| C__itt_domain | |
| C__itt_null_t | |
| C__itt_string_handle | |
| ►Cbdm::Agent | Contains code required by all agents |
| ►Cbdm::Cell | |
| Cbdm::neuroscience::NeuronSoma | |
| Cbdm::neuroscience::NeuriteElement | |
| Cbdm::SphericalAgent | |
| Cbdm::AgentContainer | |
| Cbdm::AgentFlatIdxMap | |
| Cbdm::AgentHandle | |
| Cbdm::AgentPointer< TAgent > | |
| Cbdm::AgentPointer< bdm::neuroscience::NeuriteElement > | |
| Cbdm::AgentPointer< bdm::neuroscience::NeuronOrNeurite > | |
| Cbdm::AgentUid | |
| Cbdm::AgentUidGenerator | This class generates unique ids for agents |
| Cbdm::AgentUidMap< TValue > | |
| Cbdm::AgentUidMap< bdm::AgentHandle > | |
| Cbdm::AgentUidMap< uint64_t > | |
| Cbdm::AgentVector< T > | |
| Cbdm::AgentVector< bdm::AgentHandle > | |
| ►Cbdm::experimental::Algorithm | An interface for creating new optimization algorithms |
| Cbdm::experimental::ParameterSweep | Perform an exhaustive sweep across specified parameters |
| Cbdm::experimental::ParticleSwarm | |
| Cbdm::experimental::AlgorithmRegistry | Registry of all optimization algorithms |
| Cbdm::SharedData< T >::AlignedT | Wrapper for a chacheline-size aligned T |
| Cbdm::memory_manager_detail::AllocatedBlock | Contains metadata for an allocated memory block |
| Cbdm::Aux | |
| ►Cbdm::Behavior | |
| Cbdm::Chemotaxis | Move cells along the diffusion gradient (from low concentration to high) |
| Cbdm::GeneRegulation | |
| Cbdm::GrowthDivision | |
| Cbdm::Secretion | Secrete substance at Agent position |
| Cbdm::StatelessBehavior | Simplifies the creation of behaviors without attributes. Let's assume that we want to create a behavior that divides a cell agent in each iteration. The following code example uses the StatelessBehavior: |
| ►Cbdm::BoundaryCondition | This class implements the boundary conditions. It is integrated into the diffusion grid as a smart pointer. The diffusion grid will call the Evaluate() method of the boundary condition object for Neumann and Dirichlet boundary conditions |
| Cbdm::ConstantBoundaryCondition | This class implements constant boundary conditions (Dirichlet and Neumann). The value of the boundary condition is constant and independent of the position and time, i.e. u = const or du/dn = const on the boundary |
| Cbdm::UniformGridEnvironment::Box | A single unit cube of the grid |
| Cbdm::CommandLineOptions | Class to contain and parse command line options |
| ►Cbdm::Continuum | Continuum class to interface with BioDynaMo for hybrid simulations |
| ►Cbdm::ScalarField | Interface for scalar fields. See Continuum for more information |
| ►Cbdm::DiffusionGrid | |
| ►Cbdm::EulerGrid | Continuum model for the 3D heat equation with exponential decay  |
| Cbdm::EulerDepletionGrid | Continuum model for the 3D diffusion equation with exponential decay and substance depletion  |
| Cbdm::VectorField | Interface for vector fields. See Continuum for more information |
| Cbdm::CreateVtkDataArray< TClass, TDataMember > | |
| Cbdm::CSVReader | Reads in a CSV file using rapidcsv |
| Cbdm::AgentPointer< TAgent >::Data | TODO. Replace with std::variant once we move to >= c++17 |
| Cbdm::experimental::TimeSeries::Data | |
| Cbdm::experimental::Database | |
| ►Cbdm::experimental::DataTransformer | |
| Cbdm::experimental::LinearTransformer | |
| Cbdm::DistributionRng< TSample > | Random number generator that generates samples from a distribution |
| ►Cbdm::DistributionRng< int > | |
| Cbdm::BinomialRng | |
| Cbdm::PoissonRng | |
| ►Cbdm::DistributionRng< real_t > | |
| Cbdm::BreitWignerRng | |
| Cbdm::ExpRng | |
| Cbdm::GausRng | |
| Cbdm::LandauRng | |
| Cbdm::PoissonDRng | |
| Cbdm::UniformRng | |
| Cbdm::UserDefinedDistRng1D | |
| Cbdm::UserDefinedDistRng2D | |
| Cbdm::UserDefinedDistRng3D | |
| ►Cbdm::Environment | |
| Cbdm::KDTreeEnvironment | |
| Cbdm::OctreeEnvironment | |
| Cbdm::UniformGridEnvironment | A class that represents Cartesian 3D grid |
| ►Cbdm::ExecutionContext | |
| ►Cbdm::InPlaceExecutionContext | |
| Cbdm::experimental::CopyExecutionContext | |
| ►Cbdm::Exporter | |
| Cbdm::BasicExporter | |
| Cbdm::MatlabExporter | |
| Cbdm::NeuroMLExporter | |
| Cbdm::ParaviewExporter | |
| Cbdm::ExporterFactory | |
| Cbdm::detail::ExtractUid | |
| ►Cfalse_type | |
| Cbdm::IsArray< T > | Checks whether T is std::array or bdm::MathArray |
| Cbdm::FixedSizeVector< T, N > | |
| Cbdm::FixedSizeVector< const bdm::UniformGridEnvironment::Box *, 27 > | |
| Cbdm::FixedSizeVector< real_t, 10 > | |
| Cbdm::FixedSizeVector< uint64_t, 27 > | |
| Cbdm::Functor< TReturn, TArgs > | |
| Cbdm::Functor< T, const bdm::SharedData< T > & > | |
| ►Cbdm::Functor< T, const SharedData< T > & > | |
| Cbdm::SumReduction< T > | |
| ►Cbdm::Functor< TReturn, TArgs... > | |
| Cbdm::LambdaFunctor< TReturn(TLambda::*)(TArgs...) const > | |
| Cbdm::LambdaFunctor< TReturn(TLambda::*)(TArgs...)> | |
| ►Cbdm::Functor< void, Agent * > | |
| Cbdm::experimental::Reducer< TResult > | |
| Cbdm::experimental::Reducer< real_t > | |
| ►Cbdm::experimental::Reducer< T > | |
| Cbdm::experimental::GenericReducer< T, TResult > | |
| ►Cbdm::experimental::Reducer< uint64_t > | |
| Cbdm::experimental::Counter< TResult > | |
| ►Cbdm::Functor< void, Agent *, AgentHandle > | |
| Cbdm::detail::InitializeGPUData | |
| Cbdm::Environment::SimDimensionAndLargestAgentFunctor | |
| Cbdm::Fea | |
| Cbdm::ForEachAgentParallelFunctor< TFunctor > | |
| Cbdm::RunAllScheduledOps | |
| Cbdm::UniformGridEnvironment::AssignToBoxesFunctor | |
| Cbdm::UpdateCPUResults | |
| ►Cbdm::Functor< void, Agent *, real_t > | |
| Cbdm::Fen | |
| Cbdm::neuroscience::NeuriteElement::MechanicalForcesFunctor | |
| Cbdm::Functor< void, bdm::Agent *, T * > | |
| ►Cbdm::Functor< void, Iterator< AgentHandle > * > | |
| Cbdm::LoadBalanceFunctor | |
| ►Cbdm::Functor< void, Iterator< uint64_t > * > | |
| Cbdm::UniformGridEnvironment::LoadBalanceInfoUG::InitializeVectorFunctor | |
| Cbdm::GaussianBand | |
| Cbdm::GetDataMemberForVis< TReturn, TClass, TDataMember > | |
| Cbdm::GetDataMemberForVis< TScalar *, TClass, TDataMember > | |
| Cbdm::detail::GetIndexImpl< T, Counter, Types > | |
| Cbdm::detail::GetIndexImpl< T, Counter, FirstType > | |
| Cbdm::detail::GetIndexImpl< T, Counter, FirstType, RemainingTypes... > | |
| Cbdm::GetNumberOfComponents< T > | |
| Cbdm::GetNumberOfComponents< MathArray< T, N > > | |
| Cbdm::GetNumberOfComponents< std::array< T, N > > | |
| Cbdm::GetVtkValueType< T > | |
| Cbdm::GetVtkValueType< AgentPointer< T > > | |
| Cbdm::GetVtkValueType< AgentUid > | |
| Cbdm::GetVtkValueType< int > | |
| Cbdm::GetVtkValueType< MathArray< T, N > > | |
| Cbdm::GetVtkValueType< real_t > | |
| Cbdm::GetVtkValueType< uint64_t > | |
| Cbdm::GpuHelper | |
| Cstd::hash< bdm::AgentUid > | |
| Cstd::hash< bdm::UserDefinedDist > | |
| Cbdm::InlineVector< T, N > | |
| Cbdm::InlineVector< bdm::Agent *, 3 > | |
| Cbdm::InlineVector< bdm::Behavior *, 2 > | |
| Cbdm::InlineVector< bdm::Behavior *, 3 > | |
| Cbdm::IntegralTypeWrapper< T > | |
| Cbdm::InteractionForce | |
| Cbdm::is_agent_ptr< T > | |
| Cbdm::is_agent_ptr< AgentPointer< T > > | |
| Cbdm::AgentUidMap< TValue >::Iterator | |
| Cbdm::UniformGridEnvironment::Box::Iterator | An iterator that iterates over the cells in this box |
| Cbdm::InlineVector< T, N >::Iterator< TT, TIV > | |
| Cbdm::Iterator< T > | |
| Cbdm::SharedData< T >::Iterator | |
| ►Cbdm::Iterator< AgentHandle > | |
| Cbdm::AgentHandleIterator | |
| ►Cbdm::Iterator< uint64_t > | |
| Cbdm::MortonIterator | |
| Cbdm::JitForEachDataMemberFunctor | |
| Cbdm::JitHeaders | |
| Cbdm::LambdaFunctor< TLambda > | |
| Cbdm::experimental::LineGraph | |
| Cbdm::memory_manager_detail::List | |
| ►Cbdm::LoadBalanceInfo | |
| Cbdm::UniformGridEnvironment::LoadBalanceInfoUG | |
| Cbdm::Log | Wrapper class over ROOT logging module |
| ►Cbdm::MappedDataArrayInterface | |
| Cbdm::MappedDataArray< TScalar, TClass, TDataMember > | |
| Cbdm::Math | |
| Cbdm::MathArray< T, N > | |
| Cbdm::MathArray< real_t, 3 > | |
| Cbdm::MechanicalForcesOpCudaKernel | |
| Cbdm::MemoryManager | |
| Cbdm::ModelInitializer | |
| Cbdm::MortonOrder | |
| Cbdm::UniformGridEnvironment::GridNeighborMutexBuilder::MutexWrapper | |
| Cbdm::NanoFlannAdapter | |
| Cbdm::KDTreeEnvironment::NanoflannImpl | |
| Cbdm::UniformGridEnvironment::NeighborIterator | An iterator that iterates over the boxes in this grid |
| ►Cbdm::Environment::NeighborMutexBuilder::NeighborMutex | |
| Cbdm::UniformGridEnvironment::GridNeighborMutexBuilder::GridNeighborMutex | |
| ►Cbdm::Environment::NeighborMutexBuilder | |
| Cbdm::UniformGridEnvironment::GridNeighborMutexBuilder | |
| ►Cbdm::neuroscience::NeuronOrNeurite | |
| Cbdm::neuroscience::NeuriteElement | |
| Cbdm::neuroscience::NeuronSoma | |
| ►Cbdm::NewAgentEvent | |
| Cbdm::CellDivisionEvent | Contains the parameters to perform a cell division |
| Cbdm::neuroscience::NeuriteBifurcationEvent | Contains the parameters to bifurcate a growth cone |
| Cbdm::neuroscience::NeuriteBranchingEvent | This event splits the current neurite element into two elements and adds a new side branch as daughter right at the proximal half |
| Cbdm::neuroscience::NewNeuriteExtensionEvent | Contains the parameters to extend a new neurite from a neuron soma |
| Cbdm::neuroscience::SideNeuriteExtensionEvent | Contains the parameters to add a side neurite element |
| Cbdm::neuroscience::SplitNeuriteElementEvent | Contains the parameters to split a neurite element into two segments |
| Cbdm::NewAgentEventUidGenerator | |
| Cbdm::memory_manager_detail::Node | |
| Cbdm::memory_manager_detail::NumaPoolAllocator | Pool allocator for a specific allocation size and numa node.
|
| ►COp | |
| Cbdm::VTuneOpWrapper< Op > | |
| Cbdm::OpenCLState::OpenCLImpl | |
| Cbdm::OpenCLState::OpenCLImplDestructor | |
| Cbdm::OpenCLState | |
| Cbdm::Operation | |
| ►Cbdm::OperationImpl | |
| ►Cbdm::AgentOperationImpl | Interface for implementing an operation |
| Cbdm::BehaviorOp | |
| Cbdm::BoundSpace | |
| Cbdm::DiscretizationOp | |
| Cbdm::DividingCellOp | |
| Cbdm::MechanicalForcesOp | Defines the 3D physical interactions between physical objects |
| Cbdm::PropagateStaticnessAgentOp | |
| Cbdm::ReductionOp< T > | |
| Cbdm::UpdateStaticnessOp | |
| ►Cbdm::StandaloneOperationImpl | Interface for implementing an operation that should run on a GPU |
| Cbdm::ContinuumOp | A class that sets up diffusion grids of the substances in this simulation |
| Cbdm::LoadBalancingOp | |
| Cbdm::MechanicalForcesOpCuda | Defines the 3D physical interactions between physical objects |
| Cbdm::MechanicalForcesOpOpenCL | Defines the 3D physical interactions between physical objects |
| Cbdm::PropagateStaticnessOp | |
| Cbdm::SetUpIterationOp | |
| Cbdm::TearDownIterationOp | |
| Cbdm::UpdateEnvironmentOp | |
| Cbdm::UpdateTimeSeriesOp | |
| Cbdm::VisualizationOp | |
| Cbdm::OperationRegistry | |
| Cbdm::OpTimer< TOp > | Decorator for Operations to measure runtime |
| ►Cbdm::OptimizationParamType | An interface for creating different types of optimization parameters |
| Cbdm::LogRangeParam | A uniform range of logarithmically scaled values (e.g. 1, 10, 100, 1000) |
| Cbdm::ParticleSwarmParam | |
| Cbdm::RangeParam | |
| Cbdm::SetParam | |
| Cbdm::ResourceManager::ParallelRemovalAuxData | |
| Cbdm::ParallelResizeVector< T > | Std::vector with parallel resize |
| Cbdm::ParallelResizeVector< bdm::MathArray > | |
| Cbdm::ParallelResizeVector< bdm::Spinlock > | |
| Cbdm::ParallelResizeVector< bdm::UniformGridEnvironment::Box * > | |
| Cbdm::ParallelResizeVector< bdm::UniformGridEnvironment::Box > | |
| Cbdm::ParallelResizeVector< real_t > | |
| Cbdm::ParallelResizeVector< uint64_t > | |
| Cbdm::ParallelVtiWriter | |
| Cbdm::ParallelVtuWriter | |
| Cbdm::Param | |
| ►Cbdm::ParamGroup | Interface for parameter groups |
| Cbdm::neuroscience::Param | |
| Cbdm::OptimizationParam | |
| Cbdm::ParamGroupUidGenerator | This class generates unique ids for parameter groups. Thread safe |
| Cbdm::ParaviewAdaptor::ParaviewImpl | |
| Cbdm::PoissonBand | |
| Cbdm::memory_manager_detail::PoolAllocator | |
| Cbdm::ProgressBar | This class implements a progress bar that can be used to track the progress of a simulation |
| Cbdm::PvtiWriter | |
| Cbdm::Random | |
| Cbdm::ResourceManager | |
| Cbdm::RootAdaptor | The class that bridges the simulation code with ROOT Visualization |
| Cbdm::RuntimeVariables | |
| Cbdm::Scheduler | |
| Cbdm::SharedData< T > | The SharedData class avoids false sharing between threads |
| Cbdm::SharedData< std::vector< bdm::AgentUid > > | |
| Cbdm::SharedData< uint64_t > | |
| Cbdm::Simulation | |
| Cbdm::SimulationBackup | |
| Cbdm::Spinlock | |
| Cbdm::Stack< T > | |
| ►CTAttFill | |
| Cbdm::experimental::Style | |
| ►CTAttLine | |
| Cbdm::experimental::Style | |
| ►CTAttMarker | |
| Cbdm::experimental::Style | |
| ►CTAttText | |
| Cbdm::experimental::Style | |
| ►CTBaseRm | |
| Cbdm::RandomizedRm< TBaseRm > | |
| Cbdm::TFileRaii | Automatically close a TFile object using RAII pattern |
| Cbdm::ThreadInfo | This class stores information about each thread. (e.g. to which NUMA node it belongs to.) NB: Threads must be bound to CPUs using OMP_PROC_BIND=true |
| Cbdm::InPlaceExecutionContext::ThreadSafeAgentUidMap | |
| Cbdm::experimental::TimeSeries | |
| Cbdm::Timing | |
| Cbdm::TimingAggregator | |
| ►CTNamed | |
| Cbdm::experimental::Style | |
| ►Ctrue_type | |
| Cbdm::IsArray< MathArray< T, N > > | |
| Cbdm::IsArray< std::array< T, N > > | |
| Cbdm::type_ternary_operator< Condition, T, U > | |
| Cbdm::type_ternary_operator< false, T, U > | |
| Cbdm::type_ternary_operator< true, T, U > | |
| Cbdm::TypeIndex | |
| Cbdm::Ubrng | |
| Cbdm::OctreeEnvironment::UnibnImpl | |
| Cbdm::Uniform | |
| Cbdm::UnorderedFlatmap< TKey, TValue > | |
| Cbdm::UnorderedFlatmap< std::size_t, bdm::memory_manager_detail::PoolAllocator * > | |
| Cbdm::UnorderedFlatmap< TClass *, std::vector< bdm::Agent * > > | |
| Cbdm::UserDefinedDist | |
| Cbdm::VectorTypeWrapper< T > | |
| ►Cbdm::VisualizationAdaptor | |
| Cbdm::ParaviewAdaptor | The class that bridges the simulation code with ParaView |
| Cbdm::Param::VisualizeDiffusion | |
| Cbdm::VtkAgents | |
| Cbdm::VtkDiffusionGrid | |
| ►CvtkMappedDataArray | |
| Cbdm::MappedDataArray< TScalar, TClass, TDataMember > | |
| ►CvtkXMLImageDataWriter | |
| Cbdm::VtiWriter | |
| Cbdm::VTuneTask | |
1.8.17