ChargedBondedInteraction Class Reference

#include <ChargedBondedInteraction.h>

Inheritance diagram for ChargedBondedInteraction:

Public Types
typedef ChargedBondedSpecies	SpeciesType
	Setting an alias name for ChargedBondedSpecies. More...

Public Member Functions
	ChargedBondedInteraction (BaseInteractable *P, BaseInteractable *I, unsigned timeStamp)
	Constructor. More...
	ChargedBondedInteraction (const ChargedBondedInteraction &p)
	Copy constructor. More...
	ChargedBondedInteraction ()
	~ChargedBondedInteraction () override
	Destructor. More...
void	computeAdhesionForce ()
	Computes the adhesive forces. 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...
Mdouble	getElasticEnergy () const override
	Returns the amount of Elastic energy involved in an interaction. Basically used in case you want to write the elastic energy into an output file. More...
const ChargedBondedSpecies *	getSpecies () const
	Returns a pointer to the adhesive force species ChargedBondedSpecies. More...
std::string	getBaseName () const
	Returns the name of the interaction, see Interaction.h. More...
void	bond ()
	A pair of functions which can be used to fix or unfix a pair of overlapping particles. More...
void	unbond ()
bool	isBonded () const override
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. Setting bonded_ to 'true' for a given pair of (overlapping) particles will cause these particles to become fixed together, resulting in larger, composite particles that can be used to model aspherical geometries. 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 ChargedBondedSpecies ChargedBondedInteraction::SpeciesType

Setting an alias name for ChargedBondedSpecies.

Constructor & Destructor Documentation

ChargedBondedInteraction() [1/3]

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

Constructor.

Todo:

Clean up this file by using the logger instead of cout, //cout, cerr and assert, and by motivating why the commented out code needs to be here.

Complete the documentation of these methods

Parameters

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

        : BaseInteraction(P, I, timeStamp)
{
    //ensuring that, by default, particles are not 'bonded'
    //i.e. they will not unintentionally 'stick' to any overlapping particles!
    bonded_ = false;
#ifdef DEBUG_CONSTRUCTOR
    std::cout<<"ChargedBondedInteraction::ChargedBondedInteraction() finished"<<std::endl;
#endif
}

References bonded_.

ChargedBondedInteraction() [2/3]

ChargedBondedInteraction::ChargedBondedInteraction

(

const ChargedBondedInteraction &

p

)

Copy constructor.

Parameters

[in]

p

        : BaseInteraction(p)
{
    //carrying the history parameter over for copied particles to ensure that any bonded particles
    //remain bonded!
    bonded_ = p.bonded_;
#ifdef DEBUG_CONSTRUCTOR
    std::cout<<"ChargedBondedInteraction::ChargedBondedInteraction(const ChargedBondedInteraction &p finished"<<std::endl;
#endif
}

References bonded_, and p.

ChargedBondedInteraction() [3/3]

ChargedBondedInteraction::ChargedBondedInteraction

(

)

Todo:

MX: add to MPI

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

References FATAL, and logger.

~ChargedBondedInteraction()

ChargedBondedInteraction::~ChargedBondedInteraction ( )

override

Destructor.

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

Member Function Documentation

bond()

void ChargedBondedInteraction::bond

(

)

A pair of functions which can be used to fix or unfix a pair of overlapping particles.

Used to set the private variable 'bonded' to true, thus allowing the user to choose to fix a given pair of interacting, overlapping particles together

{
    bonded_ = true;
}

References bonded_.

Referenced by ChargedBondedInteractionSelfTest::setupInitialConditions(), and ChargedBondedParticleUnitTest::setupInitialConditions().

computeAdhesionForce()

void ChargedBondedInteraction::computeAdhesionForce

(

)

Computes the adhesive forces.

TW: I added the vdW force; KW, why was that force not active? Note, this change also shows up in energy

{
    
    const ChargedBondedSpecies* species = getSpecies();
    //std::cout << getSpecies()->getCharge() << std::endl;
    
    //creating local parameters to store the charges of both particles
    //involved in the interaction to allow for quick calculation
    const auto pSpecies = dynamic_cast<const ChargedBondedSpecies*>(getP()->getSpecies());
    const auto iSpecies = dynamic_cast<const ChargedBondedSpecies*>(getI()->getSpecies());
    logger.assert_debug(pSpecies,"No ChargedBondedSpecies");
    logger.assert_debug(iSpecies,"No ChargedBondedSpecies");
    const int pCharge = pSpecies->getCharge();
    const int iCharge = iSpecies->getCharge();
    
    //similarly, creating local parameters to store the relevant stiffness
    //and max force values
    const Mdouble k = species->getAdhesionStiffness();
    const Mdouble fMax = species->getAdhesionForceMax();
    
    const Mdouble kWaals = species->getVanDerWaalsStiffness();
    const Mdouble fMaxWaals = species->getVanDerWaalsForceMax();
    const Mdouble rWaals = fMaxWaals / kWaals;
    
    
    //First, adding bonded force if applicable
    if (bonded_ && getOverlap() >= 0)
    {
        addForce(getNormal() * (-species->getBondForceMax()
                                - species->getBondDissipation() * getNormalRelativeVelocity()));
        return;
    }
    
    
    //determining which of the three possible cases for force based on charge -
    //repulsive (like charges), attractive (unlike charges) or none (1 or more uncharged) -
    //is relevant for the current combination of particle charges...
    //(Note that the charge set function contains a safety check that means charge can only be
    // +/- 1, i.e. the expressions used below should not produce errors!
    
    //case 1 - 1 or more particles has no charge, i.e. no EM force between them
    if ((pCharge == 0) or (iCharge == 0))
    {
        //No need to write anything here as nothing needs to be returned!
        //std::cout << "no charge" << std::endl;
    }
        //case 2: unlike charges --> attractive force
    else if (pCharge == -iCharge)
    {
        //std::cout << "dissimilar charge" << std::endl;
        //in the case of particles with opposing charges, simply implements the
        //standard attractive force used for adhesive particle interactions
        if (getOverlap() >= 0)
        {
            addForce(getNormal() * -fMax);
            addForce(getNormal() * -fMaxWaals);
        }
        else if (getOverlap() >= -rWaals)
        {
            addForce(getNormal() * (-kWaals * getOverlap() - fMaxWaals));
            addForce(getNormal() * (-k * getOverlap() - fMax));
        }
        else
        {
            addForce(getNormal() * (-k * getOverlap() - fMax));
        }
    }
        //case 3: like charges --> repulsive force
    else if (pCharge == iCharge)
    {
        //std::cout << "similar charge" << std::endl;
        //in the case of particles with like charges, reverse the direction of the force applied
        //such that particles repel one another
        if (getOverlap() >= 0)
        {
            addForce(getNormal() * +fMax);
            addForce(getNormal() * -fMaxWaals);
        }
        else if (getOverlap() >= -rWaals)
        {
            addForce(getNormal() * (-kWaals * getOverlap() - fMaxWaals));
            addForce(getNormal() * (+k * getOverlap() + fMax));
            //std::cout << "Waals = " << getNormal() * (-kWaals * getOverlap() - fMaxWaals) << std::endl;
        }
        else
        {
            addForce(getNormal() * (+k * getOverlap() + fMax));
        }
    }
        //if none of the above are satisfied, something must have gone very wrong!
    else
    {
        logger(ERROR, "Particle charge has erroneous value");
    }
}

References BaseInteraction::addForce(), bonded_, ERROR, ChargedBondedSpecies::getAdhesionForceMax(), ChargedBondedSpecies::getAdhesionStiffness(), ChargedBondedSpecies::getBondDissipation(), ChargedBondedSpecies::getBondForceMax(), BaseInteraction::getI(), BaseInteraction::getNormal(), BaseInteraction::getNormalRelativeVelocity(), BaseInteraction::getOverlap(), BaseInteraction::getP(), BaseInteractable::getSpecies(), getSpecies(), ChargedBondedSpecies::getVanDerWaalsForceMax(), ChargedBondedSpecies::getVanDerWaalsStiffness(), k, and logger.

getBaseName()

std::string ChargedBondedInteraction::getBaseName

(

)

const

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

Returns

std::string

{
    return "ChargedBonded";
}

getElasticEnergy()

Mdouble ChargedBondedInteraction::getElasticEnergy ( ) const

overridevirtual

Returns the amount of Elastic energy involved in an interaction. Basically used in case you want to write the elastic energy into an output file.

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.

{
    const ChargedBondedSpecies* species = getSpecies();
    const auto pSpecies = static_cast<const ChargedBondedSpecies*>(getP()->getSpecies()->getAdhesiveForce());
    const auto iSpecies = static_cast<const ChargedBondedSpecies*>(getI()->getSpecies()->getAdhesiveForce());
    logger.assert_debug(pSpecies,"No ChargedBondedSpecies");
    logger.assert_debug(iSpecies,"No ChargedBondedSpecies");
    const int pCharge = pSpecies->getCharge();
    const int iCharge = iSpecies->getCharge();
    
    const Mdouble k = species->getAdhesionStiffness();
    const Mdouble fMax = species->getAdhesionForceMax();
    const Mdouble r = getBaseSpecies()->getInteractionDistance();
    
    const Mdouble kWaals = species->getVanDerWaalsStiffness();
    const Mdouble fMaxWaals = species->getVanDerWaalsForceMax();
    const Mdouble rWaals = (fMaxWaals == 0) ? 0 : (fMaxWaals / kWaals);
    
    
    //First, adding bonded force if applicable
    if (bonded_ && getOverlap() >= 0)
    {
        //comment to ignore BondForce
        Mdouble elasticEnergyAtEquilibrium = getElasticEnergyAtEquilibrium(species->getBondForceMax());
        return -species->getBondForceMax() * getOverlap() + elasticEnergyAtEquilibrium;
    }
    
    Mdouble elasticEnergy = 0.0;
    if ((pCharge != 0) && (iCharge != 0))
    {
        if (pCharge == -iCharge)
        {
            if (getOverlap() >= 0)
            {
                elasticEnergy -= (0.5 * rWaals + getOverlap()) * fMaxWaals
                                 + (0.5 * r + getOverlap()) * fMax;
            }
            else if (getOverlap() >= -rWaals)
            {
                elasticEnergy -= (0.5 * kWaals * mathsFunc::square(getOverlap() + rWaals)) +
                                 (0.5 * k * mathsFunc::square(getOverlap() + r));
            }
            else
            {
                elasticEnergy -= (0.5 * k * mathsFunc::square(getOverlap() + r));
            }
        }
            //case 3: like charges --> repulsive force
        else if (pCharge == iCharge)
        {
            if (getOverlap() >= 0)
            {
                elasticEnergy -= (0.5 * rWaals + getOverlap()) * fMaxWaals
                                 - (0.5 * r + getOverlap()) * fMax;
            }
            else if (getOverlap() >= -rWaals)
            {
                elasticEnergy -= (0.5 * kWaals * mathsFunc::square(getOverlap() + rWaals)) -
                                 (0.5 * k * mathsFunc::square(getOverlap() + r));
            }
            else
            {
                elasticEnergy += (0.5 * k * mathsFunc::square(getOverlap() + r));
            }
        }
        else
        {
            logger(ERROR, "Particle charge has erroneous value");
        }
    }
    return elasticEnergy;
}

References bonded_, ERROR, ChargedBondedSpecies::getAdhesionForceMax(), ChargedBondedSpecies::getAdhesionStiffness(), BaseSpecies::getAdhesiveForce(), BaseInteraction::getBaseSpecies(), ChargedBondedSpecies::getBondForceMax(), BaseInteraction::getElasticEnergyAtEquilibrium(), BaseInteraction::getI(), BaseSpecies::getInteractionDistance(), BaseInteraction::getOverlap(), BaseInteraction::getP(), BaseInteractable::getSpecies(), getSpecies(), ChargedBondedSpecies::getVanDerWaalsForceMax(), ChargedBondedSpecies::getVanDerWaalsStiffness(), k, logger, UniformPSDSelfTest::r, and mathsFunc::square().

getSpecies()

const ChargedBondedSpecies * ChargedBondedInteraction::getSpecies

(

)

const

Returns a pointer to the adhesive force species ChargedBondedSpecies.

Returns

a constant pointer to an instance of this class.

{
    return static_cast<const ChargedBondedSpecies*> (getBaseSpecies()->getAdhesiveForce()); //downcast
}

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

Referenced by computeAdhesionForce(), and getElasticEnergy().

isBonded()

bool ChargedBondedInteraction::isBonded ( ) const

inlineoverridevirtual

Reimplemented from BaseInteraction.

{return bonded_;}

References bonded_.

read()

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

overridevirtual

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

Parameters

[in]

is

Implements BaseObject.

{
    std::string dummy;
    //logger(INFO,"ChargedBondedSpecies %",dummy);
    is >> dummy >> bonded_;
}

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

unbond()

void ChargedBondedInteraction::unbond

(

)

Used to set the private variable 'bonded' to false, thus allowing the user to choose to separate (or 'unbond') a given pair of interacting, overlapping particles together which were previously fixed (bonded) together Useful, for example, in implementing breakage mechanisms.

{
    bonded_ = false;
}

References bonded_.

write()

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

overridevirtual

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

Parameters

[in]

os

Implements BaseObject.

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

References bonded_.

Member Data Documentation

bonded_

bool ChargedBondedInteraction::bonded_

private

A history parameter to store if the particles were in contact or not. Useful to compute adhesive forces. Setting bonded_ to 'true' for a given pair of (overlapping) particles will cause these particles to become fixed together, resulting in larger, composite particles that can be used to model aspherical geometries.

Referenced by bond(), ChargedBondedInteraction(), computeAdhesionForce(), getElasticEnergy(), isBonded(), read(), unbond(), and write().

---

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

• ChargedBondedInteraction.h
• ChargedBondedInteraction.cc