bdm::Agent Class Reference

Contains code required by all agents. More...

#include <agent.h>

Inheritance diagram for bdm::Agent:

Collaboration diagram for bdm::Agent:

Public Member Functions
	Agent ()
	Agent (TRootIOCtor *io_ctor)
	Agent (const Agent &other)
virtual	~Agent ()
virtual Agent *	New () const =0
	Create a new instance of this object using the default constructor. More...
virtual Agent *	NewCopy () const =0
	Create a copy of this object. More...
virtual void	Initialize (const NewAgentEvent &event)
virtual void	Update (const NewAgentEvent &event)
void	CreateNewAgents (const NewAgentEvent &event, const std::initializer_list< Agent * > &prototypes)
virtual const char *	GetTypeName () const
virtual Shape	GetShape () const =0
virtual std::set< std::string >	GetRequiredVisDataMembers () const
virtual void	RunDiscretization ()
void	AssignNewUid ()
const AgentUid &	GetUid () const
Spinlock *	GetLock ()
virtual void	CriticalRegion (std::vector< AgentPointer<>> *aptrs)
uint32_t	GetBoxIdx () const
void	SetBoxIdx (uint32_t idx)
void	SetStaticnessNextTimestep (bool value) const
bool	GetPropagateStaticness () const
void	SetPropagateStaticness (bool value=true)
void	PropagateStaticness (bool beginning=false)
void	UpdateStaticness ()
bool	IsStatic () const
template<typename TAgent = Agent>
AgentPointer< TAgent >	GetAgentPtr () const
	Return agent pointer. More...
void	AddBehavior (Behavior *behavior)
	Add a behavior to this agent. More...
void	RemoveBehavior (const Behavior *behavior)
void	RunBehaviors ()
	Execute all behaviorsq. More...
const InlineVector< Behavior *, 2 > &	GetAllBehaviors () const
	Return all behaviors. More...
virtual Real3	CalculateDisplacement (const InteractionForce *force, real_t squared_radius, real_t dt)=0
virtual void	ApplyDisplacement (const Real3 &displacement)=0
virtual const Real3 &	GetPosition () const =0
virtual void	SetPosition (const Real3 &pos)=0
virtual real_t	GetDiameter () const =0
virtual void	SetDiameter (real_t diameter)=0
virtual void	RemoveFromSimulation ()
void *	operator new (size_t size)
void	operator delete (void *p)

Protected Member Functions
template<typename TFrom , typename TTo >
std::enable_if< std::is_base_of< TFrom, TTo >::value, TTo * >::type	Cast (TFrom *agent) const
template<typename TFrom , typename TTo >
std::enable_if<!std::is_base_of< TFrom, TTo >::value, TTo * >::type	Cast (TFrom *agent) const

Protected Attributes
AgentUid	uid_
	unique id More...
uint32_t	box_idx_ = std::numeric_limits<uint32_t>::max()
	Grid box index. More...
InlineVector< Behavior *, 2 >	behaviors_
	collection of behaviors which define the internal behavior More...

Private Member Functions
void	InitializeBehaviors (const NewAgentEvent &event)
void	UpdateBehaviors (const NewAgentEvent &event)
	Function to invoke the Update method of the behavior or remove it from current. Forwards the call to Update to each behavior of the existing agent and removes behaviors if they are flagged. This function sets the attributes NewAgentEvent::existing_behavior and NewAgentEvent::new_behaviors to their correct value. More...

Private Attributes
Spinlock	lock_
uint16_t	run_behavior_loop_idx_ = 0
bool	is_static_ = false
	If an agent is static, we should not compute the mechanical forces. More...
bool	propagate_staticness_neighborhood_ = true
bool	is_static_next_ts_ = false
	Flag to determine of an agent is static in the next timestep. More...

Detailed Description

Contains code required by all agents.

Definition at line 79 of file agent.h.

Constructor & Destructor Documentation

Agent() [1/3]

bdm::Agent::Agent

(

)

Definition at line 41 of file agent.cc.

Agent() [2/3]

bdm::Agent::Agent ( TRootIOCtor *  io_ctor )

explicit

Definition at line 45 of file agent.cc.

Agent() [3/3]

bdm::Agent::Agent

(

const Agent &

other

)

Definition at line 47 of file agent.cc.

~Agent()

bdm::Agent::~Agent ( )

virtual

Definition at line 59 of file agent.cc.

Member Function Documentation

AddBehavior()

void bdm::Agent::AddBehavior

(

Behavior *

behavior

)

Add a behavior to this agent.

Definition at line 132 of file agent.cc.

ApplyDisplacement()

virtual void bdm::Agent::ApplyDisplacement ( const Real3 &  displacement )

pure virtual

Implemented in bdm::Cell, bdm::neuroscience::NeuriteElement, and bdm::SphericalAgent.

AssignNewUid()

void bdm::Agent::AssignNewUid

(

)

Definition at line 119 of file agent.cc.

CalculateDisplacement()

virtual Real3 bdm::Agent::CalculateDisplacement ( const InteractionForce *  force, real_t  squared_radius, real_t  dt  )

pure virtual

Implemented in bdm::neuroscience::NeuriteElement, bdm::Cell, and bdm::SphericalAgent.

Cast() [1/2]

template<typename TFrom , typename TTo >

std::enable_if<std::is_base_of<TFrom, TTo>::value, TTo*>::type bdm::Agent::Cast ( TFrom *  agent ) const

inlineprotected

Definition at line 278 of file agent.h.

Cast() [2/2]

template<typename TFrom , typename TTo >

std::enable_if<!std::is_base_of<TFrom, TTo>::value, TTo*>::type bdm::Agent::Cast ( TFrom *  agent ) const

inlineprotected

Definition at line 284 of file agent.h.

CreateNewAgents()

void bdm::Agent::CreateNewAgents ( const NewAgentEvent &  event, const std::initializer_list< Agent * > &  prototypes  )

inline

This method creates a new agent for each entry in prototypes.
The prototypes list defines the type of the new agent. This function calls prototype->New() internally. New agents are automatically added to the execution context right after they are initialized. This function sets the attributes NewAgentEvent::existing_agent and NewAgentEvent::new_agents to their correct values. Lastly, this function calls this->Update(event)
The newly created and initialized agents can be found in event.new_agents.

Definition at line 121 of file agent.h.

CriticalRegion()

virtual void bdm::Agent::CriticalRegion ( std::vector< AgentPointer<>> *  aptrs )

inlinevirtual

If the thread-safety mechanism is set to user-specified this function will be called before the operations are executed for this agent.
Subclasses define the critical region by adding the AgentPointers of all agents that must not be processed in parallel.
Don't forget to add the current agent.
Here an example from NeuronSoma.

void NeuronSoma::CriticalRegion(std::vector<AgentPointer<>>* aptrs) {
  aptrs->reserve(daughters_.size() + 1);
  aptrs->push_back(Agent::GetAgentPtr<>());
  for (auto& daughter : daughters_) {
    aptrs->push_back(daughter);
  }
}

See also

Param::thread_safety_mechanism

AgentPointer

NeuronSoma::CriticalRegion

Reimplemented in bdm::neuroscience::NeuriteElement, and bdm::neuroscience::NeuronSoma.

Definition at line 170 of file agent.h.

GetAgentPtr()

template<typename TAgent = Agent>

AgentPointer<TAgent> bdm::Agent::GetAgentPtr ( ) const

inline

Return agent pointer.

Definition at line 208 of file agent.h.

GetAllBehaviors()

const InlineVector< Behavior *, 2 > & bdm::Agent::GetAllBehaviors

(

)

const

Return all behaviors.

Definition at line 154 of file agent.cc.

GetBoxIdx()

uint32_t bdm::Agent::GetBoxIdx

(

)

const

Definition at line 125 of file agent.cc.

GetDiameter()

virtual real_t bdm::Agent::GetDiameter ( ) const

pure virtual

Implemented in bdm::Cell, bdm::neuroscience::NeuriteElement, and bdm::SphericalAgent.

GetLock()

Spinlock* bdm::Agent::GetLock ( )

inline

Definition at line 150 of file agent.h.

GetPosition()

virtual const Real3& bdm::Agent::GetPosition ( ) const

pure virtual

Implemented in bdm::Cell, bdm::neuroscience::NeuriteElement, and bdm::SphericalAgent.

GetPropagateStaticness()

bool bdm::Agent::GetPropagateStaticness ( ) const

inline

Definition at line 180 of file agent.h.

GetRequiredVisDataMembers()

virtual std::set<std::string> bdm::Agent::GetRequiredVisDataMembers ( ) const

inlinevirtual

Returns the data members that are required to visualize this simulation object.

Reimplemented in bdm::neuroscience::NeuriteElement.

Definition at line 140 of file agent.h.

GetShape()

virtual Shape bdm::Agent::GetShape ( ) const

pure virtual

Implemented in bdm::Cell, bdm::neuroscience::NeuriteElement, and bdm::SphericalAgent.

GetTypeName()

virtual const char* bdm::Agent::GetTypeName ( ) const

inlinevirtual

Definition at line 134 of file agent.h.

GetUid()

const AgentUid & bdm::Agent::GetUid

(

)

const

Definition at line 123 of file agent.cc.

Initialize()

void bdm::Agent::Initialize ( const NewAgentEvent &  event )

virtual

This method is called to initialize new agents that are created during a NewAgentEvent. Override this method to initialize attributes of your own Agent subclasses. NB: Don't forget to call the implementation of the base class first. Base::Initialize(event); Failing to do so will result in errors.

Reimplemented in bdm::Cell, bdm::neuroscience::NeuriteElement, and bdm::neuroscience::NeuronSoma.

Definition at line 65 of file agent.cc.

InitializeBehaviors()

void bdm::Agent::InitializeBehaviors ( const NewAgentEvent &  event )

private

Function to copy behaviors from existing Agent to this one and to initialize them. This function sets the attributes NewAgentEvent::existing_behavior and NewAgentEvent::new_behaviors to their correct value.

Definition at line 163 of file agent.cc.

IsStatic()

bool bdm::Agent::IsStatic ( ) const

inline

Definition at line 204 of file agent.h.

New()

virtual Agent* bdm::Agent::New ( ) const

pure virtual

Create a new instance of this object using the default constructor.

NewCopy()

virtual Agent* bdm::Agent::NewCopy ( ) const

pure virtual

Create a copy of this object.

operator delete()

void bdm::Agent::operator delete ( void *  p )

inline

Definition at line 260 of file agent.h.

operator new()

void* bdm::Agent::operator new ( size_t  size )

inline

Definition at line 251 of file agent.h.

PropagateStaticness()

void bdm::Agent::PropagateStaticness

(

bool

beginning = false

)

If the agent is not static, a call to this method sets all neighbors to 'not static'.
This method will be called twice: 1) At the end of the iteration using an agent op (beginning=false).
2) At the beginning of the iteration as pre_scheduled op (beginning=true).
1 is faster because it can use cached neighbors, but it might miss some conditions. (Neighbors modifying an agent after PropagateStaticness has been called. Agent which is larger than the largest agent.) 2 is slower but able to process all conditions. Therefore, we use 1 whenever possible and 2 for the remaining conditions.

Definition at line 77 of file agent.cc.

RemoveBehavior()

void bdm::Agent::RemoveBehavior

(

const Behavior *

behavior

)

Remove a behavior from this agent The parameter behavior will be deleted if the instance is stored in this agent and must not be used after the call to RemoveBehavior.

Definition at line 134 of file agent.cc.

RemoveFromSimulation()

void bdm::Agent::RemoveFromSimulation ( )

virtual

Definition at line 159 of file agent.cc.

RunBehaviors()

void bdm::Agent::RunBehaviors

(

)

Execute all behaviorsq.

Definition at line 146 of file agent.cc.

RunDiscretization()

void bdm::Agent::RunDiscretization ( )

virtual

Reimplemented in bdm::neuroscience::NeuriteElement.

Definition at line 117 of file agent.cc.

SetBoxIdx()

void bdm::Agent::SetBoxIdx

(

uint32_t

idx

)

Definition at line 127 of file agent.cc.

SetDiameter()

virtual void bdm::Agent::SetDiameter ( real_t  diameter )

pure virtual

Implemented in bdm::Cell, bdm::neuroscience::NeuriteElement, and bdm::SphericalAgent.

SetPosition()

virtual void bdm::Agent::SetPosition ( const Real3 &  pos )

pure virtual

Implemented in bdm::Cell, bdm::neuroscience::NeuriteElement, and bdm::SphericalAgent.

SetPropagateStaticness()

void bdm::Agent::SetPropagateStaticness ( bool  value = true )

inline

Definition at line 184 of file agent.h.

SetStaticnessNextTimestep()

void bdm::Agent::SetStaticnessNextTimestep ( bool  value ) const

inline

Definition at line 176 of file agent.h.

Update()

void bdm::Agent::Update ( const NewAgentEvent &  event )

virtual

This method is called to update the existing agent at the end of a NewAgentEvent. Override this method to update attributes of your own Agent subclasses. NB: Don't forget to call the implementation of the base class first. Base::Update(event); Failing to do so will result in errors.

Reimplemented in bdm::neuroscience::NeuriteElement, and bdm::neuroscience::NeuronSoma.

Definition at line 71 of file agent.cc.

UpdateBehaviors()

void bdm::Agent::UpdateBehaviors ( const NewAgentEvent &  event )

private

Function to invoke the Update method of the behavior or remove it from current. Forwards the call to Update to each behavior of the existing agent and removes behaviors if they are flagged. This function sets the attributes NewAgentEvent::existing_behavior and NewAgentEvent::new_behaviors to their correct value.

Definition at line 183 of file agent.cc.

UpdateStaticness()

void bdm::Agent::UpdateStaticness

(

)

Definition at line 111 of file agent.cc.

Member Data Documentation

behaviors_

InlineVector<Behavior*, 2> bdm::Agent::behaviors_

protected

collection of behaviors which define the internal behavior

Definition at line 275 of file agent.h.

box_idx_

uint32_t bdm::Agent::box_idx_ = std::numeric_limits<uint32_t>::max()

protected

Grid box index.

Definition at line 273 of file agent.h.

is_static_

bool bdm::Agent::is_static_ = false

private

If an agent is static, we should not compute the mechanical forces.

Definition at line 297 of file agent.h.

is_static_next_ts_

bool bdm::Agent::is_static_next_ts_ = false

mutableprivate

Flag to determine of an agent is static in the next timestep.

Definition at line 302 of file agent.h.

lock_

Spinlock bdm::Agent::lock_

private

Definition at line 290 of file agent.h.

propagate_staticness_neighborhood_

bool bdm::Agent::propagate_staticness_neighborhood_ = true

private

If an agent becomes non-static (i.e. it moved or grew), we should set this flag to true to also compute mechanical forces on the neighboring agents

Definition at line 300 of file agent.h.

run_behavior_loop_idx_

uint16_t bdm::Agent::run_behavior_loop_idx_ = 0

private

Helper variable used to support removal of behaviors while RunBehaviors iterates over them.

Definition at line 294 of file agent.h.

uid_

AgentUid bdm::Agent::uid_

protected

unique id

Definition at line 271 of file agent.h.

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

• core/agent/agent.h
• core/agent/agent.cc