Particle class modeling a particle's position, velocity, force, mass and type. More...

#include <Particle.h>

Public Member Functions
	Particle (int type=0)
	Construct a new Particle object by optionally passing its type. Prevents implicit conversions.

	Particle (const Particle &other)
	Construct a new Particle object using another Particle's data.

	Particle (const std::array< double, 3 > &x, const std::array< double, 3 > &v, double m, int type=TYPE_DEFAULT, double eps=EPSILON_DEFAULT, double sigma=SIGMA_DEFAULT, double k=K_DEFAULT, double r_0=R0_DEFAULT, double fzup=FZUP_DEFAULT)
	Construct a new Particle object using explicit values for each new data field.

	Particle (const std::array< double, 3 > &x, const std::array< double, 3 > &v, const std::array< double, 3 > &f, const std::array< double, 3 > &old_f, double m, int type, double eps, double sigma, double k, double r_0, double fzup, int cellIndex)
	Construct a new Particle object using explicit values for every data field.

virtual	~Particle ()
	Destroys the Particle object.

std::array< double, 3 > &	getX ()
	Gets the position \( x \) of this particle.

std::array< double, 3 > &	getV ()
	Gets the velocity \( v \) of this particle.

std::array< double, 3 > &	getF ()
	Gets the force \( F \) effective on this particle.

std::array< double, 3 > &	getOldF ()
	Gets the force \( F_\text{old} \) previously effective on this particle.

std::vector< std::reference_wrapper< Particle > > &	getDirectNeighbours ()
	Gets the direct neighbours of this particle.

const std::vector< std::reference_wrapper< Particle > > &	getDirectNeighbours () const
	Gets the direct neighbours of this particle (const).

std::vector< std::reference_wrapper< Particle > > &	getDiagonalNeighbours ()
	Gets the diagonal neighbours of this particle.

const std::vector< std::reference_wrapper< Particle > > &	getDiagonalNeighbours () const
	Gets the diagonal neighbours of this particle (const).

const std::array< double, 3 > &	getX () const
	Gets the position \( x \) of this particle (const).

const std::array< double, 3 > &	getV () const
	Gets the velocity \( v \) of this particle (const).

const std::array< double, 3 > &	getThermalMotion () const
	Gets the thermal motion \( \hat v \) of this particle (const).

const std::array< double, 3 > &	getF () const
	Gets the force \( F \) effective on this particle (const).

const std::array< double, 3 > &	getOldF () const
	Gets the force \( F_\text{old} \) previously effective on this particle (const).

double	getM () const
	Gets the mass \( m \) of the particle.

int	getType () const
	Gets the type of the particle.

double	getEpsilon () const
	Gets the Lennard-Jones parameter \( \epsilon \) of the particle.

double	getSigma () const
	Gets the Lennard-Jones parameter \( \sigma \) of the particle.

double	getK () const
	Gets the stiffness constant \( k \).

double	getR0 () const
	Gets the average bond length of a molecule pair \( r_0 \).

double	getFZUP () const
	Gets the constant upward force \( F_{Z-UP} \).

int	getCellIndex () const
	Get the index of the particle in a CellContainer.

bool	isActive () const
	Checks if the particle is currently active.

int	getId () const
	Get the ID of this particle.

omp_lock_t &	getLock ()
	Get a reference to the Lock object.

void	setX (const std::array< double, 3 > &new_x)
	Sets the new position \( x \) of the particle to a given value.

void	setV (const std::array< double, 3 > &new_v)
	Sets the new velocity \( v \) of the particle to a given value.

void	setDirectNeighbours (const std::vector< std::reference_wrapper< Particle > > &neighbours)
	Sets the direct neighbours of the particle.

void	setDiagonalNeighbours (const std::vector< std::reference_wrapper< Particle > > &neighbours)
	Sets the diagonal neighbours of the particle.

void	setThermalMotion (const std::array< double, 3 > &new_thermal_motion)
	Sets the new thermal motion \( \hat v \) of the particle to a given value.

void	setF (const std::array< double, 3 > &new_f)
	Sets the new force effective on the particle \( F \) to a given value.

void	setOldF (const std::array< double, 3 > &new_old_f)
	Sets the new previously effective force on the particle \( F_\text{old} \) to a given value.

void	setFToZero ()
	Resets the force of the particle \( F \) to 0,0,0.

void	setM (double new_m)
	Sets the new mass \( m \) of the particle to a given value.

void	setType (double new_type)
	Sets the new type of the particle to a given value.

void	setEpsilon (double new_eps)
	Sets the new Lennard-Jones parameter \( \epsilon \) of the particle to a given value.

void	setSigma (double new_sigma)
	Sets the new Lennard-Jones parameter \( \sigma \) of the particle to a given value.

void	setK (double new_k)
	Sets the new stiffness constant \( k \) to a given value.

void	setFZUP (double new_fzup)
	Sets the new upward force \( F_{Z-UP} \) to a given value.

void	setR0 (double new_r_0)
	Sets the new average bond length \( r_0 \) to a given value.

void	setCellIndex (int new_index)
	Sets the new index in a CellContainer.

void	markInactive ()
	Sets the Particle's active status to "inactive".

std::string	toString () const
	Returns a string representation of this particle.

bool	operator== (const Particle &other) const
	Overload of the equality operator for Particle objects.

bool	operator!= (const Particle &other) const
	Overload of the inequality operator for Particle objects.

Private Attributes
std::array< double, 3 >	x
	Position \( x \) of the particle.

std::array< double, 3 >	v
	Velocity \( v \) of the particle.

std::array< double, 3 >	thermal_motion
	Thermal motion \( \hat v \) of the particle.

std::array< double, 3 >	f
	Force \( F \) effective on this particle.

std::array< double, 3 >	old_f
	Force \( F_\text{old} \) which was effective on this particle.

std::vector< std::reference_wrapper< Particle > >	direct_neighbours
	Direct (up-down, left-right) neighbours of the particle (for membranes).

std::vector< std::reference_wrapper< Particle > >	diagonal_neighbours
	Diagonal neighbours of the particle (for membranes).

double	m
	Mass \( m \) of this particle.

int	type
	Type of the particle. 1 if wall, 0 otherwise.

double	epsilon
	Depth \( \epsilon \) of the potential well. Lennard-Jones parameter.

double	sigma
	Distance \( \sigma \) where the Lennard-Jones potential reaches zero. Lennard-Jones parameter.

double	k
	The stiffness constant \( k \) for membrane simulations.

double	r_0
	The average bond length \( r_0 \) for membrane simulations.

double	fzup
	The constant upward force \( F_{Z-UP} \) for membrane simulations.

int	cellIndex
	The cell index of the particle, to be used with the linked cell method.

omp_lock_t	lock
	A mutual exclusion lock, used alongside parallelization.

bool	active {true}
	The status of the particle.

int	id
	A unique ID for this particle. Currently only used for debug purposes.

Detailed Description

Particle class modeling a particle's position, velocity, force, mass and type.

Constructor & Destructor Documentation

◆ Particle() [1/4]

Particle::Particle ( int type = 0 )

explicit

Construct a new Particle object by optionally passing its type. Prevents implicit conversions.

Given that the current simulations make use of the particle mass as the divisor in some formulas, the mass may not be negative or 0.

Parameters

type	The type of the Particle object to be constructed.

◆ Particle() [2/4]

Particle::Particle ( const Particle & other )

Construct a new Particle object using another Particle's data.

Parameters

other A reference to the Particle object to copy the data from.

◆ Particle() [3/4]

Particle::Particle	(	const std::array< double, 3 > &	x,
		const std::array< double, 3 > &	v,
		double	m,
		int	type = `TYPE_DEFAULT`,
		double	eps = `EPSILON_DEFAULT`,
		double	sigma = `SIGMA_DEFAULT`,
		double	k = `K_DEFAULT`,
		double	r_0 = `R0_DEFAULT`,
		double	fzup = `FZUP_DEFAULT`
	)

Construct a new Particle object using explicit values for each new data field.

Given that the current simulations make use of the particle mass as the divisor in some formulas, the mass may not be negative or 0.

Parameters

x	A reference to the array containing data for the position \( x \).
v	A reference to the array containing data for the velocity \( v \).
m	The mass \( m \) of the particle.
type	The type of the particle. (optional)
eps	The Lennard-Jones parameter \( \epsilon \) of the particle. (optional)
sigma	The Lennard-Jones parameter \( \sigma \) of the particle. (optional)
k	The stiffness constant \( k \), used for membrane simulations. (optional)
r_0	The average bond length \( r_0 \), used for membrane simulations. (optional)
fzup	The constant upward force \( F_{Z-UP} \), used for membrane simulations. (optional)

◆ Particle() [4/4]

Particle::Particle	(	const std::array< double, 3 > &	x,
		const std::array< double, 3 > &	v,
		const std::array< double, 3 > &	f,
		const std::array< double, 3 > &	old_f,
		double	m,
		int	type,
		double	eps,
		double	sigma,
		double	k,
		double	r_0,
		double	fzup,
		int	cellIndex
	)

Construct a new Particle object using explicit values for every data field.

There are no default parameters here; every value must be initialized.

Parameters

x	A reference to the array containing data for the position \( x \).
v	A reference to the array containing data for the velocity \( v \).
f	A reference to the array containing data for the force \( F \) effective on this particle.
old_f	A reference to the array containing data for the old force \( F \) effective on this particle.
m	The mass \( m \) of the particle.
type	The type of the particle.
eps	The Lennard-Jones parameter \( \epsilon \) of the particle.
sigma	The Lennard-Jones parameter \( \sigma \) of the particle.
k	The stiffness constant \( k \), used for membrane simulations.
r_0	The average bond length \( r_0 \), used for membrane simulations.
fzup	The constant upward force \( F_{Z-UP} \), used for membrane simulations.
cellIndex	The index of this particle inside a cell. For use with the linked cell method.

◆ ~Particle()

virtual Particle::~Particle ( )

virtual

Destroys the Particle object.

Member Function Documentation

◆ getCellIndex()

int Particle::getCellIndex ( ) const

inline

Get the index of the particle in a CellContainer.

For use with the linked cell method.

Returns: The index of the particle in a grid of cells.

◆ getDiagonalNeighbours() [1/2]

std::vector< std::reference_wrapper< Particle > > & Particle::getDiagonalNeighbours ( )

inline

Gets the diagonal neighbours of this particle.

Returns: A reference to the vector of diagonal neighbour particle references of this particle.

◆ getDiagonalNeighbours() [2/2]

const std::vector< std::reference_wrapper< Particle > > & Particle::getDiagonalNeighbours ( ) const

inline

Gets the diagonal neighbours of this particle (const).

Returns: A const reference to the vector of diagonal neighbour particle references of this particle.

◆ getDirectNeighbours() [1/2]

std::vector< std::reference_wrapper< Particle > > & Particle::getDirectNeighbours ( )

inline

Gets the direct neighbours of this particle.

Returns: A reference to the vector of direct neighbour particle references of this particle.

◆ getDirectNeighbours() [2/2]

const std::vector< std::reference_wrapper< Particle > > & Particle::getDirectNeighbours ( ) const

inline

Gets the direct neighbours of this particle (const).

Returns: A const reference to the vector of direct neighbour particle references of this particle.

◆ getEpsilon()

double Particle::getEpsilon ( ) const

inline

Gets the Lennard-Jones parameter \( \epsilon \) of the particle.

Returns: The Lennard-Jones parameter \( \epsilon \) of the particle.

◆ getF() [1/2]

std::array< double, 3 > & Particle::getF ( )

inline

Gets the force \( F \) effective on this particle.

Returns: A reference to the force array of this particle.

◆ getF() [2/2]

const std::array< double, 3 > & Particle::getF ( ) const

inline

Gets the force \( F \) effective on this particle (const).

Returns: A const reference to the force array of this particle.

◆ getFZUP()

double Particle::getFZUP ( ) const

inline

Gets the constant upward force \( F_{Z-UP} \).

Returns: The constant upward force \( F_{Z-UP} \).

◆ getId()

int Particle::getId ( ) const

inline

Get the ID of this particle.

Currently only used for debugging purposes.

Returns: The ID of this particle.

◆ getK()

double Particle::getK ( ) const

inline

Gets the stiffness constant \( k \).

Returns: The stiffness constant \( k \).

◆ getLock()

omp_lock_t & Particle::getLock ( )

inline

Get a reference to the Lock object.

Returns: A reference to the Lock object.

◆ getM()

double Particle::getM ( ) const

inline

Gets the mass \( m \) of the particle.

Returns: The mass of the particle.

◆ getOldF() [1/2]

std::array< double, 3 > & Particle::getOldF ( )

inline

Gets the force \( F_\text{old} \) previously effective on this particle.

Returns: A reference to the old force array of this particle.

◆ getOldF() [2/2]

const std::array< double, 3 > & Particle::getOldF ( ) const

inline

Gets the force \( F_\text{old} \) previously effective on this particle (const).

Returns: A const reference to the old force array of this particle.

◆ getR0()

double Particle::getR0 ( ) const

inline

Gets the average bond length of a molecule pair \( r_0 \).

Returns: The average bond length \( r_0 \).

◆ getSigma()

double Particle::getSigma ( ) const

inline

Gets the Lennard-Jones parameter \( \sigma \) of the particle.

Returns: The Lennard-Jones parameter \( \sigma \) of the particle.

◆ getThermalMotion()

const std::array< double, 3 > & Particle::getThermalMotion ( ) const

inline

Gets the thermal motion \( \hat v \) of this particle (const).

Returns: A const reference to the thermal motion array of this particle.

◆ getType()

int Particle::getType ( ) const

inline

Gets the type of the particle.

Returns: The type of the particle.

◆ getV() [1/2]

std::array< double, 3 > & Particle::getV ( )

inline

Gets the velocity \( v \) of this particle.

Returns: A reference to the velocity array of this particle.

◆ getV() [2/2]

const std::array< double, 3 > & Particle::getV ( ) const

inline

Gets the velocity \( v \) of this particle (const).

Returns: A const reference to the velocity array of this particle.

◆ getX() [1/2]

std::array< double, 3 > & Particle::getX ( )

inline

Gets the position \( x \) of this particle.

Returns: A reference to the position array of this particle.

◆ getX() [2/2]

const std::array< double, 3 > & Particle::getX ( ) const

inline

Gets the position \( x \) of this particle (const).

Returns: A const reference to the position array of this particle.

◆ isActive()

bool Particle::isActive ( ) const

inline

Checks if the particle is currently active.

Returns: true if the particle is currently active.; false if the particle is currently inactive.

◆ markInactive()

void Particle::markInactive ( )

Sets the Particle's active status to "inactive".

◆ operator!=()

bool Particle::operator!= ( const Particle & other ) const

Overload of the inequality operator for Particle objects.

Parameters

other A reference to the Particle object to compare the current object with.

Returns: true if both particles have at least one differing attribute.; false if both particles' data (attributes) contain the same values.

◆ operator==()

bool Particle::operator== ( const Particle & other ) const

Overload of the equality operator for Particle objects.

Parameters

other A reference to the Particle object to compare the current object with.

Returns: true if both particles' data (attributes) contain the same values.; false if both particles have at least one differing attribute.

◆ setCellIndex()

void Particle::setCellIndex ( int new_index )

Sets the new index in a CellContainer.

For use with the linked cell method.

Parameters

new_index The new index in a grid of cells.

◆ setDiagonalNeighbours()

void Particle::setDiagonalNeighbours ( const std::vector< std::reference_wrapper< Particle > > & neighbours )

Sets the diagonal neighbours of the particle.

Parameters

neighbours A reference to the vector of references to the neighbours.

◆ setDirectNeighbours()

void Particle::setDirectNeighbours ( const std::vector< std::reference_wrapper< Particle > > & neighbours )

Sets the direct neighbours of the particle.

Parameters

neighbours A reference to the vector of references to the neighbours.

◆ setEpsilon()

void Particle::setEpsilon ( double new_eps )

Sets the new Lennard-Jones parameter \( \epsilon \) of the particle to a given value.

Parameters

new_eps The new Lennard-Jones parameter \( \epsilon \) of this particle.

◆ setF()

void Particle::setF ( const std::array< double, 3 > & new_f )

Sets the new force effective on the particle \( F \) to a given value.

Parameters

new_f A reference to the array containing the new force effective on this particle.

◆ setFToZero()

void Particle::setFToZero ( )

Resets the force of the particle \( F \) to 0,0,0.

◆ setFZUP()

void Particle::setFZUP ( double new_fzup )

Sets the new upward force \( F_{Z-UP} \) to a given value.

Parameters

new_fzup The new upward force \( F_{Z-UP} \).

◆ setK()

void Particle::setK ( double new_k )

Sets the new stiffness constant \( k \) to a given value.

Parameters

new_k The new stiffness constant \( k \).

◆ setM()

void Particle::setM ( double new_m )

Sets the new mass \( m \) of the particle to a given value.

Given that the current simulations make use of the particle mass as the divisor in some formulas, the mass may not be negative or 0.

Parameters

new_m The new mass of this particle.

◆ setOldF()

void Particle::setOldF ( const std::array< double, 3 > & new_old_f )

Sets the new previously effective force on the particle \( F_\text{old} \) to a given value.

Parameters

new_old_f A reference to the array containing the new previously effective force on this particle.

◆ setR0()

void Particle::setR0 ( double new_r_0 )

Sets the new average bond length \( r_0 \) to a given value.

Parameters

new_r_0 The new average bond length \( r_0 \).

◆ setSigma()

void Particle::setSigma ( double new_sigma )

Sets the new Lennard-Jones parameter \( \sigma \) of the particle to a given value.

Parameters

new_sigma The new Lennard-Jones parameter \( \sigma \) of this particle.

◆ setThermalMotion()

void Particle::setThermalMotion ( const std::array< double, 3 > & new_thermal_motion )

Sets the new thermal motion \( \hat v \) of the particle to a given value.

Parameters

new_thermal_motion A reference to the array containing the new thermal motion of this particle.

◆ setType()

void Particle::setType ( double new_type )

Sets the new type of the particle to a given value.

Parameters

new_type The new type of this particle.

◆ setV()

void Particle::setV ( const std::array< double, 3 > & new_v )

Sets the new velocity \( v \) of the particle to a given value.

Parameters

new_v A reference to the array containing the new velocity of this particle.

◆ setX()

void Particle::setX ( const std::array< double, 3 > & new_x )

Sets the new position \( x \) of the particle to a given value.

Parameters

new_x A reference to the array containing the new position of this particle.

◆ toString()

std::string Particle::toString ( ) const

Returns a string representation of this particle.

Returns: The formatted particle data as a std::string.

Member Data Documentation

◆ active

bool Particle::active {true}

private

The status of the particle.

If the particle is marked "active", it will be considered in the time integration calculation. Otherwise, it is ignored.

◆ cellIndex

int Particle::cellIndex

private

The cell index of the particle, to be used with the linked cell method.

◆ diagonal_neighbours

std::vector<std::reference_wrapper<Particle> > Particle::diagonal_neighbours

private

Diagonal neighbours of the particle (for membranes).

◆ direct_neighbours

std::vector<std::reference_wrapper<Particle> > Particle::direct_neighbours

private

Direct (up-down, left-right) neighbours of the particle (for membranes).

◆ epsilon

double Particle::epsilon

private

Depth \( \epsilon \) of the potential well. Lennard-Jones parameter.

◆ f

std::array<double, 3> Particle::f

private

Force \( F \) effective on this particle.

◆ fzup

double Particle::fzup

private

The constant upward force \( F_{Z-UP} \) for membrane simulations.

◆ id

int Particle::id

private

A unique ID for this particle. Currently only used for debug purposes.

◆ k

double Particle::k

private

The stiffness constant \( k \) for membrane simulations.

◆ lock

omp_lock_t Particle::lock

private

A mutual exclusion lock, used alongside parallelization.

◆ m

double Particle::m

private

Mass \( m \) of this particle.

◆ old_f

std::array<double, 3> Particle::old_f

private

Force \( F_\text{old} \) which was effective on this particle.

◆ r_0

double Particle::r_0

private

The average bond length \( r_0 \) for membrane simulations.

◆ sigma

double Particle::sigma

private

Distance \( \sigma \) where the Lennard-Jones potential reaches zero. Lennard-Jones parameter.

◆ thermal_motion

std::array<double, 3> Particle::thermal_motion

private

Thermal motion \( \hat v \) of the particle.

◆ type

int Particle::type

private

Type of the particle. 1 if wall, 0 otherwise.

◆ v

std::array<double, 3> Particle::v

private

Velocity \( v \) of the particle.

◆ x

std::array<double, 3> Particle::x

private

Position \( x \) of the particle.

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

src/objects/Particle.h

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Particle() [1/4]

◆ Particle() [2/4]

◆ Particle() [3/4]

◆ Particle() [4/4]

◆ ~Particle()

Member Function Documentation

◆ getCellIndex()

◆ getDiagonalNeighbours() [1/2]

◆ getDiagonalNeighbours() [2/2]

◆ getDirectNeighbours() [1/2]

◆ getDirectNeighbours() [2/2]

◆ getEpsilon()

◆ getF() [1/2]

◆ getF() [2/2]

◆ getFZUP()

◆ getId()

◆ getK()

◆ getLock()

◆ getM()

◆ getOldF() [1/2]

◆ getOldF() [2/2]

◆ getR0()

◆ getSigma()

◆ getThermalMotion()

◆ getType()

◆ getV() [1/2]

◆ getV() [2/2]

◆ getX() [1/2]

◆ getX() [2/2]

◆ isActive()

◆ markInactive()

◆ operator!=()

◆ operator==()

◆ setCellIndex()

◆ setDiagonalNeighbours()

◆ setDirectNeighbours()

◆ setEpsilon()

◆ setF()

◆ setFToZero()

◆ setFZUP()

◆ setK()

◆ setM()

◆ setOldF()

◆ setR0()

◆ setSigma()

◆ setThermalMotion()

◆ setType()

◆ setV()

◆ setX()

◆ toString()

Member Data Documentation

◆ active

◆ cellIndex

◆ diagonal_neighbours

◆ direct_neighbours

◆ epsilon

◆ f

◆ fzup

◆ id

◆ k

◆ lock

◆ m

◆ old_f

◆ r_0

◆ sigma

◆ thermal_motion

◆ type

◆ v

◆ x