ChargedBondedSpecies Class Reference

ChargedBondedSpecies contains the parameters used to describe a linear reversible short-range force. More...

#include <ChargedBondedSpecies.h>

Inheritance diagram for ChargedBondedSpecies:

Public Types
typedef ChargedBondedInteraction	InteractionType
	The correct Interaction type for this AdhesiveForceSpecies. More...

Public Member Functions
	ChargedBondedSpecies ()
	The default constructor. More...
	ChargedBondedSpecies (const ChargedBondedSpecies &s)
	The default constructor. More...
	~ChargedBondedSpecies ()=default
	The default constructor. More...
void	read (std::istream &is)
	Reads the species properties from an input stream. More...
void	write (std::ostream &os) const
	Writes the species properties to an output stream. More...
std::string	getBaseName () const
	Used in Species::getName to obtain a unique name for each Species. More...
void	mix (ChargedBondedSpecies *S, ChargedBondedSpecies *T)
	creates default values for mixed species More...
void	setInteractionDistance ()
	returns the largest separation distance at which adhesive short-range forces can occur. More...
void	setAdhesionStiffness (Mdouble new_k0)
	Allows the spring constant to be changed. More...
Mdouble	getAdhesionStiffness () const
	Allows the spring constant to be accessed. More...
void	setAdhesionForceMax (Mdouble new_f0)
	Allows the spring constant to be changed. More...
Mdouble	getAdhesionForceMax () const
	Allows the spring constant to be accessed. More...
int	getCharge () const
void	setCharge (int newCharge)
void	setBondForceMax (Mdouble new_f0)
	Allows the spring constant for the BOND to be changed (Do not confuse with the charged interaction strength!) More...
Mdouble	getBondForceMax () const
	Allows the maximal force for 'bonding' particles together to be accessed. More...
void	setBondDissipation (Mdouble disp)
	Allows the additional dissipation used to damp oscillations between bondd particles to be changed. More...
Mdouble	getBondDissipation () const
	Allows the additional dissipation used to damp oscillations between bondd particles to be accessed. More...
Mdouble	getVanDerWaalsStiffness () const
Mdouble	getVanDerWaalsForceMax () const
void	setVanDerWaalsStiffness (Mdouble)
void	setVanDerWaalsForceMax (Mdouble)
Public Member Functions inherited from BaseForce
BaseSpecies *	getBaseSpecies () const
void	setBaseSpecies (BaseSpecies *baseSpecies)

Private Attributes
Mdouble	adhesionStiffness_
	stiffness of linear adhesion force More...
Mdouble	adhesionForceMax_
	adhesion force at zero overlap More...
int	charge_
Mdouble	bondForceMax_
	The maximal force which acts to bind together particles which are "bondd" into a single body. More...
Mdouble	bondDissipation_
	dissipation in bond More...
Mdouble	vanDerWaalsForceMax_
Mdouble	vanDerWaalsStiffness_

Detailed Description

ChargedBondedSpecies contains the parameters used to describe a linear reversible short-range force.

See ChargedBondedInteraction::computeForce for a description of the force law.

Member Typedef Documentation

InteractionType

typedef ChargedBondedInteraction ChargedBondedSpecies::InteractionType

The correct Interaction type for this AdhesiveForceSpecies.

Constructor & Destructor Documentation

ChargedBondedSpecies() [1/2]

ChargedBondedSpecies::ChargedBondedSpecies

(

)

The default constructor.

Default constructor for charged species. Sets default values for all relevant parameters. Note: if the stiffness of particles is left as zero, no force will be felt during interaction with other particles

Parameters

[in]

s

the species that is copied

{
    //setting adhesion values initially to zero such that, by default, particles do not experience
    //long range forces
    adhesionForceMax_ = 0;
    adhesionStiffness_ = 1;
    //similarly, setting bond properties to zero such that, by default, particles cannot be 'bondd'...
    bondForceMax_ = 0;
    //...and do not impart any excess dissipation!
    bondDissipation_ = 0;
    //Setting also parameters corresponding to the van der Waals force to zero by default
    vanDerWaalsForceMax_ = 0;
    vanDerWaalsStiffness_ = 1;
    charge_ = 0;
#ifdef DEBUG_CONSTRUCTOR
    std::cout<<"ChargedBondedSpecies::ChargedBondedSpecies() finished"<<std::endl;
#endif
}

References adhesionForceMax_, adhesionStiffness_, bondDissipation_, bondForceMax_, charge_, vanDerWaalsForceMax_, and vanDerWaalsStiffness_.

ChargedBondedSpecies() [2/2]

ChargedBondedSpecies::ChargedBondedSpecies

(

const ChargedBondedSpecies &

s

)

The default constructor.

Copy constructor for charged species

Parameters

[in]

s

the species that is copied

{
    adhesionForceMax_ = s.adhesionForceMax_;
    adhesionStiffness_ = s.adhesionStiffness_;
    bondForceMax_ = s.bondForceMax_;
    bondDissipation_ = s.bondDissipation_;
    vanDerWaalsForceMax_ = s.vanDerWaalsForceMax_;
    vanDerWaalsStiffness_ = s.vanDerWaalsStiffness_;
    charge_ = s.charge_;
#ifdef DEBUG_CONSTRUCTOR
    std::cout<<"ChargedBondedSpecies::ChargedBondedSpecies(const ChargedBondedSpecies &p) finished"<<std::endl;
#endif
}

References adhesionForceMax_, adhesionStiffness_, bondDissipation_, bondForceMax_, charge_, vanDerWaalsForceMax_, and vanDerWaalsStiffness_.

~ChargedBondedSpecies()

ChargedBondedSpecies::~ChargedBondedSpecies ( )

default

The default constructor.

Member Function Documentation

getAdhesionForceMax()

Mdouble ChargedBondedSpecies::getAdhesionForceMax

(

)

const

Allows the spring constant to be accessed.

{
    return adhesionForceMax_;
}

References adhesionForceMax_.

Referenced by ChargedBondedInteraction::computeAdhesionForce(), ChargedBondedInteraction::getElasticEnergy(), and mix().

getAdhesionStiffness()

Mdouble ChargedBondedSpecies::getAdhesionStiffness

(

)

const

Allows the spring constant to be accessed.

{
    return adhesionStiffness_;
}

References adhesionStiffness_.

Referenced by ChargedBondedInteraction::computeAdhesionForce(), ChargedBondedInteraction::getElasticEnergy(), and mix().

getBaseName()

std::string ChargedBondedSpecies::getBaseName

(

)

const

Used in Species::getName to obtain a unique name for each Species.

Returns the name of thebcurrent species

Returns

a string containing the name of the species (minus the word "Species")

{
    return "ChargedBonded";
}

getBondDissipation()

Mdouble ChargedBondedSpecies::getBondDissipation

(

)

const

Allows the additional dissipation used to damp oscillations between bondd particles to be accessed.

Allows the value of the dissipation between bondd particles to be accessed. This can be used to eliminate oscillations which may arise due to the forces holding the particles together competing with the usual forces which act to push particles in contact apart!

{
    return bondDissipation_;
}

References bondDissipation_.

Referenced by ChargedBondedInteraction::computeAdhesionForce(), and mix().

getBondForceMax()

Mdouble ChargedBondedSpecies::getBondForceMax

(

)

const

Allows the maximal force for 'bonding' particles together to be accessed.

Allows the the maximal force of the 'bond' used to bond particles together to be accessed.

{
    return bondForceMax_;
}

References bondForceMax_.

Referenced by ChargedBondedInteraction::computeAdhesionForce(), ChargedBondedInteraction::getElasticEnergy(), and mix().

getCharge()

int ChargedBondedSpecies::getCharge

(

)

const

{
    return charge_;
}

References charge_.

getVanDerWaalsForceMax()

Mdouble ChargedBondedSpecies::getVanDerWaalsForceMax

(

)

const

{
    return vanDerWaalsForceMax_;
}

References vanDerWaalsForceMax_.

Referenced by ChargedBondedInteraction::computeAdhesionForce(), ChargedBondedInteraction::getElasticEnergy(), and mix().

getVanDerWaalsStiffness()

Mdouble ChargedBondedSpecies::getVanDerWaalsStiffness

(

)

const

{
    return vanDerWaalsStiffness_;
}

References vanDerWaalsStiffness_.

Referenced by ChargedBondedInteraction::computeAdhesionForce(), ChargedBondedInteraction::getElasticEnergy(), and mix().

mix()

void ChargedBondedSpecies::mix	(	ChargedBondedSpecies *	S,
		ChargedBondedSpecies *	T
	)

creates default values for mixed species

Calling this function acts to assign values of maximum adhesion force and stiffness for mixed species interactions. For all parameters we assume that the harmonic mean of the parameters of the original two species is a sensible default.

Parameters

[in]

S,T

the two species whose properties are mixed to create the new species

{
    //'mixing' properties relating to the charged force interactions between particles
    setAdhesionForceMax(BaseSpecies::average(S->getAdhesionForceMax(), T->getAdhesionForceMax()));
    setAdhesionStiffness(BaseSpecies::average(S->getAdhesionStiffness(), T->getAdhesionStiffness()));
    
    //ensuring that, in addition, bond properties are also 'mixed'
    bondForceMax_ = BaseSpecies::average(S->getBondForceMax(), T->getBondForceMax());
    bondDissipation_ = BaseSpecies::average(S->getBondDissipation(), T->getBondDissipation());
    
    //and that the van der Waals force also is computed correctly
    vanDerWaalsForceMax_ = BaseSpecies::average(S->getVanDerWaalsForceMax(), T->getVanDerWaalsForceMax());
    vanDerWaalsStiffness_ = BaseSpecies::average(S->getVanDerWaalsStiffness(), T->getVanDerWaalsStiffness());
    
    charge_ = 0; //note mixedSpecies dont need charge, it's a particle property.
}

References BaseSpecies::average(), bondDissipation_, bondForceMax_, charge_, getAdhesionForceMax(), getAdhesionStiffness(), getBondDissipation(), getBondForceMax(), getVanDerWaalsForceMax(), getVanDerWaalsStiffness(), setAdhesionForceMax(), setAdhesionStiffness(), vanDerWaalsForceMax_, and vanDerWaalsStiffness_.

read()

void ChargedBondedSpecies::read

(

std::istream &

is

)

Reads the species properties from an input stream.

Parameters

[in]

is

input stream (typically the restart file)

{
    std::string dummy;
    is >> dummy >> adhesionForceMax_;
    is >> dummy >> adhesionStiffness_;
    is >> dummy >> charge_;
    is >> dummy >> bondForceMax_;
    is >> dummy >> bondDissipation_;
    is >> dummy >> vanDerWaalsForceMax_;
    is >> dummy >> vanDerWaalsStiffness_;
}

References adhesionForceMax_, adhesionStiffness_, bondDissipation_, bondForceMax_, charge_, vanDerWaalsForceMax_, and vanDerWaalsStiffness_.

setAdhesionForceMax()

void ChargedBondedSpecies::setAdhesionForceMax

(

Mdouble

new_f0

)

Allows the spring constant to be changed.

{
    if (new_f0 >= 0) {
        adhesionForceMax_ = new_f0;
        setInteractionDistance();
    } else {
        logger(ERROR, "Error in setAdhesionForceMax");
    }
}

References adhesionForceMax_, ERROR, logger, and setInteractionDistance().

Referenced by mix().

setAdhesionStiffness()

void ChargedBondedSpecies::setAdhesionStiffness

(

Mdouble

new_k0

)

Allows the spring constant to be changed.

{
    if (new_k0 >= 0) {
        adhesionStiffness_ = new_k0;
        setInteractionDistance();
    } else {
        logger(ERROR, "Error in setAdhesionStiffness");
    }
}

References adhesionStiffness_, ERROR, logger, and setInteractionDistance().

Referenced by mix().

setBondDissipation()

void ChargedBondedSpecies::setBondDissipation

(

Mdouble

disp

)

Allows the additional dissipation used to damp oscillations between bondd particles to be changed.

Allows the value of the dissipation between bondd particles to be changed. This can be used to eliminate oscillations which may arise due to the forces holding the particles together competing with the usual forces which act to push particles in contact apart!

{
    if (disp >= 0)
        bondDissipation_ = disp;
    else
    {
        logger(ERROR, "Error in setAdhesionDissipation");
    }
}

References bondDissipation_, ERROR, and logger.

setBondForceMax()

void ChargedBondedSpecies::setBondForceMax

(

Mdouble

new_f0

)

Allows the spring constant for the BOND to be changed (Do not confuse with the charged interaction strength!)

Allows the spring constant to be changed This means that we can alter the strength with which particles are "bondd" together and, thus, the mean distance by which bondd particles overlap by. As such, we can alter the geometry of multi-particle structures formed.

{
    if (new_f0 >= 0)
    {
        bondForceMax_ = new_f0;
    }
    else
    {
        logger(ERROR, "Error in setBondForceMax");
    }
}

References bondForceMax_, ERROR, and logger.

setCharge()

void ChargedBondedSpecies::setCharge

(

int

newCharge

)

{
    //making sure that the user can only enter 1 (positive charge) -1 (negative charge)
    //or zero (no charge)
    if (newCharge == 0 || newCharge == 1 || newCharge == -1)
        charge_ = newCharge;
    else
    {
        logger(ERROR, "Error in setCharge - charge must be +1, -1 or zero");
    }
}

References charge_, ERROR, and logger.

setInteractionDistance()

void ChargedBondedSpecies::setInteractionDistance

(

)

returns the largest separation distance at which adhesive short-range forces can occur.

Returns

the maximum separation distance below which adhesive forces can occur (needed for contact detection)

{
    logger.assert_debug(adhesionStiffness_ != 0.0,"ChargedBondedSpecies::getInteractionDistance(): adhesionStiffness cannot be zero");
    getBaseSpecies()->setInteractionDistance(adhesionForceMax_ / adhesionStiffness_);
}

References adhesionForceMax_, adhesionStiffness_, BaseForce::getBaseSpecies(), logger, and BaseSpecies::setInteractionDistance().

Referenced by setAdhesionForceMax(), and setAdhesionStiffness().

setVanDerWaalsForceMax()

void ChargedBondedSpecies::setVanDerWaalsForceMax

(

Mdouble

fMax

)

{
    if (fMax < 0)
    {
        logger(ERROR, "Error in setVanDerWaalsForceMax.");
    }
    else
    {
        vanDerWaalsForceMax_ = fMax;
    }
}

References ERROR, logger, and vanDerWaalsForceMax_.

setVanDerWaalsStiffness()

void ChargedBondedSpecies::setVanDerWaalsStiffness

(

Mdouble

stiffness

)

{
    vanDerWaalsStiffness_ = stiffness;
}

References vanDerWaalsStiffness_.

write()

void ChargedBondedSpecies::write

(

std::ostream &

os

)

const

Writes the species properties to an output stream.

Parameters

[out]

os

output stream (typically the restart file)

{
    os << " adhesionForceMax " << adhesionForceMax_;
    os << " adhesionStiffness " << adhesionStiffness_;
    os << " charge " << charge_;
    os << " bondForceMax " << bondForceMax_;
    os << " bondDissipation " << bondDissipation_;
    os << " vanDerWaalsForceMax " << vanDerWaalsForceMax_;
    os << " vanDerWaalsStiffness " << vanDerWaalsStiffness_;
}

References adhesionForceMax_, adhesionStiffness_, bondDissipation_, bondForceMax_, charge_, vanDerWaalsForceMax_, and vanDerWaalsStiffness_.

Member Data Documentation

adhesionForceMax_

Mdouble ChargedBondedSpecies::adhesionForceMax_

private

adhesion force at zero overlap

Referenced by ChargedBondedSpecies(), getAdhesionForceMax(), read(), setAdhesionForceMax(), setInteractionDistance(), and write().

adhesionStiffness_

Mdouble ChargedBondedSpecies::adhesionStiffness_

private

stiffness of linear adhesion force

Referenced by ChargedBondedSpecies(), getAdhesionStiffness(), read(), setAdhesionStiffness(), setInteractionDistance(), and write().

bondDissipation_

Mdouble ChargedBondedSpecies::bondDissipation_

private

dissipation in bond

the additional dissipation used to 'damp' oscillations between bondd particles

Referenced by ChargedBondedSpecies(), getBondDissipation(), mix(), read(), setBondDissipation(), and write().

bondForceMax_

Mdouble ChargedBondedSpecies::bondForceMax_

private

The maximal force which acts to bind together particles which are "bondd" into a single body.

Referenced by ChargedBondedSpecies(), getBondForceMax(), mix(), read(), setBondForceMax(), and write().

charge_

int ChargedBondedSpecies::charge_

private

Referenced by ChargedBondedSpecies(), getCharge(), mix(), read(), setCharge(), and write().

vanDerWaalsForceMax_

Mdouble ChargedBondedSpecies::vanDerWaalsForceMax_

private

Referenced by ChargedBondedSpecies(), getVanDerWaalsForceMax(), mix(), read(), setVanDerWaalsForceMax(), and write().

vanDerWaalsStiffness_

Mdouble ChargedBondedSpecies::vanDerWaalsStiffness_

private

Referenced by ChargedBondedSpecies(), getVanDerWaalsStiffness(), mix(), read(), setVanDerWaalsStiffness(), and write().

---

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

• ChargedBondedSpecies.h
• ChargedBondedSpecies.cc