MoleculeSystemCell Class Reference

The MoleculeSystemCell class defines a region of a MoleculeSystem and holds information about neighboring MoleculeSystemCell objects. More...

#include <moleculesystemcell.h>

Collaboration diagram for MoleculeSystemCell:

Public Member Functions
	MoleculeSystemCell (MoleculeSystem *parent)
void	setBoundaries (mat boundaries)
void	addNeighbor (MoleculeSystemCell *cell, const Vector3 &offset, const irowvec &direction)
const mat &	boundaries () const
void	addAtom (Atom *atom)
const vector< Atom * > &	atoms ()
void	setIndices (const irowvec &indices)
const irowvec &	indices () const
void	updateTwoParticleForceAndNeighborAtoms ()
void	clearAtoms ()
void	clearAlreadyCalculatedNeighbors ()
void	deleteAtomsFromCellAndSystem ()
void	setID (int id)
int	id () const
void	addAtoms (const vector< Atom * > &atoms)
void	deleteAtoms (int nAtoms)
const vector < MoleculeSystemCell * > &	neighborCells ()
void	setLocal (bool localCell)
bool	isLocal () const

Protected Attributes
mat	geometry
vector< MoleculeSystemCell * >	m_neighborCells
vector< Vector3 >	m_neighborOffsets
vector< Vector3 >	m_negativeNeighborOffsets
vector< irowvec >	m_neighborDirections
int	m_nDimensions
int	pow3nDimensions
irowvec	m_indices
MoleculeSystem *	m_moleculeSystem
mat	m_boundaries
mat	cellShiftVectors
vector< Atom * >	m_atoms
int	m_id
Vector3 &	force
Vector3	blankForce
Vector3	zeroOffset
bool	m_isOnProcessorEdge
bool	m_isLocalCell

Friends
ostream &	operator<< (ostream &os, const MoleculeSystemCell &dt)
ostream &	operator<< (ostream &os, MoleculeSystemCell *dt)

Detailed Description

The MoleculeSystemCell class defines a region of a MoleculeSystem and holds information about neighboring MoleculeSystemCell objects.

Constructor & Destructor Documentation

MoleculeSystemCell::MoleculeSystemCell

(

MoleculeSystem *

parent)

Member Function Documentation

void MoleculeSystemCell::addAtom

(

Atom *

atom)

void MoleculeSystemCell::addAtoms

(

const vector< Atom * > &

atoms)

void MoleculeSystemCell::addNeighbor	(	MoleculeSystemCell *	cell,
		const Vector3 &	offset,
		const irowvec &	direction
	)

const vector< Atom * > & MoleculeSystemCell::atoms

(

)

const mat & MoleculeSystemCell::boundaries

(

)

const

void MoleculeSystemCell::clearAlreadyCalculatedNeighbors

(

)

void MoleculeSystemCell::clearAtoms

(

)

void MoleculeSystemCell::deleteAtoms

(

int

nAtoms)

void MoleculeSystemCell::deleteAtomsFromCellAndSystem

(

)

int MoleculeSystemCell::id

(

)

const

const irowvec & MoleculeSystemCell::indices

(

)

const

bool MoleculeSystemCell::isLocal

(

)

const

const vector<MoleculeSystemCell*>& MoleculeSystemCell::neighborCells ( )

inline

void MoleculeSystemCell::setBoundaries

(

mat

boundaries)

void MoleculeSystemCell::setID

(

int

id)

void MoleculeSystemCell::setIndices

(

const irowvec &

indices)

void MoleculeSystemCell::setLocal

(

bool

localCell)

void MoleculeSystemCell::updateTwoParticleForceAndNeighborAtoms

(

)

Friends And Related Function Documentation

ostream& operator<< ( ostream &  os, const MoleculeSystemCell &  dt  )

friend

ostream& operator<< ( ostream &  os, MoleculeSystemCell *  dt  )

friend

Member Data Documentation

Vector3 MoleculeSystemCell::blankForce

protected

mat MoleculeSystemCell::cellShiftVectors

protected

Vector3& MoleculeSystemCell::force

protected

mat MoleculeSystemCell::geometry

protected

vector<Atom*> MoleculeSystemCell::m_atoms

protected

mat MoleculeSystemCell::m_boundaries

protected

int MoleculeSystemCell::m_id

protected

irowvec MoleculeSystemCell::m_indices

protected

bool MoleculeSystemCell::m_isLocalCell

protected

bool MoleculeSystemCell::m_isOnProcessorEdge

protected

MoleculeSystem* MoleculeSystemCell::m_moleculeSystem

protected

int MoleculeSystemCell::m_nDimensions

protected

vector<Vector3> MoleculeSystemCell::m_negativeNeighborOffsets

protected

vector<MoleculeSystemCell*> MoleculeSystemCell::m_neighborCells

protected

vector<irowvec> MoleculeSystemCell::m_neighborDirections

protected

vector<Vector3> MoleculeSystemCell::m_neighborOffsets

protected

int MoleculeSystemCell::pow3nDimensions

protected

Vector3 MoleculeSystemCell::zeroOffset

protected

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

• /home/svenni/Dropbox/projects/programming/emdee/emdee/src/libs/moleculesystemcell.h
• /home/svenni/Dropbox/projects/programming/emdee/emdee/src/libs/moleculesystemcell.cpp