Defines the basic properties that a interactable object can have. More...

#include <BaseInteractable.h>

Inheritance diagram for BaseInteractable:

Public Member Functions
	BaseInteractable ()
	Default BaseInteractable constructor, it simply creates an empty BaseInteractable. More...

	BaseInteractable (const BaseInteractable &p)
	Copy constructor. It copies the BaseInteractable and all objects it contains. More...

virtual	~BaseInteractable ()
	Destructor, it simply destructs the BaseInteractable and all the objects it contains. More...

virtual void	read (std::istream &is)=0
	Reads a BaseInteractable from an input stream. More...

virtual void	write (std::ostream &os) const =0
	Write a BaseInteractable to an output stream. More...

unsigned int	getIndSpecies () const
	Returns the index of the Species of this BaseInteractable. More...

virtual void	setIndSpecies (unsigned int indSpecies)
	Sets the index of the Species of this BaseInteractable. More...

const ParticleSpecies *	getSpecies () const
	Returns a pointer to the species of this BaseInteractable. More...

void	setSpecies (const ParticleSpecies *species)
	Sets the species of this BaseInteractable. More...

const Vec3D &	getForce () const
	Returns the force on this BaseInteractable. More...

const Vec3D &	getTorque () const
	Returns the torque on this BaseInteractable. More...

void	setForce (const Vec3D &force)
	Sets the force on this BaseInteractable. More...

void	setTorque (const Vec3D &torque)
	Sets the torque on this BaseInteractable. More...

void	addForce (const Vec3D &addForce)
	Adds an amount to the force on this BaseInteractable. More...

void	addTorque (const Vec3D &addTorque)
	Adds an amount to the torque on this BaseInteractable. More...

const Vec3D &	getPosition () const
	Returns the position of this BaseInteractable. More...

const Vec3D &	getOrientation () const
	Returns the orientation of this BaseInteractable. More...

void	setPosition (const Vec3D &position)
	Sets the position of this BaseInteractable. More...

void	setOrientation (const Vec3D &orientation)
	Sets the orientation of this BaseInteractable. More...

virtual void	move (const Vec3D &move)
	Moves this BaseInteractable by adding an amount to the position. More...

void	rotate (const Vec3D &rotate)
	Rotates this BaseInteractable. More...

const std::list < BaseInteraction * > &	getInteractions () const
	Returns a reference to the list of interactions in this BaseInteractable. More...

void	addInteraction (BaseInteraction *I)
	Adds an interaction to this BaseInteractable. More...

bool	removeInteraction (BaseInteraction *I)
	Removes an interaction from this BaseInteractable. More...

void	copyInteractionsForPeriodicParticles (const BaseInteractable &p)
	Copies interactions to this BaseInteractable whenever a periodic copy made. More...

void	setVelocity (const Vec3D &velocity)
	set the velocity of the BaseInteractable. More...

void	setAngularVelocity (const Vec3D &angularVelocity)
	set the angular velocity of the BaseInteractble. More...

void	addVelocity (const Vec3D &velocity)
	adds an increment to the velocity. More...

void	addAngularVelocity (const Vec3D &angularVelocity)
	add an increment to the angular velocity. More...

virtual const Vec3D &	getVelocity () const
	Returns the velocity of this interactable. More...

virtual const Vec3D &	getAngularVelocity () const
	Returns the angular velocity of this interactable. More...

void	setPrescribedPosition (const std::function< Vec3D(double)> &prescribedPosition)
	Allows the position of an infinite mass interactable to be prescribed. More...

void	applyPrescribedPosition (double time)
	Computes the position from the user defined prescribed position function. More...

void	setPrescribedVelocity (const std::function< Vec3D(double)> &prescribedVelocity)
	Allows the velocity of an infinite mass interactable to be prescribed. More...

void	applyPrescribedVelocity (double time)
	Computes the velocity from the user defined prescribed velocity function. More...

void	setPrescribedOrientation (const std::function< Vec3D(double)> &prescribedOrientation)
	Allows the orientation of the infinite mass interactbale to be prescribed. More...

void	applyPrescribedOrientation (double time)
	Computes the orientation from the user defined prescribed orientation function. More...

void	setPrescribedAngularVelocity (const std::function< Vec3D(double)> &prescribedAngularVelocity)
	Allows the angular velocity of the infinite mass interactable to be prescribed. More...

void	applyPrescribedAngularVelocity (double time)
	Computes the angular velocity from the user defined prescribed angular velocity. More...

virtual std::vector < BaseInteraction * >	getInteractionWith (BaseParticle P, Mdouble timeStamp, InteractionHandler interactionHandler)=0
	Returns the interaction between this object and a given BaseParticle. More...

virtual const Vec3D	getVelocityAtContact (const Vec3D &contact) const
	Returns the velocity at the contact point, use by many force laws. More...

void	integrateBeforeForceComputation (double time, double timeStep)
	This is part of integrate routine for objects with infinite mass. More...

void	integrateAfterForceComputation (double time, double timeStep)
	This is part of the integration routine for objects with infinite mass. More...

Public Member Functions inherited from BaseObject
	BaseObject ()
	Default constructor. More...

	BaseObject (const BaseObject &p)
	Copy constructor, copies all the objects BaseObject contains. More...

virtual	~BaseObject ()
	virtual destructor More...

virtual std::string	getName () const =0
	A purely virtual function. More...

virtual void	moveInHandler (const unsigned int index)
	Except that it is virtual, it does the same thing as setIndex() does. More...

void	setIndex (const unsigned int index)
	Allows one to assign an index to an object in the handler/container. More...

void	setId (const unsigned int id)
	Assigns a unique identifier to each object in the handler (container) which remains constant even after the object is deleted from the container/handler. More...

unsigned int	getIndex () const
	Returns the index of the object in the handler. More...

unsigned int	getId () const
	Returns the unique identifier of any particular object. More...

Private Attributes
std::function< Vec3D(double)>	prescribedPosition_

std::function< Vec3D(double)>	prescribedVelocity_

std::function< Vec3D(double)>	prescribedOrientation_

std::function< Vec3D(double)>	prescribedAngularVelocity_

Vec3D	position_

Vec3D	orientation_

Vec3D	angularVelocity_

Vec3D	force_

Vec3D	torque_

const ParticleSpecies *	species_

unsigned int	indSpecies_

Vec3D	velocity_

std::list< BaseInteraction * >	interactions_

Detailed Description

Defines the basic properties that a interactable object can have.

Inherits from class BaseObject (public) Also it includes a lot of code to deal with interactable objects that have a prescibed motion. Most of the code in here is MercuryDPM internal. The only place an user will interface with this code is for setting the lambda functions that prescribe the motion of infinite mass particles.

Todo:: Check prescribed objects have infinite mass.

Definition at line 51 of file BaseInteractable.h.

Constructor & Destructor Documentation

BaseInteractable::BaseInteractable ( )

Default BaseInteractable constructor, it simply creates an empty BaseInteractable.

Todo:: TW: why do some constructors (e.g. BaseInteractable, BaseParticle)not explicitly call the constructor from the inherited class?

Sets all vectors to zero and all point to nullptr.

Definition at line 38 of file BaseInteractable.cc.

References angularVelocity_, DEBUG, force_, indSpecies_, logger, orientation_, position_, prescribedAngularVelocity_, prescribedOrientation_, prescribedPosition_, prescribedVelocity_, Vec3D::setZero(), species_, torque_, and velocity_.

 {
     position_.setZero();
     orientation_.setZero();
     velocity_.setZero();
     angularVelocity_.setZero();
     force_.setZero();
     torque_.setZero();
     indSpecies_ = 0;
     species_ = nullptr;
     prescribedPosition_ = nullptr;
     prescribedVelocity_ = nullptr;
     prescribedOrientation_ = nullptr;
     prescribedAngularVelocity_ = nullptr;
     logger(DEBUG, "BaseInteractable::BaseInteractable() finished");
 }

BaseInteractable::BaseInteractable ( const BaseInteractable & p )

Copy constructor. It copies the BaseInteractable and all objects it contains.

Note, this does not copy interactions of a interactable. As these often require extra work. All the other properties are copied normally. Please use this copy with care.

Definition at line 61 of file BaseInteractable.cc.

References angularVelocity_, DEBUG, force_, indSpecies_, interactions_, logger, orientation_, position_, prescribedAngularVelocity_, prescribedOrientation_, prescribedPosition_, prescribedVelocity_, species_, torque_, and velocity_.

         : BaseObject(p)
 {
     interactions_.clear();
     position_ = p.position_;
     orientation_ = p.orientation_;
     velocity_ = p.velocity_;
     angularVelocity_ = p.angularVelocity_;
     force_ = p.force_;
     torque_ = p.torque_;
     species_ = p.species_;
     indSpecies_ = p.indSpecies_;
     prescribedPosition_ = p.prescribedPosition_;
     prescribedVelocity_ = p.prescribedVelocity_;
     prescribedOrientation_ = p.prescribedOrientation_;
     prescribedAngularVelocity_ = p.prescribedAngularVelocity_;
     logger(DEBUG,"BaseInteractable::BaseInteractable(const BaseInteractable &p finished");
 }

BaseInteractable::~BaseInteractable ( )

virtual

Destructor, it simply destructs the BaseInteractable and all the objects it contains.

Removes all the interactions from the interactable.

Definition at line 83 of file BaseInteractable.cc.

References DEBUG, BaseObject::getId(), BaseObject::getIndex(), interactions_, logger, and VERBOSE.

 {
     logger(VERBOSE, "Deleting BaseInteractable with index= % and id = % size = %", getIndex(),getId(),interactions_.size());
     while (interactions_.size() > 0)
     {
         interactions_.front()->removeFromHandler();
     }
     logger(DEBUG,"BaseInteractable::~BaseInteractable() finished");
 }

Member Function Documentation

void BaseInteractable::addAngularVelocity ( const Vec3D & angularVelocity )

add an increment to the angular velocity.

Parameters

[in] angularVelocity increment which to increase the angularVelocity by.

Definition at line 444 of file BaseInteractable.cc.

References angularVelocity_.

Referenced by BaseParticle::angularAccelerate().

 {
     angularVelocity_ += angularVelocity;
 }

void BaseInteractable::addForce ( const Vec3D & addForce )

Adds an amount to the force on this BaseInteractable.

Incremental version of BaseInteractable::setForce. Also see BaseInteraction::setForce for were this is used.

Parameters

[in] addForce Vec3D incremental force which is added to the total force of the interactable.

Definition at line 203 of file BaseInteractable.cc.

References force_.

Referenced by DPMBase::computeExternalForces(), DPMBase::computeForcesDueToWalls(), and DPMBase::computeInternalForces().

 {
     force_ += addForce;
 }

void BaseInteractable::addInteraction ( BaseInteraction * I )

Adds an interaction to this BaseInteractable.

Added a new interactions to the current interactable.

Parameters

[in] I Pointer to the new interaction which is to be added to the list of interactions of this interactable.

Definition at line 355 of file BaseInteractable.cc.

References interactions_.

Referenced by BaseInteraction::BaseInteraction(), BaseInteraction::copySwitchPointer(), BaseInteraction::setI(), and BaseInteraction::setP().

 {
     interactions_.push_back(I);
 }

void BaseInteractable::addTorque ( const Vec3D & addTorque )

Adds an amount to the torque on this BaseInteractable.

Incremental version of BaseInteractable::setTorque. Also see BaseInteraction::setTorque for were this is used.

Parameters

[in] addTorque Vec3D incremental force which is added to the total torque of the interactable.

Definition at line 214 of file BaseInteractable.cc.

References torque_.

Referenced by DPMBase::computeForcesDueToWalls(), and DPMBase::computeInternalForces().

 {
     torque_ += addTorque;
 }

void BaseInteractable::addVelocity ( const Vec3D & velocity )

adds an increment to the velocity.

See also BaseInteractable::setVelocity

Parameters

[in] velocity Vec3D containing the velocity increment which to increase the velocity by.

Definition at line 434 of file BaseInteractable.cc.

References velocity_.

Referenced by BaseParticle::accelerate(), ShearBoxBoundary::shiftHorizontalPosition(), and LeesEdwardsBoundary::shiftVerticalPosition().

 {
     velocity_ += velocity;
 }

void BaseInteractable::applyPrescribedAngularVelocity ( double time )

Computes the angular velocity from the user defined prescribed angular velocity.

This calls the prescribedAngularVelocity function if one has been defined. See also BaseInteractable::setPrescribedAngularVelocity

Parameters

[in] time double which is the current time of the simulation.

Definition at line 585 of file BaseInteractable.cc.

References prescribedAngularVelocity_, and setAngularVelocity().

Referenced by integrateAfterForceComputation(), and integrateBeforeForceComputation().

 {
     if(prescribedAngularVelocity_)
     {
         setAngularVelocity(prescribedAngularVelocity_(time));
     }
 }

void BaseInteractable::applyPrescribedOrientation ( double time )

Computes the orientation from the user defined prescribed orientation function.

This calls the prescribedOrientation function if one has been defined. See also BaseInteractable::setPrescribedOrientation

Parameters

[in] time double which is the current time of the simulation.

Definition at line 558 of file BaseInteractable.cc.

References prescribedOrientation_, and setOrientation().

Referenced by integrateBeforeForceComputation().

 {
     if(prescribedOrientation_)
     {
         setOrientation(prescribedOrientation_(time));
     }
 }

void BaseInteractable::applyPrescribedPosition ( double time )

Computes the position from the user defined prescribed position function.

This calls the prescribedPosition function if one has been defined. See also BaseInteractable::setPrescribedPosition

Parameters

[in] time double which is the current time of the simulation.

Definition at line 496 of file BaseInteractable.cc.

References prescribedPosition_, and setPosition().

Referenced by integrateBeforeForceComputation().

 {
     if(prescribedPosition_)
     {
         setPosition(prescribedPosition_(time));
     }
 }

void BaseInteractable::applyPrescribedVelocity ( double time )

Computes the velocity from the user defined prescribed velocity function.

This calls the prescribedVeclocity function if one has been defined. See also BaseInteractable::setPrescribedVelocity

Parameters

[in] time double which is the current time of the simulation.

Definition at line 527 of file BaseInteractable.cc.

References prescribedVelocity_, and setVelocity().

Referenced by integrateAfterForceComputation(), and integrateBeforeForceComputation().

 {
     if(prescribedVelocity_)
     {
         setVelocity(prescribedVelocity_(time));
     }
 }

void BaseInteractable::copyInteractionsForPeriodicParticles ( const BaseInteractable & pOriginal )

Copies interactions to this BaseInteractable whenever a periodic copy made.

This loops over all interactions of periodic (particle) and calls copySwitchPointer, which copies the interactions.

Parameters

[in] pOriginal Reference to the BaseInteractable which is to be copied to create the ghost particles.

Definition at line 459 of file BaseInteractable.cc.

References BaseInteraction::copySwitchPointer(), and interactions_.

Referenced by LeesEdwardsBoundary::createHorizontalPeriodicParticles(), ShearBoxBoundary::createHorizontalPeriodicParticles(), MaserBoundary::createPeriodicParticles(), AngledPeriodicBoundary::createPeriodicParticles(), PeriodicBoundary::createPeriodicParticles(), ShearBoxBoundary::createVerticalPeriodicParticles(), and LeesEdwardsBoundary::createVerticalPeriodicParticles().

 {
     for (BaseInteraction* interaction : pOriginal.interactions_)
     {
         //So here this is the ghost and it is the interaction of the ghost/
         interaction->copySwitchPointer(&pOriginal, this);
     }
 }

const Vec3D & BaseInteractable::getAngularVelocity ( ) const

virtual

Returns the angular velocity of this interactable.

Returns the angular velocity of the BaseInteractbale. Note, this is the same for all BaseInteractables; it is the direction the object is moving in.

Returns: Vec3D reference which contains the current angular velocity of the current BaseInteractable.

Definition at line 405 of file BaseInteractable.cc.

References angularVelocity_.

Referenced by getVelocityAtContact(), integrateBeforeForceComputation(), BaseParticle::integrateBeforeForceComputation(), helpers::objectivenessTest(), and AngledPeriodicBoundary::shiftPosition().

 {
     return angularVelocity_;
 }

const Vec3D & BaseInteractable::getForce ( ) const

Returns the force on this BaseInteractable.

Return the current force being to the BaseInteractable. Note, the code works by first computing the forces of each interaction and then it loops over all BaseInteracables applying forces to them from the interactions they are involved in.

Returns: const Vec3D reference that is the total force applied to this interactable.

Definition at line 154 of file BaseInteractable.cc.

References force_.

Referenced by BaseParticle::integrateAfterForceComputation(), and BaseParticle::integrateBeforeForceComputation().

 {
     return force_;
 }

unsigned int BaseInteractable::getIndSpecies ( ) const

Returns the index of the Species of this BaseInteractable.

Returns the unsigned int to the index of the species associated with the interactable object.

Returns: Unsigned int which is the unique index of the species

Definition at line 98 of file BaseInteractable.cc.

References indSpecies_.

Referenced by InteractionHandler::getInteraction(), ParticleHandler::readObject(), BaseWall::setHandler(), BaseParticle::setHandler(), and BaseWall::setIndSpecies().

 {
     return indSpecies_;
 }

const std::list< BaseInteraction * > & BaseInteractable::getInteractions ( ) const

Returns a reference to the list of interactions in this BaseInteractable.

Returns a list of interactions which belong to this interactable.

Returns: Returns an std::list of pointers to all the interactions which this interacable is involved in.

Definition at line 345 of file BaseInteractable.cc.

References interactions_.

Referenced by InteractionHandler::getExistingInteraction(), InteractionHandler::getInteraction(), LiquidMigrationWilletInteraction::getNumberOfContacts(), DPMBase::removeDuplicatePeriodicParticles(), LiquidMigrationWilletInteraction::rupture(), and AngledPeriodicBoundary::shiftPosition().

 {
     return interactions_;
 }

virtual std::vector<BaseInteraction*> BaseInteractable::getInteractionWith	(	BaseParticle *	P,
		Mdouble	timeStamp,
		InteractionHandler *	interactionHandler
	)

pure virtual

Returns the interaction between this object and a given BaseParticle.

Todo:

TW make sure this function sets normal, distance, overlap, contact point

AT why is this a BaseParticle and not a BaseInteratable.

Implemented in BaseParticle, BaseWall, TriangulatedWall, and RestrictedWall.

const Vec3D & BaseInteractable::getOrientation ( ) const

Returns the orientation of this BaseInteractable.

Returns the reference to a Vec3D which contains the orientation of the interactionable. Please note the interpretation of this depends on which interactable. Please see derived objects for details.

Todo:

This is not full implemented and is related to quaterians.

Returns: Returns a reference to a Vec3D returns the position of the interactable.

Definition at line 243 of file BaseInteractable.cc.

References orientation_.

Referenced by AxisymmetricIntersectionOfWalls::convertLimits(), AxisymmetricIntersectionOfWalls::getDistanceAndNormal(), helpers::objectivenessTest(), and AngledPeriodicBoundary::shiftPosition().

 {
     return orientation_;
 }

const Vec3D & BaseInteractable::getPosition ( ) const

Returns the position of this BaseInteractable.

Returns the reference to a Vec3D which contains the position of the interactionable. Please note the interpretation of this depends on which interactable. For particles this is the centre of the particle; where for walls it is one point of the wall given $r.n=p$

Returns: Returns a reference to a Vec3D returns the position of the interactable.

Definition at line 228 of file BaseInteractable.cc.

References position_.

 {
     return position_;
 }

const ParticleSpecies * BaseInteractable::getSpecies ( ) const

Returns a pointer to the species of this BaseInteractable.

This function return a ParticleSpecies* for the current interacable. Please note, this is a ParticleSpecies; not, a BaseSpecies as interactables must have physically properties as well.

Returns: constant ParticleSpecies* pointer to the species storing the physical properties of this interactable.

Definition at line 121 of file BaseInteractable.cc.

References species_.

Referenced by ParticleHandler::addObject(), WallHandler::addObject(), IntersectionOfWalls::addObject(), MaserBoundary::addParticleToMaser(), MaserBoundary::checkBoundaryAfterParticleMoved(), ChargedBondedInteraction::computeAdhesionForce(), MaserBoundary::createPeriodicParticles(), ChargedBondedInteraction::getElasticEnergy(), DPMBase::getInfo(), BaseParticle::getInteractionRadius(), BaseParticle::getWallInteractionRadius(), RestrictedWall::set(), BaseParticle::setRadius(), and BaseParticle::unfix().

 {
     //logger.assert(species_,"Species of % % has to be defined",getName(),getIndex());
     return species_;
 }

const Vec3D & BaseInteractable::getTorque ( ) const

Returns the torque on this BaseInteractable.

Return the current torque being to the BaseInteractable. Note, the code works by first computing the forces of each interaction and then it loops over all BaseInteracables applying forces to them from the interactions they are involved in.

Returns: const Vec3D reference that is the total force applied to this interactable.

Definition at line 167 of file BaseInteractable.cc.

References torque_.

Referenced by BaseParticle::integrateAfterForceComputation(), and BaseParticle::integrateBeforeForceComputation().

 {
     return torque_;
 }

const Vec3D & BaseInteractable::getVelocity ( ) const

virtual

Returns the velocity of this interactable.

Returns the velocity of the BaseInteractbale. Note, this is the same for all BaseInteractables; it is the direction the object is moving in.

Returns: Vec3D reference which contains the current velocity of the current BaseInteractable.

Definition at line 393 of file BaseInteractable.cc.

References velocity_.

Referenced by FrictionInteraction::computeFrictionForce(), MindlinRollingTorsionInteraction::computeFrictionForce(), BaseParticle::getKineticEnergy(), getVelocityAtContact(), integrateBeforeForceComputation(), BaseParticle::integrateBeforeForceComputation(), InfiniteWallWithHole::move_time(), helpers::objectivenessTest(), CircularPeriodicBoundary::rotateParticle(), and AngledPeriodicBoundary::shiftPosition().

 {
     return velocity_;
 }

const Vec3D BaseInteractable::getVelocityAtContact ( const Vec3D & contact ) const

virtual

Returns the velocity at the contact point, use by many force laws.

Definition at line 448 of file BaseInteractable.cc.

References Vec3D::cross(), getAngularVelocity(), getPosition(), and getVelocity().

 {
     return getVelocity() - Vec3D::cross(contact - getPosition(), getAngularVelocity());
 }

void BaseInteractable::integrateAfterForceComputation	(	double	time,
		double	timeStep
	)

This is part of the integration routine for objects with infinite mass.

This is the last part of time integration for interactable objects which have an infinite mass.

Parameters

[in]	time	double which is the current simulation time
[in]	timeStep	double which is the current delta time of the simulation i.e. the size of each time step.

Definition at line 680 of file BaseInteractable.cc.

References applyPrescribedAngularVelocity(), applyPrescribedVelocity(), prescribedAngularVelocity_, prescribedOrientation_, prescribedPosition_, prescribedVelocity_, setAngularVelocity(), and setVelocity().

Referenced by BaseParticle::integrateAfterForceComputation().

 {
     if (prescribedPosition_)
     {
         if (prescribedVelocity_)
         {
             applyPrescribedVelocity(time + timeStep);
         }
         else
         {
             setVelocity((prescribedPosition_(time + 1.1 * timeStep) - prescribedPosition_(time + 0.9 * timeStep)) / (0.2 * timeStep));
         }
     }
     else
     {
         if (prescribedVelocity_)
         {
             applyPrescribedVelocity(time + 0.5 * timeStep);
         }
     }
     if (prescribedOrientation_)
     {
         if (prescribedAngularVelocity_)
         {
             applyPrescribedAngularVelocity(time + timeStep);
         }
         else
         {
             setAngularVelocity((prescribedOrientation_(time + 1.1 * timeStep) - prescribedOrientation_(time + 0.9 * timeStep)) / (0.2 * timeStep));
         }
     }
     else
     {
         if (prescribedAngularVelocity_)
         {
             applyPrescribedAngularVelocity(time + 0.5 * timeStep);
         }
     }
 }

void BaseInteractable::integrateBeforeForceComputation	(	double	time,
		double	timeStep
	)

This is part of integrate routine for objects with infinite mass.

This does not first part of verlet integration but for objects with an infinite mass i.e. there motion is prescribed and not calculated from the applied forces. First it deals with the translation degrees of freedom and then secondly if deals with the angular degrees of freedom. Note, in both cases if the user has prescribed both positions and velocity these are used. If only only position is prescribed the velocity is computed from a finite difference. If only the velocity is prescribed the position is computed from integrating the velocity.

In the weird case they neither is set. The objects computed velocity is used to update its position.

Parameters

[in]	time	double which is the current simulation time
[in]	timeStep	double which is the current delta time of the simulation i.e. the size of each time step.

Definition at line 611 of file BaseInteractable.cc.

References applyPrescribedAngularVelocity(), applyPrescribedOrientation(), applyPrescribedPosition(), applyPrescribedVelocity(), getAngularVelocity(), getVelocity(), move(), prescribedAngularVelocity_, prescribedOrientation_, prescribedPosition_, prescribedVelocity_, rotate(), setAngularVelocity(), and setVelocity().

Referenced by BaseParticle::integrateBeforeForceComputation().

 {
     if (prescribedPosition_ )
     {
         if (prescribedVelocity_ )
         {
             //Both the velocity and position are defined; as we are using leap
             //frog method so the velocity is evaluated half a time later.
             applyPrescribedPosition(time + timeStep);
             applyPrescribedVelocity(time + 0.5 * timeStep);
         }
         else
         {
             //Only the position is defined.
             //Velocity is evaluated from a finite different of the Position
             //Note, we use 0.5 +- 0.1 timeStep for the velocity eval.
             applyPrescribedPosition(time + timeStep);
             setVelocity((prescribedPosition_(time + 0.6 * timeStep) - prescribedPosition_(time + 0.4 * timeStep)) / (0.2 * timeStep));
         }
     }
     else
     {
         if (prescribedVelocity_ )
         {
             //Only the velocity is set. The position is calculated from the
             //the integral of velocity.
             applyPrescribedVelocity(time + 0.5 * timeStep);
             move(getVelocity() * timeStep);
         }
         else
         {
             //Neither is set move based on the computed velocity of the object.
             move(getVelocity() * timeStep);
         }
     }
     if (prescribedOrientation_)
     {
         if (prescribedAngularVelocity_)
         {
             applyPrescribedOrientation(time + timeStep);
             applyPrescribedAngularVelocity(time + 0.5 * timeStep);
         }
         else
         {
             applyPrescribedOrientation(time + timeStep);
             setAngularVelocity((prescribedOrientation_(time + 0.6 * timeStep) - prescribedOrientation_(time + 0.4 * timeStep)) / (0.2 * timeStep));
         }
     }
     else
     {
         if (prescribedAngularVelocity_)
         {
             applyPrescribedAngularVelocity(time + 0.5 * timeStep);
             rotate(getAngularVelocity() * timeStep);
         }
         else
         {
             rotate(getAngularVelocity() * timeStep);
         }
     }
 }

void BaseInteractable::move ( const Vec3D & move )

virtual

Moves this BaseInteractable by adding an amount to the position.

Moves (displaces) the interacable a given distance. Note, this just updates the position by the move.

Parameters

[in] move Reference to Vec3D which is the distance to move the interactable.

Reimplemented in IntersectionOfWalls, and TriangulatedWall.

Definition at line 278 of file BaseInteractable.cc.

References position_.

Referenced by HopperInsertionBoundary::generateParticle(), integrateBeforeForceComputation(), BaseParticle::integrateBeforeForceComputation(), TriangulatedWall::move(), IntersectionOfWalls::move(), ShearBoxBoundary::shiftHorizontalPosition(), LeesEdwardsBoundary::shiftHorizontalPosition(), AngledPeriodicBoundary::shiftPosition(), MaserBoundary::shiftPosition(), PeriodicBoundary::shiftPosition(), ShearBoxBoundary::shiftVerticalPosition(), and LeesEdwardsBoundary::shiftVerticalPosition().

 {
     position_ += move;
 }

void BaseInteractable::read ( std::istream & is )

pure virtual

Reads a BaseInteractable from an input stream.

BaseInteacatable read functions. Reads in all the information about an interacatable. Note, this can be from any istream but would normally be a file See also BaseInteractable::write

Parameters

[in] is std::istream to which the information is read from.

Implements BaseObject.

Implemented in IntersectionOfWalls, TriangulatedWall, InfiniteWall, InfiniteWallWithHole, AxisymmetricIntersectionOfWalls, SphericalWall, BaseParticle, Coil, RestrictedWall, Screw, CylindricalWall, BaseWall, LiquidFilmParticle, and ThermalParticle.

Definition at line 301 of file BaseInteractable.cc.

References angularVelocity_, force_, indSpecies_, orientation_, position_, BaseObject::read(), torque_, and velocity_.

Referenced by BaseWall::read(), and BaseParticle::read().

 {
     BaseObject::read(is);
     std::string dummy;
     is >> dummy >> indSpecies_;
     is >> dummy >> position_;
     is >> dummy;
     //this if-statement is added to read Kasper van der Vaart's data files, which contain an additional variable named positionAbsolute
     if (dummy.compare("positionAbsolute") == 0)
     {
         is >> dummy >> dummy >> dummy  >> dummy;
     }
     is >> orientation_ >> dummy;
     is >> dummy >> velocity_;
     is >> dummy >> angularVelocity_ >> dummy;
     is >> dummy >> force_;
     is >> dummy >> torque_;
 }

bool BaseInteractable::removeInteraction ( BaseInteraction * I )

Removes an interaction from this BaseInteractable.

Removes a given interaction form the list of interactions belonging to the current interacable. This functions returns true to the interaction was found and returns false if the given interaction did not exist and the interaction was not removed. Note that this cannot be done with a range-based for, since we need the iterator to erase the interaction.

Parameters

[in] I BaseInteraction pointer which is the interaction to be removed.

Returns: bool True if the interaction was found and removed; false if the interaction did not exist for that interactable.

Definition at line 371 of file BaseInteractable.cc.

References BaseInteraction::getI(), BaseObject::getId(), BaseInteraction::getP(), interactions_, logger, VERBOSE, and WARN.

Referenced by BaseInteraction::setI(), BaseInteraction::setP(), and BaseInteraction::~BaseInteraction().

 {
     for (std::list<BaseInteraction*>::iterator it = interactions_.begin(); it != interactions_.end(); ++it)
     {
         if (I == (*it))
         {
             logger(VERBOSE, "Removing interaction from % between % and %",getId(),I->getI()->getId(),I->getP()->getId());
             interactions_.erase(it);
             return true;
         }
     }
     logger(WARN, "Error in BaseInteractable::removeInteraction: Interaction could not be removed");
     return false;
 }

void BaseInteractable::rotate ( const Vec3D & rotate )

Rotates this BaseInteractable.

Rotates the interacable a given solid angle. Note, this just updates the orientation by the angle.

Parameters

[in] rotate Reference to Vec3D which is the solid angle through which the interactable is rotated.

Definition at line 289 of file BaseInteractable.cc.

References orientation_.

Referenced by integrateBeforeForceComputation(), BaseParticle::integrateBeforeForceComputation(), and AngledPeriodicBoundary::shiftPosition().

 {
     orientation_ += rotate;
 }

void BaseInteractable::setAngularVelocity ( const Vec3D & angularVelocity )

set the angular velocity of the BaseInteractble.

Parameters

[in] angularVelocity Vec3D which is the angularVelocity of the interactable.

Definition at line 424 of file BaseInteractable.cc.

References angularVelocity_.

Referenced by applyPrescribedAngularVelocity(), BaseParticle::fixParticle(), integrateAfterForceComputation(), integrateBeforeForceComputation(), helpers::loadingTest(), helpers::normalAndTangentialLoadingTest(), helpers::objectivenessTest(), and ChuteBottom::setupInitialConditions().

 {
     angularVelocity_ = angularVelocity;
 }

void BaseInteractable::setForce ( const Vec3D & force )

Sets the force on this BaseInteractable.

This sets the force being applied to this interactable. Note, first the code computes all forces in the interactions and then loops over all interactable objects applying the forces from the interactions to the interactables involved in the interaction.

Parameters

[in] force Vec3D which is the force to be applied.

Definition at line 179 of file BaseInteractable.cc.

References force_.

 {
     force_ = force;
 }

MERCURY_DEPRECATED void BaseInteractable::setIndSpecies ( unsigned int indSpecies )

virtual

Sets the index of the Species of this BaseInteractable.

This set the species associated with this interactable. This function should not be used and BaseInteractable::setSpecies should be used instead. See also BaseInteractable::setSpecies

Reimplemented in BaseParticle, and BaseWall.

Definition at line 109 of file BaseInteractable.cc.

References indSpecies_.

Referenced by BaseWall::setIndSpecies(), and BaseParticle::setIndSpecies().

 {
     indSpecies_ = indSpecies;
 }

void BaseInteractable::setOrientation ( const Vec3D & orientation )

Sets the orientation of this BaseInteractable.

Sets the orientation of the interactable. interpretation depends on which interactable is being considered See also BaseInteractable::getOrientation.

Parameters

[in] orientation Reference to Vec3D storing the orientation of the particle.

Definition at line 267 of file BaseInteractable.cc.

References orientation_.

Referenced by applyPrescribedOrientation(), AxisymmetricIntersectionOfWalls::AxisymmetricIntersectionOfWalls(), helpers::objectivenessTest(), BaseParticle::oldRead(), and ChuteBottom::setupInitialConditions().

 {
     orientation_ = orientation;
 }

void BaseInteractable::setPosition ( const Vec3D & position )

Sets the position of this BaseInteractable.

Sets the positions of the interactable. interpretation depends on which interactable is being considered See also BaseInteractable::getPosistion.

Parameters

[in] position Reference to Vec3D storing the position of the particle.

Definition at line 254 of file BaseInteractable.cc.

References position_.

Referenced by applyPrescribedPosition(), AxisymmetricIntersectionOfWalls::AxisymmetricIntersectionOfWalls(), Chute::createBottom(), ChuteInsertionBoundary::generateParticle(), CubeInsertionBoundary::generateParticle(), HopperInsertionBoundary::generateParticle(), InfiniteWall::InfiniteWall(), helpers::loadingTest(), InfiniteWall::move(), helpers::normalAndTangentialLoadingTest(), helpers::objectivenessTest(), BaseParticle::oldRead(), InfiniteWall::oldRead(), FileReader::read(), CircularPeriodicBoundary::rotateParticle(), InfiniteWall::set(), and ChuteBottom::setupInitialConditions().

 {
     position_ = position;
 }

void BaseInteractable::setPrescribedAngularVelocity ( const std::function< Vec3D(double)> & prescribedAngularVelocity )

Allows the angular velocity of the infinite mass interactable to be prescribed.

Definition at line 574 of file BaseInteractable.cc.

References prescribedAngularVelocity_.

 {
     prescribedAngularVelocity_ = prescribedAngularVelocity;
 }

void BaseInteractable::setPrescribedOrientation ( const std::function< Vec3D(double)> & prescribedOrientation )

Allows the orientation of the infinite mass interactbale to be prescribed.

This is similar to the BaseInteractable::setPrescribedPosition and works the same way. See BaseInteractable::setPrescibedPosition and BaseInteractable::setPrescribedVelocity for more details how it works. Note, the rate of change of the orientation can also be set using the function BaseInteractable::setPrescribedAngularVelocity.

Parameters

[in] prescribedOrientation std::function which is the lambda function and takes a double the time and returns a Vec 3D which is the orientation of the interactable for that time.

Definition at line 547 of file BaseInteractable.cc.

References prescribedOrientation_.

 {
     prescribedOrientation_ = prescribedOrientation;
 }

void BaseInteractable::setPrescribedPosition ( const std::function< Vec3D(double)> & prescribedPosition )

Allows the position of an infinite mass interactable to be prescribed.

This functions is used to give an interactable a prescribed motion, which is defined by a std::function. This is the new moving walls interface. A demo of the use would be: setPrescribedPosition([this] (double time) { return Vec3D(getXMin(),0.0,shaker_amp * std::sin(t * 2.0 * shaker_freq * constants::pi)); } ); This example moves the wall sinusoidally with time.

Parameters

[in] prescribedPosition std::function which is the lambda function and takes a double the time and returns a Vec 3D which is the position of the interactable for that time. See also BaseInteractable::setPrescribedVelocity for more information.

Definition at line 486 of file BaseInteractable.cc.

References prescribedPosition_.

 {
     prescribedPosition_ = prescribedPosition;
 }

void BaseInteractable::setPrescribedVelocity ( const std::function< Vec3D(double)> & prescribedVelocity )

Allows the velocity of an infinite mass interactable to be prescribed.

In a similar manner to BaseInteractable::setPrescribedPosition this sets the velocity of the BaseInteactable. See also BaseInteractable::setPrescribedPosition Note, it is valid to set both the velocity and the position. No checking if these are consist is done at all. If you only set one of these function the other is automatically calculated using a by numerically differentiating or integrating the functions will is prescribed.

Parameters

[in] prescribedVelocity std::function which is the lambda function and takes a double the time and returns a Vec 3D which is the velocity of the intertable for that time.

Definition at line 517 of file BaseInteractable.cc.

References prescribedVelocity_.

 {
     prescribedVelocity_ = prescribedVelocity;
 }

void BaseInteractable::setSpecies ( const ParticleSpecies * species )

Sets the species of this BaseInteractable.

This function sets the species associated with this interactable object. Again this must be a ParticleSpecies. Note, it also automatically sets the index on the indSpecies_ by working up the correct index. However, index should be carefully used

Parameters

[in] species ParticleSpcies pointer which is species holding the physical properties.

Definition at line 135 of file BaseInteractable.cc.

References ERROR, BaseSpecies::getHandler(), BaseObject::getIndex(), indSpecies_, logger, and species_.

Referenced by BaseWall::setSpecies(), and BaseParticle::setSpecies().

 {
     if (species->getHandler() == nullptr)
     {
         logger(ERROR, "Error: Species is not part of any handler yet");
     }
     
     species_ = species;
     indSpecies_ = species->getIndex();
 }

void BaseInteractable::setTorque ( const Vec3D & torque )

Sets the torque on this BaseInteractable.

This sets the torque being applied to this interactable. Note, first the code computes all force/torques in the interactions and then loops over all interactable objects applying the torques from the interactions to the interactables involved in the interaction.

Parameters

[in] torque Vec3D which is the force to be applied.

Definition at line 192 of file BaseInteractable.cc.

References torque_.