BondedInteraction Class Reference

#include <BondedInteraction.h>

Inheritance diagram for BondedInteraction:

Public Types
typedef BondedSpecies	SpeciesType
	An alias name for BondedSpecies data type. More...

Public Member Functions
	BondedInteraction (BaseInteractable *P, BaseInteractable *I, unsigned timeStamp)
	Constructor. More...
	BondedInteraction (const BondedInteraction &p)
	Copy constructor. More...
	BondedInteraction ()
	~BondedInteraction () override
	Destructor. More...
void	computeAdhesionForce ()
	Computes the Adhesive force. More...
void	read (std::istream &is) override
	Interaction read function, which accepts an std::istream as input. More...
void	write (std::ostream &os) const override
	Interaction print function, which accepts an std::ostream as input. More...
const BondedSpecies *	getSpecies () const
	Returns a pointer to the adhesive force species BondedSpecies. More...
std::string	getBaseName () const
	Returns the name of the interaction, see Interaction.h. More...
Mdouble	getElasticEnergy () const override
	Returns the elastic energy stored in the adhesive spring. More...
bool	getBonded () const
	Get function. More...
bool	isBonded () const override
void	setBonded (bool bonded)
	Set function. More...
void	bond ()
void	bondInPlace ()
void	unbond ()
Mdouble	getBondForce () const
	Simple access function to return the force of the bond. More...
Public Member Functions inherited from BaseInteraction
	BaseInteraction (BaseInteractable *P, BaseInteractable *I, unsigned timeStamp)
	A constructor takes the BaseInteractable objects which are interacting (come into contact) and time the interaction starts. More...
	BaseInteraction ()
	BaseInteraction (const BaseInteraction &p)
	Copy constructor. More...
	~BaseInteraction () override
	The destructor. It removes this interactions from the objects that were interacting, and writes the time to a file when needed. More...
virtual void	actionsOnErase ()
	If an interaction needs to do something before it gets erased, add it here. E.g. Liquid bridges rupture at the end of their lifetime, and the liquid bridge volume has to be redistributed. The reason this action is not done in the destructor is that this action should not be taken when erasing ghost interactions. More...
virtual void	computeForce ()
	Virtual function that contains the force law between the two objects interacting. More...
void	read (std::istream &is) override
	Interaction read function, which accepts an std::istream as input. More...
void	write (std::ostream &os) const override
	Interaction print function, which accepts an std::ostream as input. More...
void	writeToFStat (std::ostream &os, Mdouble time) const
	Writes forces data to the FStat file. More...
std::string	getName () const override
	Virtual function which allows interactions to be named. More...
void	setDistance (Mdouble distance)
	Sets the interaction distance between the two interacting objects. More...
void	setNormal (Vec3D normal)
	Sets the normal vector between the two interacting objects. More...
void	setOverlap (Mdouble overlap)
	Set the overlap between the two interacting object. More...
void	setContactPoint (Vec3D contactPoint)
	Set the location of the contact point between the two interacting objects. More...
void	setTimeStamp (unsigned timeStamp)
	Updates the time step of the interacting. Note, time steps used to find completed interactions. More...
void	setSpecies (const BaseSpecies *species)
	Set the Species of the interaction; note this can either be a Species or MixedSpecies. More...
void	setP (BaseInteractable *P)
	Sets the first object involved in the interaction (normally a particle). More...
void	setI (BaseInteractable *I)
	Sets the second object involved in the interaction (often particle or wall). More...
void	importP (BaseInteractable *P)
	Sets the first object involved in the interaction (normally a particle). More...
void	importI (BaseInteractable *I)
	Sets the second object involved in the interaction (often particle or wall). More...
Vec3D	getIP () const
Vec3D	getIC () const
Vec3D	getCP () const
void	setLagrangeMultiplier (Mdouble multiplier)
Mdouble	getLagrangeMultiplier ()
void	setHandler (InteractionHandler *handler)
	Sets the pointer to the interaction hander which is storing this interaction. More...
InteractionHandler *	getHandler () const
	Gets a point to the interaction handlers to which this interaction belongs. More...
const Vec3D &	getForce () const
	Gets the current force (vector) between the two interacting objects. More...
const Vec3D &	getTorque () const
	Gets the current torque (vector) between the two interacting objects. More...
const Vec3D &	getNormal () const
	Gets the normal vector between the two interacting objects. More...
const Vec3D &	getContactPoint () const
	Gets constant reference to contact point (vector). More...
Mdouble	getOverlap () const
	Returns a Mdouble with the current overlap between the two interacting objects. More...
Mdouble	getOverlapVolume () const
	Returns the overlap volume between two interacting objects. More...
Mdouble	getContactRadius () const
	Returns a Mdouble with the current contact between the two interacting objects. More...
void	removeFromHandler ()
	Removes this interaction from its interaction hander. More...
void	copySwitchPointer (const BaseInteractable *original, BaseInteractable *ghost) const
	This copies the interactions of the original particle and replaces the original with the ghost copy. More...
void	gatherContactStatistics ()
BaseInteractable *	getP ()
	Returns a pointer to first object involved in the interaction (normally a particle). More...
BaseInteractable *	getI ()
	Returns a pointer to the second object involved in the interaction (often a wall or a particle). More...
const BaseInteractable *	getP () const
	Returns a constant pointer to the first object involved in the interaction. More...
const BaseInteractable *	getI () const
	Returns a constant pointer to the second object involved in the interaction. More...
Mdouble	getTimeStamp () const
	Returns an Mdouble which is the time stamp of the interaction. More...
virtual void	integrate (Mdouble timeStep)
	integrates variables of the interaction which need to be integrate e.g. the tangential overlap. More...
virtual Mdouble	getTangentialOverlap () const
	get the length of the current tangential overlap More...
Mdouble	getDistance () const
	Returns an Mdouble which is the norm (length) of distance vector. More...
const Vec3D &	getRelativeVelocity () const
	Returns a constant reference to a vector of relative velocity. More...
Mdouble	getNormalRelativeVelocity () const
	Returns a double which is the norm (length) of the relative velocity vector. More...
Mdouble	getAbsoluteNormalForce () const
	Returns the absolute value of the norm (length) of the Normal force vector. More...
virtual BaseInteraction *	copy () const =0
	Makes a copy of the interaction and returns a pointer to the copy. More...
void	setFStatData (std::fstream &fstat, BaseParticle *P, BaseWall *I)
void	setFStatData (std::fstream &fstat, BaseParticle *P, BaseParticle *I)
unsigned int	getMultiContactIdentifier () const
void	setMultiContactIdentifier (unsigned int multiContactIdentifier_)
virtual void	rotateHistory (Matrix3D &rotationMatrix)
	When periodic particles are used, some interactions need certain history properties rotated (e.g. tangential springs). This is the function for that. More...
virtual void	actionsAfterTimeStep ()
virtual unsigned	getNumberOfFieldsVTK () const
virtual std::string	getTypeVTK (unsigned i) const
virtual std::string	getNameVTK (unsigned i) const
virtual std::vector< Mdouble >	getFieldVTK (unsigned i) const
void	addForce (Vec3D force)
	add an force increment to the total force. More...
void	addTorque (Vec3D torque)
	add a torque increment to the total torque. More...
void	setForce (Vec3D force)
	set total force (this is used by the normal force, tangential forces are added use addForce) More...
void	setTorque (Vec3D torque)
	set the total force (this is used by the normal force, tangential torques are added use addTorque) More...
const BaseSpecies *	getBaseSpecies () const
	Return a constant point to BaseSpecies of the interaction. More...
virtual void	createMPIType ()
virtual void *	createMPIInteractionDataArray (unsigned int numberOfInteractions) const
virtual void	deleteMPIInteractionDataArray (void *dataArray)
virtual void	getMPIInteraction (void *historyDataArray, unsigned int index) const
	copies the history interactions into the data array More...
virtual void	getInteractionDetails (void *interactionDataArray, unsigned int index, unsigned int &identificationP, unsigned int &identificationI, bool &isWallInteraction, unsigned &timeStamp)
virtual void	setMPIInteraction (void *interactionDataArray, unsigned int index, bool resetPointers)
void	setBasicMPIInteractionValues (int P, int I, unsigned timeStamp, Vec3D force, Vec3D torque, bool isWallInteraction, bool resetPointers)
void	setIdentificationP (unsigned int identification)
void	setIdentificationI (int identification)
void	setWallInteraction (bool flag)
unsigned int	getIdentificationP ()
int	getIdentificationI ()
bool	isWallInteraction ()
Public Member Functions inherited from BaseObject
	BaseObject ()=default
	Default constructor. More...
	BaseObject (const BaseObject &p)=default
	Copy constructor, copies all the objects BaseObject contains. More...
virtual	~BaseObject ()=default
	virtual destructor More...
virtual void	moveInHandler (unsigned int index)
	Except that it is virtual, it does the same thing as setIndex() does. More...
void	setIndex (unsigned int index)
	Allows one to assign an index to an object in the handler/container. More...
void	setId (unsigned long 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...
void	setGroupId (unsigned groupId)
unsigned	getGroupId () const

Private Attributes
bool	bonded_
	A history parameter to store if the particles were in contact or not. Useful to compute adhesive forces. More...
Mdouble	bondForce_
	This stores the extra force created by the bond. More...

Additional Inherited Members
Protected Member Functions inherited from BaseInteraction
virtual const Vec3D	getTangentialForce () const
Mdouble	getEffectiveRadius () const
	Returns a Mdouble to the effective radius of the interaction. (Not corrected for the overlap) More...
Mdouble	getEffectiveMass () const
	Returns a Mdouble to the effective radius of the interaction. (Not corrected for the overlap) More...
void	setRelativeVelocity (Vec3D relativeVelocity)
	set the relative velocity of the current of the interactions. More...
void	setNormalRelativeVelocity (Mdouble normalRelativeVelocit)
	set the normal component of the relative velocity. More...
void	setAbsoluteNormalForce (Mdouble absoluteNormalForce)
	the absolute values of the norm (length) of the normal force More...
virtual Mdouble	getElasticEnergyAtEquilibrium (Mdouble adhesiveForce) const
virtual void	reverseHistory ()
	When periodic particles some interaction need certain history properties reversing. This is the function for that. More...
void	writeInteraction (std::ostream &os, bool created) const
	Writes information about a interaction to the interaction file. More...

Member Typedef Documentation

SpeciesType

typedef BondedSpecies BondedInteraction::SpeciesType

An alias name for BondedSpecies data type.

Constructor & Destructor Documentation

BondedInteraction() [1/3]

BondedInteraction::BondedInteraction	(	BaseInteractable *	P,
		BaseInteractable *	I,
		unsigned	timeStamp
	)

Constructor.

Parameters

[in]	P
[in]	I
[in]	timeStamp

        : BaseInteraction(P, I, timeStamp)
{
    bonded_ = false;
    bondForce_ = 0;
#ifdef DEBUG_CONSTRUCTOR
    std::cout<<"BondedInteraction::BondedInteraction() finished"<<std::endl;
#endif
}

References bonded_, and bondForce_.

BondedInteraction() [2/3]

BondedInteraction::BondedInteraction

(

const BondedInteraction &

p

)

Copy constructor.

Parameters

[in]

p

Todo:

tw check if the parameters are valid when inserting the species into the handler

        : BaseInteraction(p)
{
    bonded_ = p.bonded_;
    bondForce_ = p.bondForce_;
#ifdef DEBUG_CONSTRUCTOR
    std::cout<<"BondedInteraction::BondedInteraction(const BondedInteraction &p finished"<<std::endl;
#endif
}

References bonded_, bondForce_, and p.

BondedInteraction() [3/3]

BondedInteraction::BondedInteraction

(

)

Todo:

MX: add to MPI

{
#ifdef MERCURYDPM_USE_MPI
    logger(FATAL,"ChargedBondedInteractions are currently not implemented in parallel MercuryDPM");
#endif
}

References FATAL, and logger.

~BondedInteraction()

BondedInteraction::~BondedInteraction ( )

override

Destructor.

{
#ifdef DEBUG_DESTRUCTOR
    std::cout<<"BondedInteraction::~BondedInteraction() finished"<<std::endl;
#endif
}

Member Function Documentation

bond()

void BondedInteraction::bond

(

)

This access function create a bond between the particles with the stength of the maximum bondForce

{
    bondForce_=getSpecies()->getBondForceMax();
    bonded_ = true;
}

References bonded_, bondForce_, BondedSpecies::getBondForceMax(), and getSpecies().

bondInPlace()

void BondedInteraction::bondInPlace

(

)

This access function create a bond between the particles with the stength of the current force. So the current distance should be come the equilibrum distance.

Bug:

Make have to things about dispative forces

{
    bondForce_= getForce().getLength();
    bonded_ = true;
}

References bonded_, bondForce_, BaseInteraction::getForce(), and Vec3D::getLength().

computeAdhesionForce()

void BondedInteraction::computeAdhesionForce

(

)

Computes the Adhesive force.

Uses the most basic adhesion contact model.

{
    if (bonded_ && getOverlap() >= 0)
    {
        const BondedSpecies* species = getSpecies();
        addForce(getNormal() * (-getBondForce()
                                - species->getBondDissipation() * getNormalRelativeVelocity()));
    }
}

References BaseInteraction::addForce(), bonded_, BondedSpecies::getBondDissipation(), getBondForce(), BaseInteraction::getNormal(), BaseInteraction::getNormalRelativeVelocity(), BaseInteraction::getOverlap(), and getSpecies().

getBaseName()

std::string BondedInteraction::getBaseName

(

)

const

Returns the name of the interaction, see Interaction.h.

Returns

std::string

{
    return "Bonded";
}

getBonded()

bool BondedInteraction::getBonded

(

)

const

Get function.

Todo:

replace by isBonded

{
    return bonded_;
}

References bonded_.

getBondForce()

Mdouble BondedInteraction::getBondForce ( ) const

inline

Simple access function to return the force of the bond.

                                 {
        return bondForce_;
    }

References bondForce_.

Referenced by computeAdhesionForce(), and getElasticEnergy().

getElasticEnergy()

Mdouble BondedInteraction::getElasticEnergy ( ) const

overridevirtual

Returns the elastic energy stored in the adhesive spring.

Elastic (=potential) energy is defined as the energy gained by separating two interactables. As it costs energy to separate adhesive interactables, the elastic energy is negative.

Returns

the elastic energy stored in the adhesive spring.

Reimplemented from BaseInteraction.

{
    if (!bonded_)
        return 0.0;
    else
        return -getBondForce() * getOverlap();
}

References bonded_, getBondForce(), and BaseInteraction::getOverlap().

getSpecies()

const BondedSpecies * BondedInteraction::getSpecies

(

)

const

Returns a pointer to the adhesive force species BondedSpecies.

Returns

const pointer of BondedSpecies*

{
    return static_cast<const BondedSpecies*>(getBaseSpecies()->getAdhesiveForce());
;
}

References BaseSpecies::getAdhesiveForce(), and BaseInteraction::getBaseSpecies().

Referenced by bond(), and computeAdhesionForce().

isBonded()

bool BondedInteraction::isBonded ( ) const

inlineoverridevirtual

Reimplemented from BaseInteraction.

                                   {
        return bonded_;
    };

References bonded_.

read()

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

overridevirtual

Interaction read function, which accepts an std::istream as input.

Parameters

[in,out]

is

Implements BaseObject.

{
    std::string dummy;
    is >> dummy >> bonded_;
    is >> dummy >> bondForce_;
}

References bonded_, bondForce_, and oomph::Global_string_for_annotation::string().

setBonded()

void BondedInteraction::setBonded

(

bool

bonded

)

Set function.

{
    bonded_ = bonded;
}

References bonded_.

unbond()

void BondedInteraction::unbond

(

)

{
    bonded_ = false;
}

References bonded_.

write()

void BondedInteraction::write ( std::ostream &  os ) const

overridevirtual

Interaction print function, which accepts an std::ostream as input.

Parameters

[in,out]

os

Implements BaseObject.

{
    os << " bonded " << bonded_;
    os << " bondForce " << bondForce_;
}

References bonded_, and bondForce_.

Member Data Documentation

bonded_

bool BondedInteraction::bonded_

private

A history parameter to store if the particles were in contact or not. Useful to compute adhesive forces.

Referenced by bond(), BondedInteraction(), bondInPlace(), computeAdhesionForce(), getBonded(), getElasticEnergy(), isBonded(), read(), setBonded(), unbond(), and write().

bondForce_

Mdouble BondedInteraction::bondForce_

private

This stores the extra force created by the bond.

Referenced by bond(), BondedInteraction(), bondInPlace(), getBondForce(), read(), and write().

---

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

• BondedInteraction.h
• BondedInteraction.cc