Namespaces
	detail

	experimental

	in_place_exec_ctxt_detail

	memory_manager_detail

	neuroscience

Classes
class	Agent
	Contains code required by all agents. More...

class	AgentContainer

class	AgentFlatIdxMap

class	AgentHandle

struct	AgentHandleIterator

struct	AgentOperationImpl
	Interface for implementing an operation. More...

class	AgentPointer

class	AgentUid

class	AgentUidGenerator
	This class generates unique ids for agents. More...

class	AgentUidMap

class	AgentVector

struct	Aux

class	BasicExporter

class	Behavior

struct	BehaviorOp

class	BinomialRng

class	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. More...

struct	BoundSpace

class	BreitWignerRng

class	Cell

struct	CellDivisionEvent
	Contains the parameters to perform a cell division. More...

class	Chemotaxis
	Move cells along the diffusion gradient (from low concentration to high) More...

class	CommandLineOptions
	Class to contain and parse command line options. More...

class	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. More...

class	Continuum
	Continuum class to interface with BioDynaMo for hybrid simulations. More...

class	ContinuumOp
	A class that sets up diffusion grids of the substances in this simulation. More...

struct	CreateVtkDataArray

class	CSVReader
	Reads in a CSV file using rapidcsv. More...

class	DiffusionGrid

struct	DiscretizationOp

class	DistributionRng
	Random number generator that generates samples from a distribution. More...

struct	DividingCellOp

class	Environment

class	EulerDepletionGrid
	Continuum model for the 3D diffusion equation with exponential decay and substance depletion $\partial_t u = \nabla D \nabla u - \mu u - \mu' v u$ . More...

class	EulerGrid
	Continuum model for the 3D heat equation with exponential decay $\partial_t u = \nabla D \nabla u - \mu u$ . More...

class	ExecutionContext

class	Exporter

class	ExporterFactory

class	ExpRng

struct	Fea

struct	Fen

class	FixedSizeVector

struct	ForEachAgentParallelFunctor

class	Functor

class	GausRng

class	GaussianBand

class	GeneRegulation

struct	GetDataMemberForVis

struct	GetNumberOfComponents

struct	GetNumberOfComponents< MathArray< T, N > >

struct	GetNumberOfComponents< std::array< T, N > >

struct	GetVtkValueType

struct	GetVtkValueType< AgentPointer< T > >

struct	GetVtkValueType< AgentUid >

struct	GetVtkValueType< int >

struct	GetVtkValueType< MathArray< T, N > >

struct	GetVtkValueType< real_t >

struct	GetVtkValueType< uint64_t >

class	GpuHelper

class	GrowthDivision

class	InlineVector

class	InPlaceExecutionContext

class	IntegralTypeWrapper

class	InteractionForce

struct	is_agent_ptr

struct	is_agent_ptr< AgentPointer< T > >

struct	IsArray
	Checks whether T is std::array or bdm::MathArray. More...

struct	IsArray< MathArray< T, N > >

struct	IsArray< std::array< T, N > >

class	Iterator

class	JitForEachDataMemberFunctor

class	JitHeaders

class	KDTreeEnvironment

struct	LambdaFunctor

struct	LambdaFunctor< TReturn(TLambda::*)(TArgs...) const >

struct	LambdaFunctor< TReturn(TLambda::*)(TArgs...)>

class	LandauRng

struct	LoadBalanceFunctor

class	LoadBalanceInfo

struct	LoadBalancingOp

class	Log
	Wrapper class over ROOT logging module. More...

struct	LogRangeParam
	A uniform range of logarithmically scaled values (e.g. 1, 10, 100, 1000) More...

class	MappedDataArray

struct	MappedDataArrayInterface

struct	Math

class	MathArray

class	MatlabExporter

class	MechanicalForcesOp
	Defines the 3D physical interactions between physical objects. More...

struct	MechanicalForcesOpCuda
	Defines the 3D physical interactions between physical objects. More...

class	MechanicalForcesOpCudaKernel

struct	MechanicalForcesOpOpenCL
	Defines the 3D physical interactions between physical objects. More...

class	MemoryManager

struct	ModelInitializer

class	MortonIterator

class	MortonOrder

struct	NanoFlannAdapter

class	NeuroMLExporter

struct	NewAgentEvent

class	NewAgentEventUidGenerator

class	OctreeEnvironment

class	OpenCLState

struct	Operation

struct	OperationImpl

class	OperationRegistry

class	OpTimer
	Decorator for `Operations` to measure runtime. More...

struct	OptimizationParam

struct	OptimizationParamType
	An interface for creating different types of optimization parameters. More...

class	ParallelResizeVector
	std::vector with parallel resize More...

struct	ParallelVtiWriter

struct	ParallelVtuWriter

struct	Param

struct	ParamGroup
	Interface for parameter groups. More...

class	ParamGroupUidGenerator
	This class generates unique ids for parameter groups. Thread safe. More...

class	ParaviewAdaptor
	The class that bridges the simulation code with ParaView. More...

class	ParaviewExporter

struct	ParticleSwarmParam

class	PoissonBand

class	PoissonDRng

class	PoissonRng

class	ProgressBar
	This class implements a progress bar that can be used to track the progress of a simulation. More...

struct	PropagateStaticnessAgentOp

struct	PropagateStaticnessOp

class	PvtiWriter

class	Random

class	RandomizedRm

struct	RangeParam

class	ReductionOp

class	ResourceManager

class	RootAdaptor
	The class that bridges the simulation code with ROOT Visualization. More...

struct	RunAllScheduledOps

class	RuntimeVariables

class	ScalarField
	Interface for scalar fields. See `Continuum` for more information. More...

class	Scheduler

class	Secretion
	Secrete substance at Agent position. More...

struct	SetParam

struct	SetUpIterationOp

class	SharedData
	The SharedData class avoids false sharing between threads. More...

class	Simulation

class	SimulationBackup

class	SphericalAgent

class	Spinlock

class	Stack

struct	StandaloneOperationImpl
	Interface for implementing an operation that should run on a GPU. More...

class	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: More...

struct	SumReduction

struct	TearDownIterationOp

class	TFileRaii
	Automatically close a TFile object using RAII pattern. More...

class	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`. More...

class	Timing

class	TimingAggregator

struct	type_ternary_operator

struct	type_ternary_operator< false, T, U >

struct	type_ternary_operator< true, T, U >

class	TypeIndex

struct	Ubrng

class	Uniform

class	UniformGridEnvironment
	A class that represents Cartesian 3D grid. More...

class	UniformRng

class	UnorderedFlatmap

struct	UpdateCPUResults

struct	UpdateEnvironmentOp

struct	UpdateStaticnessOp

struct	UpdateTimeSeriesOp

struct	UserDefinedDist

class	UserDefinedDistRng1D

class	UserDefinedDistRng2D

class	UserDefinedDistRng3D

class	VectorField
	Interface for vector fields. See `Continuum` for more information. More...

class	VectorTypeWrapper

class	VisualizationAdaptor

class	VisualizationOp

class	VtiWriter

class	VtkAgents

class	VtkDiffusionGrid

class	VTuneOpWrapper

class	VTuneTask

Typedefs
using	NewAgentEventUid = uint64_t

using	Real3 = MathArray< real_t, 3 >
	Aliases for a size 3 MathArray. More...

using	Float3 = MathArray< float, 3 >

using	Double3 = MathArray< double, 3 >

using	Real4 = MathArray< real_t, 4 >
	Aliases for a size 4 MathArray. More...

using	Float4 = MathArray< float, 4 >

using	Double4 = MathArray< double, 4 >

typedef KDTreeSingleIndexAdaptor< L2_Simple_Adaptor< real_t, NanoFlannAdapter >, NanoFlannAdapter, 3, uint64_t >	bdm_kd_tree_t

using	NeighborMutex = Environment::NeighborMutexBuilder::NeighborMutex

using	GridNeighborMutexBuilder = UniformGridEnvironment::GridNeighborMutexBuilder

using	ParamGroupUid = uint64_t

using	real_t = double

template<typename T >
using	raw_type = std::remove_pointer_t< std::decay_t< T > >
	Type trait that converts `T`, `T&`, `T&&`, `T&` to `T` More...

using	vtkRealArray = typename type_ternary_operator< std::is_same< real_t, double >::value, vtkDoubleArray, vtkFloatArray >::type

Enumerations
enum	AgentPointerMode { kIndirect, kDirect }

enum	BoundaryConditionType { BoundaryConditionType::kDirichlet, BoundaryConditionType::kNeumann, BoundaryConditionType::kOpenBoundaries, BoundaryConditionType::kClosedBoundaries, BoundaryConditionType::kPeriodic }
	Available boundary conditions. More...

enum	InteractionMode { InteractionMode::kAdditive = 0, InteractionMode::kExponential = 1, InteractionMode::kLogistic = 2 }

enum	ExporterType { kBasic, kMatlab, kNeuroML, kParaview }

enum	OpComputeTarget { kCpu, kCuda, kOpenCl }

enum	OpType { kSchedule, kPreSchedule, kPostSchedule }

enum	Shape { kSphere, kCylinder }

enum	Axis { kXAxis, kYAxis, kZAxis }

Functions
template<typename T >
void	InPlaceParallelPrefixSum (T &v, uint64_t n)

template<typename T >
void	ExclusivePrefixSum (T *v, uint64_t n)

template<typename TSearch , typename TContainer >
uint64_t	BinarySearch (const TSearch &search_val, const TContainer &container, uint64_t from, uint64_t to)

template<class T , std::size_t N>
std::ostream &	operator<< (std::ostream &o, const MathArray< T, N > &arr)

template<class T , std::size_t N>
MathArray< T, N >	operator* (T const &scalar, MathArray< T, N > array)
	Template function to multiply array with scalar from the left. More...

std::string	BoundaryTypeToString (const BoundaryConditionType &type)
	Transforms a BoundaryConditionType to the corresponding string. More...

BoundaryConditionType	StringToBoundaryType (const std::string &type)
	Transforms a string to the corresponding BoundaryConditionType. More...

template<typename T >
std::pair< uint64_t, uint64_t >	BinarySearch (uint64_t search_val, const T &container, uint64_t from, uint64_t to)

template<typename TLambda >
LambdaFunctor< decltype(&TLambda::operator())>	L2F (const TLambda &l)

template<typename T >
void	CudaAllocPinned (T **d, uint64_t elements)

void	CudaFreePinned (void *p)

void	ApplyBoundingBox (Agent *agent, Param::BoundSpaceMode mode, real_t lb, real_t rb)

	BDM_REGISTER_OP (BoundSpace, "bound space", kCpu)

	BDM_REGISTER_OP (ContinuumOp, "continuum", kCpu)

	BDM_REGISTER_OP_WITH_FREQ (LoadBalancingOp, "load balancing", kCpu, std::numeric_limits< uint32_t >::max())

	BDM_REGISTER_OP (MechanicalForcesOp, "mechanical forces", kCpu)

	BDM_REGISTER_OP (DividingCellOp, "DividingCellOp", kCpu)

	BDM_REGISTER_OP (UpdateStaticnessOp, "update staticness", kCpu)

	BDM_REGISTER_OP (PropagateStaticnessAgentOp, "propagate staticness agentop", kCpu)

	BDM_REGISTER_OP (BehaviorOp, "behavior", kCpu)

	BDM_REGISTER_OP (DiscretizationOp, "discretization", kCpu)

	BDM_REGISTER_OP (SetUpIterationOp, "set up iteration", kCpu)

	BDM_REGISTER_OP (TearDownIterationOp, "tear down iteration", kCpu)

	BDM_REGISTER_OP (UpdateTimeSeriesOp, "update time series", kCpu)

	BDM_REGISTER_OP (UpdateEnvironmentOp, "update environment", kCpu)

	BDM_REGISTER_OP (VisualizationOp, "visualize", kCpu)

	BDM_REGISTER_OP (PropagateStaticnessOp, "propagate staticness", kCpu)

void	IsNonSphericalObjectPresent (const Agent agent, bool answer)

std::string	OpComputeTargetString (OpComputeTarget t)

Operation *	NewOperation (const std::string &name)
	A convenient function to get a new operation from the registry by its name. More...

	BDM_REGISTER_TEMPLATE_OP (ReductionOp, int, "ReductionOpInt", kCpu)

	BDM_REGISTER_TEMPLATE_OP (ReductionOp, real_t, "ReductionOpDouble", kCpu)

	BDM_REGISTER_TEMPLATE_OP (ReductionOp, Real3, "ReductionOpReal3", kCpu)

	BDM_REGISTER_TEMPLATE_OP (ReductionOp, Real4, "ReductionOpReal4", kCpu)

std::ostream &	operator<< (std::ostream &os, const CommandLineOptions &clo)

json	FlattenGroups (const json &j_document)

json	UnflattenGroups (const json &j_flattened, const json &j_original)

void	AssignThreadSafetyMechanism (const std::shared_ptr< cpptoml::table > &config, Param *param)

void	AssignMappedDataArrayMode (const std::shared_ptr< cpptoml::table > &config, Param *param)

void	AssignBoundSpaceMode (const std::shared_ptr< cpptoml::table > &config, Param *param)

std::ostream &	operator<< (std::ostream &os, const ResourceManager &rm)

std::ostream &	operator<< (std::ostream &os, Simulation &sim)

uint64_t	RemoveDirectoryContents (const std::string &directory)

bool	FileExists (const std::string &file_name)

void	WriteToFile (const std::string &filename, const std::string &content)

template<typename T >
bool	GetPersistentObject (const char root_file, const char obj_name, T *&empty_obj)
	Gets the persistent object from the specified ROOT file. More...

template<typename T >
void	WritePersistentObject (const char root_file, const char obj_name, const T &pst_object, const char *mode="new")
	Writes a persistent object to the specified ROOT file. More...

std::vector< TClass * >	FindClassSlow (const std::string &class_name)

std::vector< TDataMember * >	FindDataMemberSlow (TClass *tclass, const std::string &data_member)

void	Partition (uint64_t elements, uint64_t batches, uint64_t batch_num, uint64_t start, uint64_t end)

void	PlotMemoryLayout (const std::vector< Agent * > &agents, int numa_node)

void	PlotMemoryHistogram (const std::vector< Agent * > &agents, int numa_node)

void	PlotNeighborMemoryHistogram (bool before)

std::string	GetExecutablePath ()
	This function returns the path of the currently running executable. More...

std::string	GetExecutableDirectory ()

std::string	GetExecutableName ()

real_t	TimeConversionFactor (const std::string &unit)

void	PrintDataMemberInfo (const std::string &class_name)
	Writes information of each data member of a class to cout. More...

std::vector< std::string >	Split (const std::string &s, const std::string &delimiter)

bool	EndsWith (const std::string &str, const std::string &suffix)

bool	StartsWith (const std::string &str, const std::string &prefix)

template<typename... Args>
std::string	Concat (const Args &... parts)
	Concatenates all arguments into a string. Equivalent to streaming all arguments into a stringstream and calling `stream.str()` More...

std::ostream &	operator<< (std::ostream &os, const TimingAggregator &ta)

template<typename TTuple , typename TFunction >
void	Apply (TTuple *t, size_t index, TFunction &&f)

template<typename T , typename... Types>
constexpr int	GetIndex ()

template<typename TTo , typename TFrom >
TTo	bdm_static_cast (TFrom from)

std::string	GenerateSimulationInfoJson (const std::unordered_map< std::string, VtkAgents * > &vtk_agents, const std::unordered_map< std::string, VtkDiffusionGrid * > &vtk_dgrids)

	vtkStandardNewMacro (VtiWriter)

void	FixPvtu (const std::string &filename, const std::string &file_prefix, uint64_t pieces)

void	VisualizeInNotebook (size_t w=300, size_t h=300, std::string opt="")
	Visualize the agents in ROOT notebooks. More...

Variables
AgentPointerMode	gAgentPointerMode = AgentPointerMode::kIndirect

constexpr const char *	kRealtName = "double"

Typedef Documentation

◆ bdm_kd_tree_t

typedef KDTreeSingleIndexAdaptor<L2_Simple_Adaptor<real_t, NanoFlannAdapter>, NanoFlannAdapter, 3, uint64_t> bdm::bdm_kd_tree_t

Definition at line 29 of file kd_tree_environment.cc.

◆ Double3

using bdm::Double3 = typedef MathArray<double, 3>

Definition at line 436 of file math_array.h.

◆ Double4

using bdm::Double4 = typedef MathArray<double, 4>

Definition at line 441 of file math_array.h.

◆ Float3

using bdm::Float3 = typedef MathArray<float, 3>

Definition at line 435 of file math_array.h.

◆ Float4

using bdm::Float4 = typedef MathArray<float, 4>

Definition at line 440 of file math_array.h.

◆ GridNeighborMutexBuilder

using bdm::GridNeighborMutexBuilder = typedef UniformGridEnvironment::GridNeighborMutexBuilder

Definition at line 293 of file uniform_grid_environment.cc.

◆ NeighborMutex

using bdm::NeighborMutex = typedef Environment::NeighborMutexBuilder::NeighborMutex

Definition at line 291 of file uniform_grid_environment.cc.

◆ NewAgentEventUid

using bdm::NewAgentEventUid = typedef uint64_t

NewAgentEventUid is used inside behaviors to determine if a behavior should be copied if a new agent is created. Possible events are cell division, neurite branching, ...
NewAgentEventUid invariant: the number of bits set to 1 must be 1.

Definition at line 29 of file new_agent_event.h.

◆ ParamGroupUid

using bdm::ParamGroupUid = typedef uint64_t

Definition at line 26 of file param_group.h.

◆ raw_type

template<typename T >

using bdm::raw_type = typedef std::remove_pointer_t<std::decay_t<T> >

Type trait that converts T*, T&, T&&, T*& to T

Definition at line 44 of file type.h.

◆ Real3

using bdm::Real3 = typedef MathArray<real_t, 3>

Aliases for a size 3 MathArray.

Definition at line 434 of file math_array.h.

◆ Real4

using bdm::Real4 = typedef MathArray<real_t, 4>

Aliases for a size 4 MathArray.

Definition at line 439 of file math_array.h.

◆ real_t

using bdm::real_t = typedef double

Definition at line 21 of file real_t.h.

◆ vtkRealArray

using bdm::vtkRealArray = typedef typename type_ternary_operator<std::is_same<real_t, double>::value, vtkDoubleArray, vtkFloatArray>::type

Definition at line 36 of file vtk_diffusion_grid.cc.

Enumeration Type Documentation

◆ AgentPointerMode

enum bdm::AgentPointerMode

Class AgentPointer supports two different modes: First, an indirect mode in which the AgentUid is used to determine an agent.
Second, a direct mode in which the raw Agent* is used. The indirect mode is necessary if the Agent* changes during the simulation. This can happen due to sorting and balancing operation to improve the memory layout, or in a distributed runtime, where an agent might reside in a different address space. If the Agent* of an agent does not change during a simulation, the direct mode can be used to achieve better performance.

Enumerator
kIndirect
kDirect

Definition at line 42 of file agent_pointer.h.

◆ Axis

enum bdm::Axis

Enumerator
kXAxis
kYAxis
kZAxis

Definition at line 33 of file substance_initializers.h.

◆ BoundaryConditionType

enum bdm::BoundaryConditionType

strong

Available boundary conditions.

Enumerator
kDirichlet
kNeumann
kOpenBoundaries
kClosedBoundaries
kPeriodic

Definition at line 35 of file diffusion_grid.h.

◆ ExporterType

enum bdm::ExporterType

Enumerator
kBasic
kMatlab
kNeuroML
kParaview

Definition at line 69 of file exporter.h.

◆ InteractionMode

enum bdm::InteractionMode

strong

Enumerator
kAdditive
kExponential
kLogistic

Definition at line 43 of file diffusion_grid.h.

◆ OpComputeTarget

enum bdm::OpComputeTarget

Enumerator
kCpu
kCuda
kOpenCl

Definition at line 31 of file operation.h.

◆ OpType

enum bdm::OpType

Enumerator
kSchedule
kPreSchedule
kPostSchedule

Definition at line 43 of file scheduler.h.

◆ Shape

enum bdm::Shape

Enumerator
kSphere
kCylinder

Definition at line 20 of file shape.h.

Function Documentation

◆ Apply()

template<typename TTuple , typename TFunction >

void bdm::Apply	(	TTuple *	t,
		size_t	index,
		TFunction &&	f
	)

This function applies the given function on tuple element index. The peculiarity is that index is a runtime parameter. std::get<N>(tuple) however, requires a compile time constant. Therefore, Apply performs the translation to a compile time index.

Parameters

t	std::tuple or similar type that supports std::get<N>
index	runtime index specifying the type within t
f	function that should be executed on the type

Definition at line 88 of file tuple.h.

◆ ApplyBoundingBox()

void bdm::ApplyBoundingBox	(	Agent *	agent,
		Param::BoundSpaceMode	mode,
		real_t	lb,
		real_t	rb
	)

inline

Definition at line 26 of file bound_space_op.h.

◆ AssignBoundSpaceMode()

void bdm::AssignBoundSpaceMode	(	const std::shared_ptr< cpptoml::table > &	config,
		Param *	param
	)

Definition at line 196 of file param.cc.

◆ AssignMappedDataArrayMode()

void bdm::AssignMappedDataArrayMode	(	const std::shared_ptr< cpptoml::table > &	config,
		Param *	param
	)

Definition at line 170 of file param.cc.

◆ AssignThreadSafetyMechanism()

void bdm::AssignThreadSafetyMechanism	(	const std::shared_ptr< cpptoml::table > &	config,
		Param *	param
	)

Definition at line 149 of file param.cc.

◆ BDM_REGISTER_OP() [1/14]

bdm::BDM_REGISTER_OP	(	BehaviorOp	,
		"behavior"	,
		kCpu
	)

◆ BDM_REGISTER_OP() [2/14]

bdm::BDM_REGISTER_OP	(	BoundSpace	,
		"bound space"	,
		kCpu
	)

◆ BDM_REGISTER_OP() [3/14]

bdm::BDM_REGISTER_OP	(	ContinuumOp	,
		"continuum"	,
		kCpu
	)

◆ BDM_REGISTER_OP() [4/14]

bdm::BDM_REGISTER_OP	(	DiscretizationOp	,
		"discretization"	,
		kCpu
	)

◆ BDM_REGISTER_OP() [5/14]

bdm::BDM_REGISTER_OP	(	DividingCellOp	,
		"DividingCellOp"	,
		kCpu
	)

◆ BDM_REGISTER_OP() [6/14]

bdm::BDM_REGISTER_OP	(	MechanicalForcesOp	,
		"mechanical forces"	,
		kCpu
	)

◆ BDM_REGISTER_OP() [7/14]

bdm::BDM_REGISTER_OP	(	PropagateStaticnessAgentOp	,
		"propagate staticness agentop"	,
		kCpu
	)

◆ BDM_REGISTER_OP() [8/14]

bdm::BDM_REGISTER_OP	(	PropagateStaticnessOp	,
		"propagate staticness"	,
		kCpu
	)

◆ BDM_REGISTER_OP() [9/14]

bdm::BDM_REGISTER_OP	(	SetUpIterationOp	,
		"set up iteration"	,
		kCpu
	)

◆ BDM_REGISTER_OP() [10/14]

bdm::BDM_REGISTER_OP	(	TearDownIterationOp	,
		"tear down iteration"	,
		kCpu
	)

◆ BDM_REGISTER_OP() [11/14]

bdm::BDM_REGISTER_OP	(	UpdateEnvironmentOp	,
		"update environment"	,
		kCpu
	)

◆ BDM_REGISTER_OP() [12/14]

bdm::BDM_REGISTER_OP	(	UpdateStaticnessOp	,
		"update staticness"	,
		kCpu
	)

◆ BDM_REGISTER_OP() [13/14]

bdm::BDM_REGISTER_OP	(	UpdateTimeSeriesOp	,
		"update time series"	,
		kCpu
	)

◆ BDM_REGISTER_OP() [14/14]

bdm::BDM_REGISTER_OP	(	VisualizationOp	,
		"visualize"	,
		kCpu
	)

◆ BDM_REGISTER_OP_WITH_FREQ()

bdm::BDM_REGISTER_OP_WITH_FREQ	(	LoadBalancingOp	,
		"load balancing"	,
		kCpu	,
		std::numeric_limits< uint32_t >	::max()
	)

◆ BDM_REGISTER_TEMPLATE_OP() [1/4]

bdm::BDM_REGISTER_TEMPLATE_OP	(	ReductionOp	,
		int	,
		"ReductionOpInt"	,
		kCpu
	)

◆ BDM_REGISTER_TEMPLATE_OP() [2/4]

bdm::BDM_REGISTER_TEMPLATE_OP	(	ReductionOp	,
		Real3	,
		"ReductionOpReal3"	,
		kCpu
	)

◆ BDM_REGISTER_TEMPLATE_OP() [3/4]

bdm::BDM_REGISTER_TEMPLATE_OP	(	ReductionOp	,
		Real4	,
		"ReductionOpReal4"	,
		kCpu
	)

◆ BDM_REGISTER_TEMPLATE_OP() [4/4]

bdm::BDM_REGISTER_TEMPLATE_OP	(	ReductionOp	,
		real_t	,
		"ReductionOpDouble"	,
		kCpu
	)

◆ bdm_static_cast()

template<typename TTo , typename TFrom >

TTo bdm::bdm_static_cast ( TFrom from )

Use this cast if you want to downcast an object to a known type with extra safety. The extra safety check will only be performed in Debug mode.

Definition at line 60 of file type.h.

◆ BinarySearch() [1/2]

template<typename TSearch , typename TContainer >

uint64_t bdm::BinarySearch	(	const TSearch &	search_val,
		const TContainer &	container,
		uint64_t	from,
		uint64_t	to
	)

Definition at line 76 of file algorithm.h.

◆ BinarySearch() [2/2]

template<typename T >

std::pair<uint64_t, uint64_t> bdm::BinarySearch	(	uint64_t	search_val,
		const T &	container,
		uint64_t	from,
		uint64_t	to
	)

Definition at line 130 of file morton_order.cc.

◆ BoundaryTypeToString()

std::string bdm::BoundaryTypeToString ( const BoundaryConditionType & type )

Transforms a BoundaryConditionType to the corresponding string.

Definition at line 26 of file diffusion_grid.cc.

◆ Concat()

template<typename... Args>

std::string bdm::Concat ( const Args &... parts )

inline

Concatenates all arguments into a string. Equivalent to streaming all arguments into a stringstream and calling stream.str()

Parameters

[in] parts objects that compose the entire message

Returns: A unique string pointer to the message

Definition at line 70 of file string.h.

◆ CudaAllocPinned()

template<typename T >

void bdm::CudaAllocPinned	(	T **	d,
		uint64_t	elements
	)

inline

Definition at line 33 of file cuda_pinned_memory.h.

◆ CudaFreePinned()

void bdm::CudaFreePinned ( void * p )

inline

Definition at line 35 of file cuda_pinned_memory.h.

◆ EndsWith()

bool bdm::EndsWith	(	const std::string &	str,
		const std::string &	suffix
	)

inline

Definition at line 25 of file string.h.

◆ ExclusivePrefixSum()

template<typename T >

void bdm::ExclusivePrefixSum	(	T *	v,
		uint64_t	n
	)

Calculate exclusive prefix sum in-place. n must be <= t->size() - 1 This means that there must be an additional element in the vector at v[n+1]

Definition at line 61 of file algorithm.h.

◆ FileExists()

bool bdm::FileExists ( const std::string & file_name )

Definition at line 78 of file io.cc.

◆ FindClassSlow()

std::vector< TClass * > bdm::FindClassSlow ( const std::string & class_name )

Iterates over all entries in TClassTable and returns a vector of candidate TClass* that match the given class name.

Parameters

class_name does not have to be fully qualified (e.g. Cell instead of bdm::Cell).
However, Cell will also match e.g "bdm::foo::Cell"

Returns: multiple values if class_name is ambiguous and multiple classes were found in different namespaces

Definition at line 31 of file jit.cc.

◆ FindDataMemberSlow()

std::vector< TDataMember * > bdm::FindDataMemberSlow	(	TClass *	tclass,
		const std::string &	data_member
	)

Iterates over all data members of tclass and its base classes and returns TClass* that match the given class name.

Parameters

tclass	TClass for which the data members should be determined
data_member	name of the data_member (e.g. `position_` or `bdm::Cell::position_`).

Returns: multiple values if data_member name is ambiguous and multiple instances were found in tclass and its base classes

Definition at line 60 of file jit.cc.

◆ FixPvtu()

void bdm::FixPvtu	(	const std::string &	filename,
		const std::string &	file_prefix,
		uint64_t	pieces
	)

Definition at line 31 of file parallel_vtu_writer.cc.

◆ FlattenGroups()

json bdm::FlattenGroups ( const json & j_document )

Definition at line 73 of file param.cc.

◆ GenerateSimulationInfoJson()

std::string bdm::GenerateSimulationInfoJson	(	const std::unordered_map< std::string, VtkAgents * > &	vtk_agents,
		const std::unordered_map< std::string, VtkDiffusionGrid * > &	vtk_dgrids
	)

If the user selects the visualiation option export, we need to pass the information on the C++ side to a python script which generates the ParaView state file. The Json file is generated inside this function

See also: GenerateParaviewState

Definition at line 24 of file helper.cc.

◆ GetExecutableDirectory()

std::string bdm::GetExecutableDirectory ( )

Definition at line 62 of file proc.cc.

◆ GetExecutableName()

std::string bdm::GetExecutableName ( )

Definition at line 67 of file proc.cc.

◆ GetExecutablePath()

std::string bdm::GetExecutablePath ( )

This function returns the path of the currently running executable.

Definition at line 45 of file proc.cc.

◆ GetIndex()

template<typename T , typename... Types>

constexpr int bdm::GetIndex ( )

inlineconstexpr

Return the index of the first occurrence of type T within the variadic template parameter Types.

Definition at line 96 of file tuple.h.

◆ GetPersistentObject()

template<typename T >

bool bdm::GetPersistentObject	(	const char *	root_file,
		const char *	obj_name,
		T *&	empty_obj
	)

Gets the persistent object from the specified ROOT file.

Parameters

[in]	root_file	The root file
[in]	obj_name	The object name
	empty_obj	The empty object

Template Parameters

T	{ The object class type }

Returns: The persistent object.

Definition at line 101 of file io.h.

◆ InPlaceParallelPrefixSum()

template<typename T >

void bdm::InPlaceParallelPrefixSum	(	T &	v,
		uint64_t	n
	)

Calculate work-efficient inclusive prefix sum. Calculation is parallel and in-place.

Definition at line 27 of file algorithm.h.

◆ IsNonSphericalObjectPresent()

void bdm::IsNonSphericalObjectPresent	(	const Agent *	agent,
		bool *	answer
	)

Definition at line 36 of file mechanical_forces_op_cuda.cc.

◆ L2F()

template<typename TLambda >

LambdaFunctor<decltype(&TLambda::operator())> bdm::L2F ( const TLambda & l )

Wraps a lambda inside a LambdaFunctor with the same signature as the lambda. Assume the following example using L2F

void PrintSmallNeighbors(Agent* agent, real_t threshold) {
  auto functor = L2F([&](Agent* neighbor, real_t squared_distance)) {
     if (neighbor->GetDiameter() < threshold) {
       std::cout << neighbor->GetUid() << std::endl;
     }
  });
  auto* ctxt = Simulation::GetActive()->GetExecutionContext();
  ctxt->ForEachNeighbor(functor, *agent);
}

The base class of functor in the example above is Functor<void, Agent*, real_t>
The wrapped lambda is allowed to capture variables.
Without bdm::LambdaFunctor and bdm::L2F the following code is needed to achieve the same result as above. Notice the extra class MyFunctor that has to be defined outside PrintSmallNeighbors.

class MyFunctor : public Functor<void, Agent*, real_t> {
 public:
  MyFunctor(real_t threshold) : threshold_(threshold) {}
  virtual ~MyFunctor() = default;
  void operator()(Agent* neighbor, real_t squared_distance) override {
    if (neighbor->GetDiameter() < threshold_) {
      std::cout << agent->GetUid() << std::endl;
    }
  }
 private:
  real_t threshold_;
};

void PrintSmallNeighbors(Agent* agent, real_t threshold) {
  MyFunctor functor(threshold);
  auto* ctxt = Simulation::GetActive()->GetExecutionContext();
  ctxt->ForEachNeighbor(functor, *agent);
}

Definition at line 110 of file functor.h.

◆ NewOperation()

Operation* bdm::NewOperation ( const std::string & name )

inline

A convenient function to get a new operation from the registry by its name.

Definition at line 85 of file operation_registry.h.

◆ OpComputeTargetString()

std::string bdm::OpComputeTargetString ( OpComputeTarget t )

inline

Definition at line 33 of file operation.h.

◆ operator*()

template<class T , std::size_t N>

MathArray<T, N> bdm::operator*	(	T const &	scalar,
		MathArray< T, N >	array
	)

Template function to multiply array with scalar from the left.

Definition at line 429 of file math_array.h.

◆ operator<<() [1/5]

template<class T , std::size_t N>

std::ostream& bdm::operator<<	(	std::ostream &	o,
		const MathArray< T, N > &	arr
	)

Definition at line 412 of file math_array.h.

◆ operator<<() [2/5]

std::ostream& bdm::operator<<	(	std::ostream &	os,
		const CommandLineOptions &	clo
	)

Definition at line 212 of file command_line_options.cc.

◆ operator<<() [3/5]

std::ostream& bdm::operator<<	(	std::ostream &	os,
		const ResourceManager &	rm
	)

inline

Definition at line 529 of file resource_manager.h.

◆ operator<<() [4/5]

std::ostream& bdm::operator<<	(	std::ostream &	os,
		const TimingAggregator &	ta
	)

inline

Definition at line 62 of file timing_aggregator.h.

◆ operator<<() [5/5]

std::ostream& bdm::operator<<	(	std::ostream &	os,
		Simulation &	sim
	)

Definition at line 138 of file simulation.cc.

◆ Partition()

void bdm::Partition	(	uint64_t	elements,
		uint64_t	batches,
		uint64_t	batch_num,
		uint64_t *	start,
		uint64_t *	end
	)

inline

Definition at line 22 of file partition.h.

◆ PlotMemoryHistogram()

void bdm::PlotMemoryHistogram	(	const std::vector< Agent * > &	agents,
		int	numa_node
	)

Definition at line 74 of file plot_memory_layout.cc.

◆ PlotMemoryLayout()

void bdm::PlotMemoryLayout	(	const std::vector< Agent * > &	agents,
		int	numa_node
	)

Definition at line 42 of file plot_memory_layout.cc.

◆ PlotNeighborMemoryHistogram()

void bdm::PlotNeighborMemoryHistogram ( bool before )

Definition at line 137 of file plot_memory_layout.cc.

◆ PrintDataMemberInfo()

void bdm::PrintDataMemberInfo ( const std::string & class_name )

Writes information of each data member of a class to cout.

Definition at line 25 of file root.cc.

◆ RemoveDirectoryContents()

uint64_t bdm::RemoveDirectoryContents ( const std::string & directory )

Removes all contents inside the directory and returns the number of deleted files and directories that were deleted.

Definition at line 21 of file filesystem.cc.

◆ Split()

std::vector< std::string > bdm::Split	(	const std::string &	s,
		const std::string &	delimiter
	)

Definition at line 21 of file string.cc.

◆ StartsWith()

bool bdm::StartsWith	(	const std::string &	str,
		const std::string &	prefix
	)

inline

Definition at line 30 of file string.h.

◆ StringToBoundaryType()

BoundaryConditionType bdm::StringToBoundaryType ( const std::string & type )

Transforms a string to the corresponding BoundaryConditionType.

Definition at line 44 of file diffusion_grid.cc.

◆ TimeConversionFactor()

real_t bdm::TimeConversionFactor ( const std::string & unit )

inline

Definition at line 24 of file progress_bar.cc.

◆ UnflattenGroups()

json bdm::UnflattenGroups	(	const json &	j_flattened,
		const json &	j_original
	)

Definition at line 89 of file param.cc.

◆ VisualizeInNotebook()

void bdm::VisualizeInNotebook	(	size_t	w = `300`,
		size_t	h = `300`,
		std::string	opt = `""`
	)

inline

Visualize the agents in ROOT notebooks.

Definition at line 26 of file notebook_util.h.

◆ vtkStandardNewMacro()

bdm::vtkStandardNewMacro ( VtiWriter )

◆ WritePersistentObject()

template<typename T >

void bdm::WritePersistentObject	(	const char *	root_file,
		const char *	obj_name,
		const T &	pst_object,
		const char *	mode = `"new"`
	)

Writes a persistent object to the specified ROOT file.

Parameters

[in]	root_file	The root file
[in]	obj_name	The object name
	pst_object	The persistent object
[in]	mode	The mode

Template Parameters

T	{ The object class type }

Option	Details
new (default)	A new root file `root_file` is created. If file already exists, an error message is printed and the function returns.
recreate	If file does not exist, it is created (like in "new"). If file already exist, the existing file is deleted before creating the new file.
update	New classes are added to the existing directory. Existing classes with the same name are replaced by the new definition. If the directory dirname doest not exist, same effect as "new".

Definition at line 130 of file io.h.

◆ WriteToFile()

void bdm::WriteToFile	(	const std::string &	filename,
		const std::string &	content
	)

Definition at line 83 of file io.cc.

Variable Documentation

◆ gAgentPointerMode

AgentPointerMode bdm::gAgentPointerMode = AgentPointerMode::kIndirect

Global variable to select the agent pointer mode.
Replacing the global variable with an attribute in Param is too costly in terms of performance.

See also: AgentPointerMode

Definition at line 19 of file agent_pointer.cc.

◆ kRealtName

constexpr const char* bdm::kRealtName = "double"

constexpr

Definition at line 22 of file real_t.h.

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ bdm_kd_tree_t

◆ Double3

◆ Double4

◆ Float3

◆ Float4

◆ GridNeighborMutexBuilder

◆ NeighborMutex

◆ NewAgentEventUid

◆ ParamGroupUid

◆ raw_type

◆ Real3

◆ Real4

◆ real_t

◆ vtkRealArray

Enumeration Type Documentation

◆ AgentPointerMode

◆ Axis

◆ BoundaryConditionType

◆ ExporterType

◆ InteractionMode

◆ OpComputeTarget

◆ OpType

◆ Shape

Function Documentation

◆ Apply()

◆ ApplyBoundingBox()

◆ AssignBoundSpaceMode()

◆ AssignMappedDataArrayMode()

◆ AssignThreadSafetyMechanism()

◆ BDM_REGISTER_OP() [1/14]

◆ BDM_REGISTER_OP() [2/14]

◆ BDM_REGISTER_OP() [3/14]

◆ BDM_REGISTER_OP() [4/14]

◆ BDM_REGISTER_OP() [5/14]

◆ BDM_REGISTER_OP() [6/14]

◆ BDM_REGISTER_OP() [7/14]

◆ BDM_REGISTER_OP() [8/14]

◆ BDM_REGISTER_OP() [9/14]

◆ BDM_REGISTER_OP() [10/14]

◆ BDM_REGISTER_OP() [11/14]

◆ BDM_REGISTER_OP() [12/14]

◆ BDM_REGISTER_OP() [13/14]

◆ BDM_REGISTER_OP() [14/14]

◆ BDM_REGISTER_OP_WITH_FREQ()

◆ BDM_REGISTER_TEMPLATE_OP() [1/4]

◆ BDM_REGISTER_TEMPLATE_OP() [2/4]

◆ BDM_REGISTER_TEMPLATE_OP() [3/4]

◆ BDM_REGISTER_TEMPLATE_OP() [4/4]

◆ bdm_static_cast()

◆ BinarySearch() [1/2]

◆ BinarySearch() [2/2]

◆ BoundaryTypeToString()

◆ Concat()

◆ CudaAllocPinned()

◆ CudaFreePinned()

◆ EndsWith()

◆ ExclusivePrefixSum()

◆ FileExists()

◆ FindClassSlow()

◆ FindDataMemberSlow()

◆ FixPvtu()

◆ FlattenGroups()

◆ GenerateSimulationInfoJson()

◆ GetExecutableDirectory()

◆ GetExecutableName()

◆ GetExecutablePath()

◆ GetIndex()

◆ GetPersistentObject()

◆ InPlaceParallelPrefixSum()

◆ IsNonSphericalObjectPresent()

◆ L2F()

◆ NewOperation()

◆ OpComputeTargetString()