#include <cell.h>

Inheritance diagram for bdm::Cell:

Collaboration diagram for bdm::Cell:

Public Member Functions
	Cell ()

	Cell (real_t diameter)

	Cell (const Real3 &position)

	~Cell () override=default

void	Initialize (const NewAgentEvent &event) override
	This method is used to initialise the values of daughter 2 for a cell division event. More...

Shape	GetShape () const override

virtual Cell *	Divide ()
	Divide this cell. More...

virtual Cell *	Divide (real_t volume_ratio)
	Divide this cell. More...

virtual Cell *	Divide (const Real3 &axis)
	Divide this cell. More...

virtual Cell *	Divide (real_t volume_ratio, const Real3 &axis)
	Divide this cell. More...

virtual Cell *	Divide (real_t volume_ratio, real_t phi, real_t theta)
	Divide this cell. More...

real_t	GetAdherence () const

real_t	GetDiameter () const override

real_t	GetMass () const

real_t	GetDensity () const

const Real3 &	GetPosition () const override

const Real3 &	GetTractorForce () const

real_t	GetVolume () const

void	SetAdherence (real_t adherence)

void	SetDiameter (real_t diameter) override

void	SetVolume (real_t volume)

void	SetMass (real_t mass)

void	SetDensity (real_t density)

void	SetPosition (const Real3 &position) override

void	SetTractorForce (const Real3 &tractor_force)

void	ChangeVolume (real_t speed)

void	UpdateDiameter ()

void	UpdateVolume ()

void	UpdatePosition (const Real3 &delta)

Real3	CalculateDisplacement (const InteractionForce *force, real_t squared_radius, real_t dt) override

void	ApplyDisplacement (const Real3 &displacement) override

void	MovePointMass (const Real3 &normalized_dir, real_t speed)

Public Member Functions inherited from bdm::Agent
	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	Update (const NewAgentEvent &event)

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

virtual const char *	GetTypeName () const

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 void	RemoveFromSimulation ()

void *	operator new (size_t size)

void	operator delete (void *p)

Static Public Attributes
static const Real3	kXAxis = {1.0, 0.0, 0.0}
	First axis of the local coordinate system. More...

static const Real3	kYAxis = {0.0, 1.0, 0.0}
	Second axis of the local coordinate system. More...

static const Real3	kZAxis = {0.0, 0.0, 1.0}
	Third axis of the local coordinate system. More...

Protected Member Functions
Real3	TransformCoordinatesGlobalToPolar (const Real3 &coord) const

Protected Member Functions inherited from bdm::Agent
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

Private Member Functions
	BDM_AGENT_HEADER (Cell, Agent, 1)

Private Attributes
Real3	position_ = {{0, 0, 0}}
	NB: Use setter and don't assign values directly. More...

Real3	tractor_force_ = {{0, 0, 0}}

real_t	diameter_ = 0
	NB: Use setter and don't assign values directly. More...

real_t	volume_ = 0

real_t	adherence_ = 0
	NB: Use setter and don't assign values directly. More...

real_t	density_ = 0
	NB: Use setter and don't assign values directly. More...

Additional Inherited Members
Protected Attributes inherited from bdm::Agent
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...

Detailed Description

Definition at line 40 of file cell.h.

Constructor & Destructor Documentation

◆ Cell() [1/3]

bdm::Cell::Cell ( )

inline

Definition at line 51 of file cell.h.

◆ Cell() [2/3]

bdm::Cell::Cell ( real_t diameter )

inlineexplicit

Definition at line 53 of file cell.h.

◆ Cell() [3/3]

bdm::Cell::Cell ( const Real3 & position )

inlineexplicit

Definition at line 57 of file cell.h.

◆ ~Cell()

bdm::Cell::~Cell ( )

overridedefault

Member Function Documentation

◆ ApplyDisplacement()

void bdm::Cell::ApplyDisplacement ( const Real3 & displacement )

overridevirtual

Implements bdm::Agent.

Definition at line 23 of file cell.cc.

◆ BDM_AGENT_HEADER()

bdm::Cell::BDM_AGENT_HEADER	(	Cell	,
		Agent	,
		1
	)

private

◆ CalculateDisplacement()

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

inlineoverridevirtual

Implements bdm::Agent.

Definition at line 262 of file cell.h.

◆ ChangeVolume()

void bdm::Cell::ChangeVolume ( real_t speed )

inline

Definition at line 232 of file cell.h.

◆ Divide() [1/5]

virtual Cell* bdm::Cell::Divide ( )

inlinevirtual

Divide this cell.

CellDivisionEvent::volume_ratio will be between 0.9 and 1.1
The axis of division is random.

See also: CellDivisionEvent

Definition at line 134 of file cell.h.

◆ Divide() [2/5]

virtual Cell* bdm::Cell::Divide ( const Real3 & axis )

inlinevirtual

Divide this cell.

CellDivisionEvent::volume_ratio will be between 0.9 and 1.1

See also: CellDivisionEvent

Definition at line 156 of file cell.h.

◆ Divide() [3/5]

virtual Cell* bdm::Cell::Divide ( real_t volume_ratio )

inlinevirtual

Divide this cell.

The axis of division is random.

See also: CellDivisionEvent

Definition at line 143 of file cell.h.

◆ Divide() [4/5]

virtual Cell* bdm::Cell::Divide	(	real_t	volume_ratio,
		const Real3 &	axis
	)

inlinevirtual

Divide this cell.

See also: CellDivisionEvent

Definition at line 166 of file cell.h.

◆ Divide() [5/5]

virtual Cell* bdm::Cell::Divide	(	real_t	volume_ratio,
		real_t	phi,
		real_t	theta
	)

inlinevirtual

Divide this cell.

See also: CellDivisionEvent

Definition at line 174 of file cell.h.

◆ GetAdherence()

real_t bdm::Cell::GetAdherence ( ) const

inline

Definition at line 180 of file cell.h.

◆ GetDensity()

real_t bdm::Cell::GetDensity ( ) const

inline

Definition at line 186 of file cell.h.

◆ GetDiameter()

real_t bdm::Cell::GetDiameter ( ) const

inlineoverridevirtual

Implements bdm::Agent.

Definition at line 182 of file cell.h.

◆ GetMass()

real_t bdm::Cell::GetMass ( ) const

inline

Definition at line 184 of file cell.h.

◆ GetPosition()

const Real3& bdm::Cell::GetPosition ( ) const

inlineoverridevirtual

Implements bdm::Agent.

Definition at line 188 of file cell.h.

◆ GetShape()

Shape bdm::Cell::GetShape ( ) const

inlineoverridevirtual

Implements bdm::Agent.

Definition at line 127 of file cell.h.

◆ GetTractorForce()

const Real3& bdm::Cell::GetTractorForce ( ) const

inline

Definition at line 190 of file cell.h.

◆ GetVolume()

real_t bdm::Cell::GetVolume ( ) const

inline

Definition at line 192 of file cell.h.

◆ Initialize()

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

inlineoverridevirtual

This method is used to initialise the values of daughter 2 for a cell division event.

See also: CellDivisionEvent

Reimplemented from bdm::Agent.

Reimplemented in bdm::neuroscience::NeuronSoma.

Definition at line 68 of file cell.h.

◆ MovePointMass()

void bdm::Cell::MovePointMass	(	const Real3 &	normalized_dir,
		real_t	speed
	)

inline

Definition at line 357 of file cell.h.

◆ SetAdherence()

void bdm::Cell::SetAdherence ( real_t adherence )

inline

Definition at line 194 of file cell.h.

◆ SetDensity()

void bdm::Cell::SetDensity ( real_t density )

inline

Definition at line 216 of file cell.h.

◆ SetDiameter()

void bdm::Cell::SetDiameter ( real_t diameter )

inlineoverridevirtual

Implements bdm::Agent.

Definition at line 201 of file cell.h.

◆ SetMass()

void bdm::Cell::SetMass ( real_t mass )

inline

Definition at line 214 of file cell.h.

◆ SetPosition()

void bdm::Cell::SetPosition ( const Real3 & position )

inlineoverridevirtual

Implements bdm::Agent.

Definition at line 223 of file cell.h.

◆ SetTractorForce()

void bdm::Cell::SetTractorForce ( const Real3 & tractor_force )

inline

Definition at line 228 of file cell.h.

◆ SetVolume()

void bdm::Cell::SetVolume ( real_t volume )

inline

Definition at line 209 of file cell.h.

◆ TransformCoordinatesGlobalToPolar()

Real3 bdm::Cell::TransformCoordinatesGlobalToPolar ( const Real3 & coord ) const

protected

Returns the position in the polar coordinate system (cylindrical or spherical) of a point expressed in global cartesian coordinates ([1,0,0],[0,1,0],[0,0,1]).

Parameters

coord position in absolute coordinates - [x,y,z] cartesian values

Returns: the position in local coordinates

Definition at line 33 of file cell.cc.

◆ UpdateDiameter()

void bdm::Cell::UpdateDiameter ( )

inline

Definition at line 243 of file cell.h.

◆ UpdatePosition()

void bdm::Cell::UpdatePosition ( const Real3 & delta )

inline

Definition at line 257 of file cell.h.

◆ UpdateVolume()

void bdm::Cell::UpdateVolume ( )

inline

Definition at line 252 of file cell.h.

Member Data Documentation

◆ adherence_

real_t bdm::Cell::adherence_ = 0

private

NB: Use setter and don't assign values directly.

Definition at line 377 of file cell.h.

◆ density_

real_t bdm::Cell::density_ = 0

private

NB: Use setter and don't assign values directly.

Definition at line 379 of file cell.h.

◆ diameter_

real_t bdm::Cell::diameter_ = 0

private

NB: Use setter and don't assign values directly.

Definition at line 374 of file cell.h.

◆ kXAxis

const Real3 bdm::Cell::kXAxis = {1.0, 0.0, 0.0}

static

First axis of the local coordinate system.

Definition at line 45 of file cell.h.

◆ kYAxis

const Real3 bdm::Cell::kYAxis = {0.0, 1.0, 0.0}

static

Second axis of the local coordinate system.

Definition at line 47 of file cell.h.

◆ kZAxis

const Real3 bdm::Cell::kZAxis = {0.0, 0.0, 1.0}

static

Third axis of the local coordinate system.

Definition at line 49 of file cell.h.

◆ position_

Real3 bdm::Cell::position_ = {{0, 0, 0}}

private

NB: Use setter and don't assign values directly.

Definition at line 371 of file cell.h.

◆ tractor_force_

Real3 bdm::Cell::tractor_force_ = {{0, 0, 0}}

private

Definition at line 372 of file cell.h.

◆ volume_

real_t bdm::Cell::volume_ = 0

private

Definition at line 375 of file cell.h.

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

core/agent/cell.h
core/agent/cell.cc

Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Cell() [1/3]

◆ Cell() [2/3]

◆ Cell() [3/3]

◆ ~Cell()

Member Function Documentation

◆ ApplyDisplacement()

◆ BDM_AGENT_HEADER()

◆ CalculateDisplacement()

◆ ChangeVolume()

◆ Divide() [1/5]

◆ Divide() [2/5]

◆ Divide() [3/5]

◆ Divide() [4/5]

◆ Divide() [5/5]

◆ GetAdherence()

◆ GetDensity()

◆ GetDiameter()

◆ GetMass()

◆ GetPosition()

◆ GetShape()

◆ GetTractorForce()

◆ GetVolume()

◆ Initialize()

◆ MovePointMass()

◆ SetAdherence()

◆ SetDensity()

◆ SetDiameter()

◆ SetMass()

◆ SetPosition()

◆ SetTractorForce()

◆ SetVolume()

◆ TransformCoordinatesGlobalToPolar()

◆ UpdateDiameter()

◆ UpdatePosition()

◆ UpdateVolume()

Member Data Documentation

◆ adherence_

◆ density_

◆ diameter_

◆ kXAxis

◆ kYAxis

◆ kZAxis

◆ position_

◆ tractor_force_

◆ volume_