdf5DataReader::GetVariableOverNodes(), Hdf5DataReader::GetVariableOverTime(), Hdf5DataReader::GetVariableOverTimeOverMultipleNodes(), HeartConfig::GetVersionFromNamespace(), StokesFlowProblemDefinition< DIM >::GetViscosity(), MeshBasedCellPopulation< DIM >::GetVoronoiEdgeLength(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex(), NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetWeightedDirectionForElement(), WntConcentration< DIM >::GetWntGradient(), Hdf5DataWriter::Hdf5DataWriter(), HeartConfigRelatedCellFactory< SPACE_DIM >::HeartConfigRelatedCellFactory(), HeartGeometryInformation< SPACE_DIM >::HeartGeometryInformation(), HoneycombMeshGenerator::HoneycombMeshGenerator(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType(), PlaneBoundaryCondition< DIM >::ImposeBoundaryCondition(), IncompressibleNonlinearElasticitySolver< DIM >::IncompressibleNonlinearElasticitySolver(), OrthotropicConductivityTensors< ELEMENT_DIM, SPACE_DIM >::Init(), AxisymmetricConductivityTensors< ELEMENT_DIM, SPACE_DIM >::Init(), CardiacElectroMechanicsProblem< DIM >::Initialise(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >::Initialise(), CellBasedPdeHandler< DIM >::InitialiseCellPdeElementMap(), ImplicitCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::InitialiseContractionModels(), ExplicitCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::InitialiseContractionModels(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::InitialiseHdf5Writer(), AbstractCardiacCell::IsFastOnly(), LinearSystem::LinearSystem(), AbstractOdeSystem::load(), AbstractCardiacProblem< ELEMENT_DIM, ELEMENT_DIM, 1 >::load(), MemfemMeshReader< ELEMENT_DIM, SPACE_DIM >::MemfemMeshReader(), CardiacSimulationArchiver< PROBLEM_CLASS >::Migrate(), MooneyRivlinMaterialLaw< DIM >::MooneyRivlinMaterialLaw(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode(), NumericFileComparison::NumericFileComparison(), OffLatticeSimulation< DIM >::OffLatticeSimulation(), OnLatticeSimulation< DIM >::OnLatticeSimulation(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::OpenElementFiles(), VertexMeshReader< ELEMENT_DIM, SPACE_DIM >::OpenElementsFile(), TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >::OpenElementsFile(), PottsMeshReader< SPACE_DIM >::OpenElementsFile(), TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >::OpenFacesFile(), VertexMeshReader< ELEMENT_DIM, SPACE_DIM >::OpenNodeFile(), TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >::OpenNodeFile(), PottsMeshReader< SPACE_DIM >::OpenNodeFile(), OutputFileHandler::OpenOutputFile(), CellBasedPdeHandler< DIM >::OpenResultsFiles(), ChastePoint< 0 >::operator[](), OutputFileHandler::OutputFileHandler(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT2Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), PolynomialMaterialLaw3d::PolynomialMaterialLaw3d(), PottsMesh< DIM >::PottsMesh(), ExtendedBidomainProblem< DIM >::PreSolveChecks(), BidomainProblem< DIM >::PreSolveChecks(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PreSolveChecks(), HeartGeometryInformation< SPACE_DIM >::ProcessLine(), Hdf5DataWriter::PutStripedVector(), Hdf5DataWriter::PutUnlimitedVariable(), ColumnDataWriter::PutVariable(), ParallelColumnDataWriter::PutVector(), Hdf5DataWriter::PutVector(), RandomCellKiller< DIM >::RandomCellKiller(), HeartConfig::ReadFile(), TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >::ReadHeaders(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), FibreReader< DIM >::ReadNumLinesOfDataFromFile(), ColumnDataReader::ReadValueFromFile(), XmlTools::ReadXmlFile(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::RefineElement(), AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::RefreshJacobian(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), Node< SPACE_DIM >::RemoveBoundaryElement(), Node< SPACE_DIM >::RemoveElement(), CellPropertyCollection::RemoveProperty(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::ReplaceNode(), PetscTools::ReplicateException(), GenericEventHandler< 1, EventHandler >::ReportImpl(), AbstractCellPopulation< DIM >::rGetCellCyclePhaseCount(), AbstractCellPopulation< DIM >::rGetCellProliferativeTypeCount(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::rGetExtracellularConductivityTensor(), NodeBasedCellPopulation< DIM >::rGetNodePairs(), LinearSystem::rGetPrecondMatrix(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RotateX(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RotateY(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RotateZ(), CardiacSimulation::Run(), CardiacSimulationArchiver< PROBLEM_CLASS >::Save(), AbstractMaterialLaw< DIM >::ScaleMaterialParameters(), LogFile::Set(), HeartConfig::SetAdaptivityParameters(), AbstractParameterisedSystem< VECTOR >::SetAnyVariable(), StreeterFibreGenerator< SPACE_DIM >::SetApexToBase(), CellwiseData< DIM >::SetCellPopulation(), AxisymmetricConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetConstantConductivities(), AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >::SetConstantConductivities(), AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::SetConstantFibreSheetDirections(), WntConcentration< DIM >::SetConstantWntValueForTesting(), WntConcentration< DIM >::SetCryptLength(), AbstractParameterisedSystem< VECTOR >::SetDefaultInitialCondition(), AbstractParameterisedSystem< VECTOR >::SetDefaultInitialConditions(), AbstractCellCycleModel::SetDimension(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::SetDistributedVectorFactory(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetFixedExtracellularPotentialNodes(), DistributedVectorFactory::SetFromFactory(), ExtendedBidomainProblem< DIM >::SetGgapHeterogeneities(), HeartConfig::SetKSPPreconditioner(), HeartConfig::SetKSPSolver(), AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::SetMesh(), HeartConfig::SetMeshPartitioning(), AbstractCardiacCellWithModifiers< CARDIAC_CELL >::SetModifier(), Cell::SetMutationState(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode(), AbstractOnLatticeCellPopulation< DIM >::SetNode(), TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >::SetNodePermutation(), LinearSystem::SetNullBasis(), CellwiseData< DIM >::SetNumCellsAndVars(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::SetParallelFiles(), AbstractParameterisedSystem< VECTOR >::SetParameter(), PoleZeroMaterialLaw< DIM >::SetParameters(), FileFinder::SetPath(), AbstractExtendedBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetRowForAverageOfPhiZeroed(), AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::SetRowForAverageOfPhiZeroed(), S1S2Stimulus::SetS2ExperimentPeriodIndex(), AbstractCardiacCell::SetSlowValues(), AbstractCardiacCell::SetState(), AbstractParameterisedSystem< VECTOR >::SetStateVariable(), AbstractParameterisedSystem< VECTOR >::SetStateVariables(), AbstractLookupTableCollection::SetTableProperties(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetTimes(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetTimeStep(), HeartConfig::SetTissueAndBathIdentifiers(), WntConcentration< DIM >::SetType(), CvodeAdaptor::SetupCvode(), AbstractCvodeSystem::SetupCvode(), CellwiseData< DIM >::SetValue(), AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::SetVariableFibreSheetDirections(), AbstractNonlinearElasticitySolver< DIM >::SetWriteOutput(), SimpleDataWriter::SimpleDataWriter(), AbstractNonlinearAssemblerSolverHybrid< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), RungeKuttaFehlbergIvpOdeSolver::Solve(), CvodeAdaptor::Solve(), AbstractOneStepIvpOdeSolver::Solve(), SimplePetscNonlinearSolver::Solve(), SimpleNewtonNonlinearSolver::Solve(), LinearSystem::Solve(), AbstractNonlinearElasticitySolver< DIM >::Solve(), AbstractCellBasedSimulation< DIM >::Solve(), AbstractIvpOdeSolver::SolveAndUpdateStateVariable(), LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SolveAndWriteResultsToFile(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveElementMapping(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), CellPropertyRegistry::SpecifyOrdering(), SphereGeometryBoundaryCondition< DIM >::SphereGeometryBoundaryCondition(), Cell::StartApoptosis(), AbstractNonlinearElasticitySolver< DIM >::TakeNewtonStep(), SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), CommandLineArguments::TestOptionFormat(), TimeStepper::TimeStepper(), FemlabMeshReader< ELEMENT_DIM, SPACE_DIM >::TokenizeStringsToDoubles(), TrianglesMeshReader< ELEMENT_DIM, SPACE_DIM >::TrianglesMeshReader(), NodeBasedCellPopulation< DIM >::Update(), MeshBasedCellPopulation< DIM >::Update(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), AbstractCellBasedSimulation< DIM >::UpdateCellPopulation(), OffLatticeSimulation< DIM >::UpdateNodePositions(), HeartConfig::UpdateParametersFromResumeSimulation(), AbstractCardiacCellInterface::UseCellMLDefaultStimulus(), CellBasedPdeHandler< DIM >::UseCoarsePdeMesh(), ElectroMechanicsProblemDefinition< DIM >::Validate(), SolidMechanicsProblemDefinition< DIM >::Validate(), ContinuumMechanicsProblemDefinition< DIM >::Validate(), VertexBasedCellPopulation< DIM >::Validate(), PottsBasedCellPopulation< DIM >::Validate(), NodeBasedCellPopulation< DIM >::Validate(), MeshBasedCellPopulationWithGhostNodes< DIM >::Validate(), MeshBasedCellPopulation< DIM >::Validate(), CaBasedCellPopulation< DIM >::Validate(), VanLeeuwen2009WntSwatCellCycleOdeSystem::VanLeeuwen2009WntSwatCellCycleOdeSystem(), PlaneBoundaryCondition< DIM >::VerifyBoundaryCondition(), VertexBasedCellPopulation< DIM >::VertexBasedCellPopulation(), VolumeTrackedOffLatticeSimulation< DIM >::VolumeTrackedOffLatticeSimulation(), VtkMeshReader< ELEMENT_DIM, SPACE_DIM >::VtkMeshReader(), HeartConfig::Write(), CmguiDeformedSolutionsWriter< DIM >::WriteDeformationPositions(), and OdeSolution::WriteToFile().
#define EXPECT0 | ( | cmd, | |||
arg | ) |
{ \ std::string _arg(arg); \ int ret = cmd(_arg.c_str()); \ if (ret != 0) { \ EXCEPTION("Error executing command: " #cmd "(" + _arg + ")"); \ } }
Handy for calling functions like system which return non-zero on error. Throws if an error occurs.
cmd | command to call | |
arg | its argument (will be converted to std::string) |
Definition at line 219 of file Exception.hpp.
Referenced by CellMLToSharedLibraryConverter::ConvertCellmlToSo(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::DisplayRun(), and PetscSetup::setUpWorld().
#define EXPECT_NON0 | ( | cmd, | |||
arg | ) |
{ \ std::string _arg = (arg); \ int ret = cmd(_arg.c_str()); \ if (ret == 0) { \ EXCEPTION("Command: " #cmd "(" + _arg + ") succeeded and it shouldn't have"); \ } }
Handy for calling functions like system which return non-zero on error. This time we expect failure; throws if the command succeeds.
cmd | command to call | |
arg | its argument (will be converted to std::string) |
Definition at line 260 of file Exception.hpp.
#define IGNORE_RET | ( | cmd, | |||
arg | ) |
{ \
std::string _arg = (arg); \
int ret = cmd(_arg.c_str()); \
ret = ret; \
}
Handy for calling functions like system which return non-zero on error. This version ignores the return code, in case you don't care about errors for some reason...
cmd | command to call | |
arg | its argument (will be converted to std::string) |
Definition at line 273 of file Exception.hpp.
Referenced by CellMLToSharedLibraryConverter::ConvertCellmlToSo().
#define NEVER_REACHED TERMINATE("Should have been impossible to reach this line of code"); exit(EXIT_FAILURE) |
Use for control paths that will never be executed, just to make sure they aren't.
The exit statement at the end of NEVER_REACHED is not really needed but prevents g++ from complaining about uninitialised variables when you have code that looks like:
RelativeTo::Value relative_to; switch (rPath.relative_to()) { case cp::relative_to_type::cwd: relative_to = RelativeTo::CWD; break; case cp::relative_to_type::chaste_test_output: relative_to = RelativeTo::ChasteTestOutput; break; case cp::relative_to_type::chaste_source_root: relative_to = RelativeTo::ChasteSourceRoot; break; case cp::relative_to_type::absolute: relative_to = RelativeTo::Absolute; break; default: NEVER_REACHED; break; }
relative_to is considered potentially uninitialised in the default branch unless the compiler finds a exit, assert or throw statement.
Definition at line 194 of file Exception.hpp.
Referenced by AbstractCellMutationState::AbstractCellMutationState(), AdaptiveBidomainProblem::AdaptMesh(), Alarcon2004OxygenBasedCellCycleModel::AdjustOdeParameters(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::AppendLocalDataToFiles(), IncompressibleNonlinearElasticitySolver< DIM >::AssembleOnBoundaryElement(), CompressibleNonlinearElasticitySolver< DIM >::AssembleOnBoundaryElement(), IncompressibleNonlinearElasticitySolver< DIM >::AssembleOnElement(), CompressibleNonlinearElasticitySolver< DIM >::AssembleOnElement(), AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::AssembleOnElement(), OffLatticeSimulation< DIM >::CalculateCellDivisionVector(), AbstractTetrahedralElement< ELEMENT_DIM, SPACE_DIM >::CalculateWeightedDirection(), AbstractStimulusFunction::Clear(), CmguiDeformedSolutionsWriter< DIM >::CmguiDeformedSolutionsWriter(), CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::CmguiMeshWriter(), QuadraticBasisFunction< ELEMENT_DIM >::ComputeBasisFunction(), QuadraticBasisFunction< ELEMENT_DIM >::ComputeBasisFunctionDerivative(), AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ComputeCableMatrixTerm(), AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::ComputeCableVectorTerm(), DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::ComputeDistanceMap(), CellwiseSourcePde< DIM >::ComputeLinearInUCoeffInSourceTerm(), AbstractFeVolumeIntegralAssembler< DIM, DIM, 2, false, true, CARDIAC >::ComputeMatrixTerm(), AbstractFeSurfaceIntegralAssembler< ELEMENT_DIM, SPACE_DIM, 2 >::ComputeVectorSurfaceTerm(), AbstractFeVolumeIntegralAssembler< DIM, DIM, 2, false, true, CARDIAC >::ComputeVectorTerm(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), Cylindrical2dMesh::CorrectNonPeriodicMesh(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), HeartConfigRelatedCellFactory< SPACE_DIM >::CreateCellWithIntracellularStimulus(), BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::CreateFilesWithHeaders(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::CreateIntracellularConductivityTensor(), MeshBasedCellPopulation< 1 >::CreateVoronoiTessellation(), Determinant(), CardiacElectroMechanicsProblem< DIM >::DetermineWatchedNodes(), AbstractRushLarsenCardiacCell::EvaluateYDerivatives(), HeartConfigRelatedCellFactory< SPACE_DIM >::FillInCellularTransmuralAreas(), CryptCellsGenerator< CELL_CYCLE_MODEL >::Generate(), AbstractCellPopulation< DIM >::GenerateCellResults(), StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation(), ContinuumMechanicsProblemDefinition< DIM >::GetBodyForce(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfElement(), HeartGeometryInformation< SPACE_DIM >::GetDistanceToEndo(), StreeterFibreGenerator< SPACE_DIM >::GetFibreMaxAngle(), HeartConfig::GetInterNodeSpace(), HeartConfig::GetIonicModelRegions(), CaBasedCellPopulation< DIM >::GetNeighbouringNodeIndicesVector(), AdvectionCaUpdateRule< DIM >::GetNewLocationOfCell(), HeartConfig::GetStimuli(), SimpleWntCellCycleModel::GetWntLevel(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), SimpleWntCellCycleModel::GetWntType(), SpaceConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::GiveUpConvergence(), HeartFileFinder::HeartFileFinder(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType(), AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Initialise(), Alarcon2004OxygenBasedCellCycleModel::Initialise(), OperatorSplittingMonodomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), AbstractCardiacTissue< SPACE_DIM >::LoadCardiacCells(), ExtendedBidomainTissue< DIM >::LoadExtendedBidomainCells(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::MetisLibraryNodePartitioning(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes(), PottsMeshGenerator< DIM >::PottsMeshGenerator(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::ReplicateCaches(), AbstractCardiacTissue< SPACE_DIM >::save(), AbstractCardiacTissue< SPACE_DIM >::SaveCardiacCells(), ExtendedBidomainTissue< DIM >::SaveExtendedBidomainCells(), SimpleWntCellCycleModel::SetG1Duration(), StochasticDurationGenerationBasedCellCycleModel::SetG1Duration(), StochasticDurationCellCycleModel::SetG1Duration(), AbstractSimpleCellCycleModel::SetG1Duration(), FileFinder::SetPath(), LinearSystem::SetPrecondMatrixIsDifferentFromLhs(), BoxCollection< DIM >::SetupAllLocalBoxes(), CellwiseDataGradient< DIM >::SetupGradients(), BoxCollection< DIM >::SetupLocalBoxesHalfOnly(), AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Solve(), SubDeterminant(), SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::UpdateCaches(), SimpleWntCellCycleModel::UpdateCellCyclePhase(), SimpleOxygenBasedCellCycleModel::UpdateCellCyclePhase(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), PottsBasedCellPopulation< DIM >::UpdateCellLocations(), DeltaNotchCellCycleModel::UpdateDeltaNotch(), SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration(), CellBasedPdeHandler< DIM >::UseCoarsePdeMesh(), AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesFooter(), and CmguiMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteNodeFileHeader().
#define TERMINATE | ( | message | ) | Exception::Terminate(message, __FILE__, __LINE__) |
Terminate execution safely, even when running in parallel. Use for level 4 errors: execution cannot continue from this point and hence should be terminated (even when running with NDEBUG).
message | explanatory message |
Definition at line 161 of file Exception.hpp.
Referenced by AbstractBidomainSolver< ELEMENT_DIM, SPACE_DIM >::InitialiseForSolve(), PCBlockDiagonal::PCBlockDiagonalCreate(), PCLDUFactorisation::PCLDUFactorisationCreate(), PCTwoLevelsBlockDiagonal::PCTwoLevelsBlockDiagonalCreate(), LinearSystem::SetPcType(), and LinearSystem::Solve().
#define UNUSED_OPT | ( | var | ) |
This is to cope with NDEBUG causing variables to not be used, when they are only used in assert()s.
var | the "unused" variable |
Definition at line 204 of file Exception.hpp.
const double DOUBLE_UNSET = DBL_MAX |
Use when initialising a double variable that doesn't have a sensible default value.
Definition at line 49 of file Exception.hpp.
Referenced by AbstractHdf5Converter< ELEMENT_DIM, SPACE_DIM >::AbstractHdf5Converter(), AbstractCvodeCell::Compute(), CellCycleModelOdeHandler::GetDt(), AbstractOdeBasedCellCycleModel::GetOdeStopTime(), SimulationTime::GetTime(), SimulationTime::IsStartTimeSetUp(), SimulationTime::ResetEndTimeAndNumberOfTimeSteps(), SimulationTime::SetEndTimeAndNumberOfTimeSteps(), NhsContractionModel::SetInputParameters(), Nash2004ContractionModel::SetInputParameters(), Kerchoffs2003ContractionModel::SetInputParameters(), SimulationTime::SetStartTime(), AbstractCvodeCell::SolveAndUpdateState(), LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SolveAndWriteResultsToFile(), and ContactInhibitionCellCycleModel::UpdateCellCyclePhase().
const int INT_UNSET = INT_MAX |
Use when initialising an int variable that doesn't have a sensible default value.
Definition at line 47 of file Exception.hpp.
const unsigned UNSIGNED_UNSET = UINT_MAX |
Use when initialising an unsigned variable that doesn't have a sensible default value.
Definition at line 45 of file Exception.hpp.
Referenced by CardiacElectroMechanicsProblem< DIM >::CardiacElectroMechanicsProblem(), CardiacElectroMechanicsProblem< DIM >::DetermineWatchedNodes(), AbstractCellPopulation< DIM >::GenerateCellResults(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex(), CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >::Initialise(), CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >::IsSetUp(), CellCycleModelOdeSolver< CELL_CYCLE_MODEL, BackwardEulerIvpOdeSolver >::Reset(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().