#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, Mdouble timeStamp)
	Constructor. More...

	ChargedBondedInteraction (const ChargedBondedInteraction &p)
	Copy constructor. More...

virtual	~ChargedBondedInteraction ()
	Destructor. More...

void	computeAdhesionForce ()
	Computes the adhesive forces. More...

void	read (std::istream &is)
	Interaction read function, which accepts an std::istream as input. More...

void	write (std::ostream &os) const
	Interaction print function, which accepts an std::ostream as input. More...

Mdouble	getElasticEnergy () const
	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
	A dynamic_cast of BaseSpecies pointer type to a pointer to an object of type 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 ()

Public Member Functions inherited from BaseInteraction
	BaseInteraction (BaseInteractable P, BaseInteractable I, Mdouble timeStamp)
	A constructor takes the BaseInteractable objects which are interacting (come into contact) and time the interaction starts. More...

	BaseInteraction (const BaseInteraction &p)
	Copy constructor. More...

	BaseInteraction ()
	Empty constructor. More...

virtual	~BaseInteraction ()
	The default destructor. 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	writeToFStat (std::ostream &os) const
	Writes forces data to the FStat file. More...

virtual std::string	getName () const
	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 (Mdouble timeStamp)
	Updates the time step of the interacting. Note, timesteps used to find completed interactions. More...

void	setSpecies (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	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	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 ()

const BaseInteractable *	getP () const

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...

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	setForce (Vec3D force)
	set total force (this is used by the normal force, tangential forces are added use addForce) 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 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
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...

Mdouble	getEffectiveCorrectedRadius ()
	Returns a Mdouble to the effective radius corrected for the overlaps of the particles. More...

void	addForce (Vec3D force)
	add an force increment to the total force. More...

void	addTorque (Vec3D torque)

void	setTorque (Vec3D torque)
	set the total force (this is used by the normal force, tangential torques are added use addTorque) 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...

const BaseSpecies *	getBaseSpecies () const
	Return a constant point to BaseSpecies of the interaction. 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...

Detailed Description

Definition at line 39 of file ChargedBondedInteraction.h.

Member Typedef Documentation

typedef ChargedBondedSpecies ChargedBondedInteraction::SpeciesType

Setting an alias name for ChargedBondedSpecies.

Definition at line 45 of file ChargedBondedInteraction.h.

Constructor & Destructor Documentation

ChargedBondedInteraction::ChargedBondedInteraction	(	BaseInteractable *	P,
		BaseInteractable *	I,
		Mdouble	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

Definition at line 42 of file ChargedBondedInteraction.cc.

References bonded_.

     : 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
 }

ChargedBondedInteraction::ChargedBondedInteraction ( const ChargedBondedInteraction & p )

Copy constructor.

Parameters

[in] p

Definition at line 56 of file ChargedBondedInteraction.cc.

References bonded_.

     : 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
 }

ChargedBondedInteraction::~ChargedBondedInteraction ( )

virtual

Destructor.

Definition at line 70 of file ChargedBondedInteraction.cc.

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

Member Function Documentation

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

Definition at line 291 of file ChargedBondedInteraction.cc.

References bonded_.

 {
     bonded_=true;
 }

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

Definition at line 97 of file ChargedBondedInteraction.cc.

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

 {
 
     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());
     assert(pSpecies);
     assert(iSpecies);
     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
     {
         std::cerr << "Error: Particle charge has erroneous value" << std::endl;
         exit(-1);
     }
 }

std::string ChargedBondedInteraction::getBaseName ( ) const

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

Returns: std::string

Definition at line 282 of file ChargedBondedInteraction.cc.

 {
     return "ChargedBonded";
 }

Mdouble ChargedBondedInteraction::getElasticEnergy ( ) const

virtual

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.

Definition at line 200 of file ChargedBondedInteraction.cc.

References assert, bonded_, ERROR, ChargedBondedSpecies::getAdhesionForceMax(), ChargedBondedSpecies::getAdhesionStiffness(), ChargedBondedSpecies::getBondForceMax(), BaseInteraction::getElasticEnergyAtEquilibrium(), BaseInteraction::getI(), ChargedBondedSpecies::getInteractionDistance(), BaseInteraction::getOverlap(), BaseInteraction::getP(), getSpecies(), BaseInteractable::getSpecies(), ChargedBondedSpecies::getVanDerWaalsForceMax(), ChargedBondedSpecies::getVanDerWaalsStiffness(), logger, and mathsFunc::square().

 {
     const ChargedBondedSpecies* species = getSpecies();
     const auto pSpecies = dynamic_cast<const ChargedBondedSpecies*>(getP()->getSpecies());
     const auto iSpecies = dynamic_cast<const ChargedBondedSpecies*>(getI()->getSpecies());
     assert(pSpecies);
     assert(iSpecies);
     const int pCharge = pSpecies->getCharge();
     const int iCharge = iSpecies->getCharge();
 
     const Mdouble k = species->getAdhesionStiffness();
     const Mdouble fMax = species->getAdhesionForceMax();
     const Mdouble r = species->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;
 }

const ChargedBondedSpecies * ChargedBondedInteraction::getSpecies ( ) const

A dynamic_cast of BaseSpecies pointer type to a pointer to an object of type ChargedBondedSpecies.

Returns: a constant pointer to an instance of this class.

Definition at line 275 of file ChargedBondedInteraction.cc.

References BaseInteraction::getBaseSpecies().

Referenced by computeAdhesionForce(), and getElasticEnergy().

 {
     return dynamic_cast<const ChargedBondedSpecies *> (getBaseSpecies()); //downcast
 }

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

virtual

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

Parameters

[in] is

Reimplemented from BaseInteraction.

Definition at line 88 of file ChargedBondedInteraction.cc.

References bonded_.

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

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.

Definition at line 301 of file ChargedBondedInteraction.cc.

References bonded_.

 {
     bonded_=false;
 }

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

virtual

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

Parameters

[in] os

Reimplemented from BaseInteraction.

Definition at line 80 of file ChargedBondedInteraction.cc.

References bonded_.

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

Member Data Documentation

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.

Definition at line 108 of file ChargedBondedInteraction.h.

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

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

Interactions/AdhesiveForceInteractions/ChargedBondedInteraction.h
Interactions/AdhesiveForceInteractions/ChargedBondedInteraction.cc

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation