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...

virtual	~ChargedBondedSpecies ()
	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 const S, ChargedBondedSpecies const T)
	creates default values for mixed species More...

Mdouble	getInteractionDistance () const
	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 BaseSpecies
	BaseSpecies ()
	The default constructor. More...

	BaseSpecies (const BaseSpecies &p)
	The copy constructor. More...

virtual	~BaseSpecies ()
	The default destructor. More...

virtual BaseSpecies *	copy () const =0
	Creates a deep copy of the object from which it is called. More...

void	setHandler (SpeciesHandler *handler)
	Sets the pointer to the handler to which this species belongs. More...

SpeciesHandler *	getHandler () const
	Returns the pointer to the handler to which this species belongs. More...

Mdouble	average (Mdouble a, Mdouble b)
	defines the average of two variables by the harmonic mean. More...

virtual void	mixAll (BaseSpecies const S, BaseSpecies const T)=0
	creates default values for mixed species More...

virtual bool	getUseAngularDOFs () const =0
	Returns true if torques (i.e. angular degrees of freedom) have to be calculated. More...

virtual BaseInteraction *	getNewInteraction (BaseInteractable P, BaseInteractable I, Mdouble timeStamp) const =0
	returns new Interaction object. 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
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.

Definition at line 36 of file ChargedBondedSpecies.h.

Member Typedef Documentation

typedef ChargedBondedInteraction ChargedBondedSpecies::InteractionType

The correct Interaction type for this AdhesiveForceSpecies.

Definition at line 40 of file ChargedBondedSpecies.h.

Constructor & Destructor Documentation

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

Definition at line 35 of file ChargedBondedSpecies.cc.

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

 {
     //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
 }

ChargedBondedSpecies::ChargedBondedSpecies ( const ChargedBondedSpecies & s )

The default constructor.

Copy constructor for charged species

Parameters

[in] s the species that is copied

Definition at line 58 of file ChargedBondedSpecies.cc.

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

 {
     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
 }

ChargedBondedSpecies::~ChargedBondedSpecies ( )

virtual

The default constructor.

Definition at line 72 of file ChargedBondedSpecies.cc.

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

Member Function Documentation

Mdouble ChargedBondedSpecies::getAdhesionForceMax ( ) const

Allows the spring constant to be accessed.

Definition at line 185 of file ChargedBondedSpecies.cc.

References adhesionForceMax_.

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

 {
     return adhesionForceMax_;
 }

Mdouble ChargedBondedSpecies::getAdhesionStiffness ( ) const

Allows the spring constant to be accessed.

Definition at line 168 of file ChargedBondedSpecies.cc.

References adhesionStiffness_.

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

 {
     return adhesionStiffness_;
 }

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")

Definition at line 114 of file ChargedBondedSpecies.cc.

 {
     return "ChargedBonded";
 }

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!

Definition at line 249 of file ChargedBondedSpecies.cc.

References bondDissipation_.

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

 {
     return bondDissipation_;
 }

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.

Definition at line 228 of file ChargedBondedSpecies.cc.

References bondForceMax_.

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

 {
     return bondForceMax_;
 }

int ChargedBondedSpecies::getCharge ( ) const

Definition at line 192 of file ChargedBondedSpecies.cc.

References charge_.

                                           {
     return charge_;
 }

Mdouble ChargedBondedSpecies::getInteractionDistance ( ) const

virtual

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)

Implements BaseSpecies.

Definition at line 145 of file ChargedBondedSpecies.cc.

References adhesionForceMax_, and adhesionStiffness_.

Referenced by ChargedBondedInteraction::getElasticEnergy().

 {
     if (adhesionStiffness_ != 0.0)
         return adhesionForceMax_ / adhesionStiffness_;
     else
     {
         std::cerr << "ChargedBondedSpecies::getInteractionDistance(): adhesionStiffness cannot be zero" << std::endl;
         exit(-1);
     }
 }

Mdouble ChargedBondedSpecies::getVanDerWaalsForceMax ( ) const

Definition at line 276 of file ChargedBondedSpecies.cc.

References vanDerWaalsForceMax_.

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

 {
     return vanDerWaalsForceMax_;
 }

Mdouble ChargedBondedSpecies::getVanDerWaalsStiffness ( ) const

Definition at line 289 of file ChargedBondedSpecies.cc.

References vanDerWaalsStiffness_.

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

 {
     return vanDerWaalsStiffness_;
 }

void ChargedBondedSpecies::mix	(	ChargedBondedSpecies *const	S,
		ChargedBondedSpecies *const	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

Definition at line 127 of file ChargedBondedSpecies.cc.

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

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

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

virtual

Reads the species properties from an input stream.

Parameters

[in] is input stream (typically the restart file)

Implements BaseObject.

Definition at line 96 of file ChargedBondedSpecies.cc.

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

 {
     std::string dummy;
     is >> dummy >> adhesionForceMax_;
     is >> dummy >> adhesionStiffness_;
     logger(INFO,"adhesionForceMax_ %", adhesionForceMax_);
     is >> dummy >> charge_;
     logger(INFO,"charge % %", dummy, charge_);
     is >> dummy >> bondForceMax_;
     is >> dummy >> bondDissipation_;
     is >> dummy >> vanDerWaalsForceMax_;
     is >> dummy >> vanDerWaalsStiffness_;
 }

void ChargedBondedSpecies::setAdhesionForceMax ( Mdouble new_f0 )

Allows the spring constant to be changed.

Definition at line 174 of file ChargedBondedSpecies.cc.

References adhesionForceMax_.

 {
     if (new_f0 >= 0)
         adhesionForceMax_ = new_f0;
     else
     {
         std::cerr << "Error in setBondForceMax" << std::endl;
         exit(-1);
     }
 }

void ChargedBondedSpecies::setAdhesionStiffness ( Mdouble new_k0 )

Allows the spring constant to be changed.

Definition at line 157 of file ChargedBondedSpecies.cc.

References adhesionStiffness_.

 {
     if (new_k0 >= 0)
         adhesionStiffness_ = new_k0;
     else
     {
         std::cerr << "Error in setAdhesionStiffness" << std::endl;
         exit(-1);
     }
 }

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!

Definition at line 236 of file ChargedBondedSpecies.cc.

References bondDissipation_.

 {
     if (disp >= 0)
         bondDissipation_ = disp;
     else
     {
         std::cerr << "Error in setAdhesionDissipation" << std::endl;
         exit(-1);
     }
 }

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.

Definition at line 217 of file ChargedBondedSpecies.cc.

References bondForceMax_.

                                                          {
     if (new_f0 >= 0) {
         bondForceMax_ = new_f0;
     }
     else {
         std::cerr << "Error in setBondForceMax" << std::endl;
         exit(-1);
     }
 }

void ChargedBondedSpecies::setCharge ( int newCharge )

Definition at line 197 of file ChargedBondedSpecies.cc.

References charge_.

 {
     //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
     {
         std::cerr << "Error in setCharge - charge must be +1, -1 or zero" << std::endl;
         exit(-1);
     }
 }

void ChargedBondedSpecies::setVanDerWaalsForceMax ( Mdouble fMax )

Definition at line 264 of file ChargedBondedSpecies.cc.

References vanDerWaalsForceMax_.

 {
     if ( fMax < 0 ) {
         std::cerr << "Error in setVanDerWaalsForceMax." << std::endl;
         exit(-1);
     }
     else {
         vanDerWaalsForceMax_ = fMax;
     }
 }

void ChargedBondedSpecies::setVanDerWaalsStiffness ( Mdouble stiffness )

Definition at line 283 of file ChargedBondedSpecies.cc.

References vanDerWaalsStiffness_.

 {
     vanDerWaalsStiffness_ = stiffness;
 }

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

virtual

Writes the species properties to an output stream.

Parameters

[out] os output stream (typically the restart file)

Implements BaseObject.

Definition at line 82 of file ChargedBondedSpecies.cc.

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

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