Cluster Class Reference

Collaboration diagram for Cluster:

[legend]List of all members.

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Detailed Description

This class represents a cluster of atoms.

Author:

John Schneiderman

Definition at line 37 of file cluster.h.

Public Member Functions
void	addAtom (const Atom &atom)
void	calculateCentreMass ()
void	calculateKineticEnergy ()
void	calculatePotentialEnergy ()
void	clear ()
	Cluster (const Cluster &cluster)
	Cluster ()
double	kineticEnergyTotal () const
Cluster &	operator= (const Cluster &rhs)
const Atom &	operator[] (int index) const
Atom &	operator[] (int index)
Coordinate	positionCentreMass () const
double	potentialEnergyTotal () const
void	read (string baseName)
void	setKineticEnergyTotal (double kineticEnergyTotal)
void	setPositionCentreMass (Coordinate positionCentreMass)
void	setPotentialEnergyTotal (double potentialEnergyTotal)
void	setVelocityCentreMass (Coordinate velocityCentreMass)
int	size () const
Coordinate	velocityCentreMass () const
void	write (string baseName)
Static Public Attributes
static const int	PRECISION = 10
static const int	WIDTH = 18
Private Attributes
vector< Atom >	m_atoms
double	m_kineticEnergyTotal
Coordinate	m_positionCentreMass
double	m_potentialEnergyTotal
Coordinate	m_velocityCentreMass
Friends
ostream &	operator<< (ostream &outStream, const Cluster &cluster)
bool	operator== (const Cluster &lhs, const Cluster &rhs)

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Constructor & Destructor Documentation

Cluster::Cluster (   )

A default constructor. Definition at line 30 of file cluster.cpp. References m_kineticEnergyTotal, and m_potentialEnergyTotal.

Cluster::Cluster (  const Cluster &  cluster  )

Copy constructor. Parameters: cluster  is the cluster to copy into *this. Definition at line 35 of file cluster.cpp.

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Member Function Documentation

void Cluster::addAtom (  const Atom &  atom  )

Adds an atom into the cluster. Parameters: atom  this is the atom to add to the cluster. Definition at line 233 of file cluster.cpp. References m_atoms. Referenced by FCC_Lattice::createLattice().

void Cluster::calculateCentreMass (   )

The cluster's positional and velocity centre of mass are calculated. Definition at line 129 of file cluster.cpp. References m_atoms, m_positionCentreMass, m_velocityCentreMass, and size(). Referenced by FCC_Lattice::createLattice(), MDLJ_Simulation::run(), and MCLJ_Simulation::run(). Here is the call graph for this function:

void Cluster::calculateKineticEnergy (   )

Calculates the kinetic energy of the cluster and for each atom. Definition at line 116 of file cluster.cpp. References m_atoms, and m_kineticEnergyTotal. Referenced by MDLJ_Simulation::run().

void Cluster::calculatePotentialEnergy (   )

Calculates the potential energy of the cluster and for each atom. Definition at line 80 of file cluster.cpp. References m_atoms, m_potentialEnergyTotal, Coordinate::x, Coordinate::y, and Coordinate::z. Referenced by MDLJ_Simulation::run(), and MCLJ_Simulation::run().

void Cluster::clear (   )

Clears the cluster. Definition at line 197 of file cluster.cpp. References m_atoms, m_kineticEnergyTotal, m_positionCentreMass, m_potentialEnergyTotal, and m_velocityCentreMass. Referenced by FCC_Lattice::createLattice(), interactiveRun(), nonInteractiveRun(), and operator=().

double Cluster::kineticEnergyTotal (   )  const

An accessor for the total kinetic energy. Returns: Total kinetic energy in the cluster. Definition at line 45 of file cluster.cpp. References m_kineticEnergyTotal. Referenced by operator=(), and MDLJ_Simulation::run().

Cluster & Cluster::operator= (  const Cluster &  rhs  )

Assignment operator for a cluster. Parameters: rhs  is the cluster to assign to *this. Returns: *this. Definition at line 208 of file cluster.cpp. References clear(), kineticEnergyTotal(), m_atoms, m_kineticEnergyTotal, m_positionCentreMass, m_potentialEnergyTotal, m_velocityCentreMass, positionCentreMass(), potentialEnergyTotal(), size(), and velocityCentreMass(). Here is the call graph for this function:

const Atom & Cluster::operator[] (  int  index  )  const

Constant Subscript operator for the cluster. Parameters: index  is the atom within the cluster to retreive. The first atom is located at 0. Returns: a cosntant refrence to the atom. Definition at line 228 of file cluster.cpp. References m_atoms.

Atom & Cluster::operator[] (  int  index  )

Subscript operator for the cluster. Parameters: index  is the atom within the cluster to retreive. The first atom is located at 0. Returns: a refrence to the atom. Definition at line 223 of file cluster.cpp. References m_atoms.

Coordinate Cluster::positionCentreMass (   )  const

An accessor for the centre of mass' position. Returns: The cluster's centre of mass' position. Definition at line 50 of file cluster.cpp. References m_positionCentreMass. Referenced by RadialDensityHistogram::acquire(), MDLJ_Simulation::adjustPosCenMass(), FCC_Lattice::adjustPosCenMass(), and operator=().

double Cluster::potentialEnergyTotal (   )  const

An accessor for the total potential energy. Returns: The total potential energy in the cluster. Definition at line 40 of file cluster.cpp. References m_potentialEnergyTotal. Referenced by MDLJ_Simulation::calculateAccelerations(), operator=(), MDLJ_Simulation::run(), and MCLJ_Simulation::run().

void Cluster::read (  string  baseName  )

Reads in the position and velocity of a previous cluster. Exceptions: char*  if it fails to read. Parameters: baseName  is the base name for the position and velocity files. The position and velocity are read in as: baseName.pos and baseName.vel. Definition at line 144 of file cluster.cpp. References m_atoms, and Atom::properties. Referenced by interactiveRun(), and nonInteractiveRun().

void Cluster::setKineticEnergyTotal (  double  kineticEnergyTotal  )

A modifier for the total kinetic energy. Parameters: kineticEnergyTotal  is the value to set the cluster's total kinetic energy to. Definition at line 65 of file cluster.cpp. References m_kineticEnergyTotal. Referenced by MDLJ_Simulation::calculateVelocities().

void Cluster::setPositionCentreMass (  Coordinate  positionCentreMass  )

A modifier for the centre of mass' position. Parameters: positionCentreMass  is the value to set the cluster's positional centre of mass. Definition at line 70 of file cluster.cpp. References m_positionCentreMass. Referenced by FCC_Lattice::createLattice().

void Cluster::setPotentialEnergyTotal (  double  potentialEnergyTotal  )

A modifier for the total potential energy. Parameters: potentialEnergyTotal  is the value to set the cluster's total potential energy to. Definition at line 60 of file cluster.cpp. References m_potentialEnergyTotal. Referenced by MDLJ_Simulation::calculateAccelerations().

void Cluster::setVelocityCentreMass (  Coordinate  velocityCentreMass  )

A modifier for the centre of mass' velocity. Parameters: velocityCentreMass  is the value to set the cluster's velocity centre of mass. Definition at line 75 of file cluster.cpp. References m_velocityCentreMass.

int Cluster::size (   )  const

Gives the current size of the cluster. Returns: the number of atoms in the cluster. Definition at line 203 of file cluster.cpp. References m_atoms. Referenced by RadialDistributionFunction::acquire(), RadialDensityHistogram::acquire(), PotentialEnergyHistogram::acquire(), KineticEnergyHistogram::acquire(), MDLJ_Simulation::adjustPosCenMass(), FCC_Lattice::adjustPosCenMass(), MDLJ_Simulation::calculateAccelerations(), calculateCentreMass(), MDLJ_Simulation::calculatePositions(), MDLJ_Simulation::calculateVelocities(), interactiveRun(), operator<<(), operator=(), operator==(), MCLJ_Simulation::potentialEnergyDifference(), MDLJ_Simulation::run(), MCLJ_Simulation::run(), selectSimulation(), and MD_Simulation::writeAverages().

Coordinate Cluster::velocityCentreMass (   )  const

An accessor for the centre of mass' velocity. Returns: The cluster's centre of mass' velocity. Definition at line 55 of file cluster.cpp. References m_velocityCentreMass. Referenced by operator=().

void Cluster::write (  string  baseName  )

Writes out the position and velocity of the cluster. Exceptions: char*  if it fails to write. Parameters: baseName  is the base name for the position and velocity files. The position and velocity are wrote out as: baseName.pos and baseName.vel. Definition at line 169 of file cluster.cpp. References m_atoms, and PRECISION. Referenced by createCluster(), interactiveRun(), and nonInteractiveRun().

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Friends And Related Function Documentation

ostream& operator<< (  ostream &  outStream, const Cluster &  cluster )  [friend]

Outputs the contents of the cluster in the format of: Positions: x, y, z Velocity: x, y, z Acceleration: x, y, z Potential Energies: Each atoms' potential energy. Kinetic Energies: Each atoms' kinetic energy. This is useful for debuging purposes. Parameters: outStream  is the buffer to output to. cluster  is the cluster to output. Returns: a refrence to the outStream Definition at line 238 of file cluster.cpp.

bool operator== (  const Cluster &  lhs, const Cluster &  rhs )  [friend]

Equivelant operator for the cluster. Note: we assume that all values have to be equal. Parameters: lhs  is the left hand side cluster to compare to the rhs. rhs  is the right hand side cluster to compare to the lhs. Returns: True if lhs has the exact same contents as the rhs, false else wise. Definition at line 261 of file cluster.cpp.

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Member Data Documentation

vector<Atom> Cluster::m_atoms [private]

Parameters: m_atoms  is the atoms in the cluster. Definition at line 199 of file cluster.h. Referenced by addAtom(), calculateCentreMass(), calculateKineticEnergy(), calculatePotentialEnergy(), clear(), operator=(), operator[](), read(), size(), and write().

double Cluster::m_kineticEnergyTotal [private]

Parameters: m_kineticEnergyTotal  is the total kinetic energy in the cluster. Definition at line 197 of file cluster.h. Referenced by calculateKineticEnergy(), clear(), Cluster(), kineticEnergyTotal(), operator=(), operator==(), and setKineticEnergyTotal().

Coordinate Cluster::m_positionCentreMass [private]

Parameters: m_positionCentreMass  is the coordinates for the positional centre of mass. Definition at line 191 of file cluster.h. Referenced by calculateCentreMass(), clear(), operator=(), operator==(), positionCentreMass(), and setPositionCentreMass().

double Cluster::m_potentialEnergyTotal [private]

Parameters: m_potentialEnergyTotal  is the total potential energy in the cluster. Definition at line 195 of file cluster.h. Referenced by calculatePotentialEnergy(), clear(), Cluster(), operator=(), operator==(), potentialEnergyTotal(), and setPotentialEnergyTotal().

Coordinate Cluster::m_velocityCentreMass [private]

Parameters: m_velocityCentreMass  is the coordinates for the velocity centre of mass. Definition at line 193 of file cluster.h. Referenced by calculateCentreMass(), clear(), operator=(), operator==(), setVelocityCentreMass(), and velocityCentreMass().

const int Cluster::PRECISION = 10 [static]

Parameters: PRECISION  is how precise to be with all data. Note: This value are used through-out the programme. Definition at line 44 of file cluster.h. Referenced by operator<<(), MDLJ_Simulation::run(), MCLJ_Simulation::run(), RadialDistributionFunction::write(), RadialDensityHistogram::write(), PotentialEnergyHistogram::write(), KineticEnergyHistogram::write(), and write().

const int Cluster::WIDTH = 18 [static]

Parameters: WIDTH  is the output space between each number, including that number. Note: This value are used through-out the programme. Definition at line 49 of file cluster.h. Referenced by MDLJ_Simulation::run(), and MCLJ_Simulation::run().

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

• clusters/cluster.h
• clusters/cluster.cpp

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