The MoleculeSystem class is the core of the molecular dynamics simulation. It provides functions to add and remove atoms, start simulations, and sampling of statistical properties. More...

#include <moleculesystem.h>

Collaboration diagram for MoleculeSystem:

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Public Member Functions
	MoleculeSystem ()

void	addAtoms (const vector< Atom * > &atoms)

const vector< Atom * > &	atoms () const

const vector < MoleculeSystemCell * > &	globalCells () const

const vector< AtomType > &	particleTypes () const

void	updateForces ()

void	simulate ()

void	setBoundaries (double min, double max)

void	setBoundaries (double xMin, double xMax, double yMin, double yMax, double zMin, double zMax)

void	setBoundaries (mat boundaries)

void	setupCells (double requestedCellLength=0.0)

const mat &	cellShiftVectors ()

void	refreshCellContents ()

void	setIntegrator (Integrator *integrator)

void	updateStatistics ()

bool	isOutputEnabled () const

void	setOutputEnabled (bool enabled)

bool	isSaveEnabled () const

void	setSaveEnabled (bool enabled)

void	obeyBoundaries ()

void	setFileManager (FileManager *fileManager)

void	addModifier (Modifier *modifier)

void	removeModifier (Modifier *modifier)

void	applyModifiers ()

Integrator *	integrator () const

double	kineticEnergyTotal ()

double	potentialEnergyTotal ()

double	temperature () const

double	pressure () const

double	averageDisplacement () const

double	averageSquareDisplacement () const

const mat &	boundaries () const

double	time () const

const irowvec &	nCells () const

void	setTime (double currentTime)

void	setBoltzmannConstant (double boltzmannConstant)

bool	load (string fileName)

void	clearAtoms ()

void	addAtomsToCorrectCells (vector< Atom * > &atoms)

void	setStep (uint step)

void	deleteAtoms ()

void	setAverageSquareDisplacement (double averageSquareDisplacement)

void	setAverageDisplacement (double averageDisplacement)

void	setupProcessors ()

MoleculeSystemCell *	cell (int i, int j, int k)

Processor *	processor ()

void	setCalculatePressureEnabled (bool enable)

bool	isCalculatePressureEnabled ()

void	setCalculatePotentialEnabled (bool enable)

bool	isCalculatePotentialEnabled ()

void	setSaveEveryNSteps (int nSteps)

int	saveEveryNSteps ()

bool	shouldTimeStepBeSaved ()

void	setNSimulationSteps (int nSteps)

int	nSimulationSteps ()

void	setProgressReporter (ProgressReporter *progressReporter)

void	addSingleParticleForce (SingleParticleForce *force)

const vector < SingleParticleForce * > &	singleParticleForces () const

void	setParticleTypes (const vector< AtomType > &particleTypes)

const unordered_map< int, AtomType > &	particleTypesById ()

bool	isOutputEnabledForThisStep () const

void	save ()

void	save (string fileName)

void	setCreateSymlink (bool enabled)

const vector < MoleculeSystemCell * > &	localCells () const

ThreeParticleForce *	threeParticleForce () const

void	setThreeParticleForce (ThreeParticleForce *threeParticleForce)

TwoParticleForce *	twoParticleForce () const

void	setTwoParticleForce (TwoParticleForce *twoParticleForce)

int	cellIndex (int xIndex, int yIndex, int zIndex)

void	setPeriodicity (bool periodicInX, bool periodicInY, bool periodicInZ)

int	nAtomsTotal ()

const vector < MoleculeSystemCell * > &	localAndGhostCells () const

Protected Attributes
vector< Atom * >	m_atoms

Integrator *	m_integrator

mat	m_boundaries

int	m_nDimensions

mat	m_cellShiftVectors

int	pow3nDimensions

irowvec	m_globalCellsPerDimension

rowvec	m_cellLengths

vector< MoleculeSystemCell * >	m_globalCells

bool	m_isSaveEnabled

bool	m_isOutputEnabled

bool	m_areCellsSetUp

double	m_temperature

vector< Modifier * >	m_modifiers

double	m_averageDisplacement

double	m_averageSquareDisplacement

double	m_pressure

uint	m_step

double	m_time

bool	m_skipInitialize

double	m_kineticEnergyTotal

double	m_potentialEnergyTotal

Processor *	m_processor

bool	m_isCalculatePressureEnabled

bool	m_isCalculatePotentialEnabled

int	m_saveEveryNSteps

int	m_nSimulationSteps

bool	m_isFinalTimeStep

ProgressReporter *	m_progressReporter

vector< SingleParticleForce * >	m_singleParticleForces

vector< AtomType >	m_particleTypes

unordered_map< int, AtomType >	m_particleTypesByID

bool	m_isCreateSymlinkEnabled

bool	m_isPeriodicDimension [3]

TwoParticleForce *	m_twoParticleForce

ThreeParticleForce *	m_threeParticleForce

int	m_nAtomsTotal

Detailed Description

The MoleculeSystem class is the core of the molecular dynamics simulation. It provides functions to add and remove atoms, start simulations, and sampling of statistical properties.

Constructor & Destructor Documentation

MoleculeSystem::MoleculeSystem ( )

Member Function Documentation

void MoleculeSystem::addAtoms ( const vector< Atom * > & atoms)

void MoleculeSystem::addAtomsToCorrectCells ( vector< Atom * > & atoms)

void MoleculeSystem::addModifier ( Modifier * modifier)

void MoleculeSystem::addSingleParticleForce ( SingleParticleForce * force)

inline

void MoleculeSystem::applyModifiers ( )

const vector< Atom * > & MoleculeSystem::atoms ( ) const

double MoleculeSystem::averageDisplacement ( ) const

inline

double MoleculeSystem::averageSquareDisplacement ( ) const

inline

const mat& MoleculeSystem::boundaries ( ) const

inline

MoleculeSystemCell * MoleculeSystem::cell	(	int	i,
		int	j,
		int	k
	)

int MoleculeSystem::cellIndex	(	int	xIndex,
		int	yIndex,
		int	zIndex
	)

const mat & MoleculeSystem::cellShiftVectors ( )

void MoleculeSystem::clearAtoms ( )

void MoleculeSystem::deleteAtoms ( )

const vector< MoleculeSystemCell * > & MoleculeSystem::globalCells ( ) const

Integrator* MoleculeSystem::integrator ( ) const

inline

bool MoleculeSystem::isCalculatePotentialEnabled ( )

inline

bool MoleculeSystem::isCalculatePressureEnabled ( )

inline

bool MoleculeSystem::isOutputEnabled ( ) const

bool MoleculeSystem::isOutputEnabledForThisStep ( ) const

bool MoleculeSystem::isSaveEnabled ( ) const

double MoleculeSystem::kineticEnergyTotal ( )

inline

bool MoleculeSystem::load ( string fileName)

const vector< MoleculeSystemCell * > & MoleculeSystem::localAndGhostCells ( ) const

const vector< MoleculeSystemCell * > & MoleculeSystem::localCells ( ) const

int MoleculeSystem::nAtomsTotal ( )

const irowvec & MoleculeSystem::nCells ( ) const

inline

int MoleculeSystem::nSimulationSteps ( )

inline

void MoleculeSystem::obeyBoundaries ( )

const vector< AtomType > & MoleculeSystem::particleTypes ( ) const

inline

const unordered_map< int, AtomType > & MoleculeSystem::particleTypesById ( )

inline

double MoleculeSystem::potentialEnergyTotal ( )

inline

double MoleculeSystem::pressure ( ) const

inline

Processor* MoleculeSystem::processor ( )

void MoleculeSystem::refreshCellContents ( )

void MoleculeSystem::removeModifier ( Modifier * modifier)

void MoleculeSystem::save ( )

void MoleculeSystem::save ( string fileName)

int MoleculeSystem::saveEveryNSteps ( )

inline

void MoleculeSystem::setAverageDisplacement ( double averageDisplacement)

void MoleculeSystem::setAverageSquareDisplacement ( double averageSquareDisplacement)

void MoleculeSystem::setBoltzmannConstant ( double boltzmannConstant)

void MoleculeSystem::setBoundaries	(	double	min,
		double	max
	)

void MoleculeSystem::setBoundaries	(	double	xMin,
		double	xMax,
		double	yMin,
		double	yMax,
		double	zMin,
		double	zMax
	)

void MoleculeSystem::setBoundaries ( mat boundaries)

void MoleculeSystem::setCalculatePotentialEnabled ( bool enable)

inline

void MoleculeSystem::setCalculatePressureEnabled ( bool enable)

inline

void MoleculeSystem::setCreateSymlink ( bool enabled)

void MoleculeSystem::setFileManager ( FileManager * fileManager)

void MoleculeSystem::setIntegrator ( Integrator * integrator)

void MoleculeSystem::setNSimulationSteps ( int nSteps)

inline

void MoleculeSystem::setOutputEnabled ( bool enabled)

void MoleculeSystem::setParticleTypes ( const vector< AtomType > & particleTypes)

void MoleculeSystem::setPeriodicity	(	bool	periodicInX,
		bool	periodicInY,
		bool	periodicInZ
	)

void MoleculeSystem::setProgressReporter ( ProgressReporter * progressReporter)

inline

void MoleculeSystem::setSaveEnabled ( bool enabled)

void MoleculeSystem::setSaveEveryNSteps ( int nSteps)

inline

void MoleculeSystem::setStep ( uint step)

void MoleculeSystem::setThreeParticleForce ( ThreeParticleForce * threeParticleForce)

void MoleculeSystem::setTime ( double currentTime)

void MoleculeSystem::setTwoParticleForce ( TwoParticleForce * twoParticleForce)

void MoleculeSystem::setupCells ( double requestedCellLength = 0.0)

void MoleculeSystem::setupProcessors ( )

bool MoleculeSystem::shouldTimeStepBeSaved ( )

void MoleculeSystem::simulate ( )

const vector< SingleParticleForce * > & MoleculeSystem::singleParticleForces ( ) const

inline

double MoleculeSystem::temperature ( ) const

inline

ThreeParticleForce * MoleculeSystem::threeParticleForce ( ) const

double MoleculeSystem::time ( ) const

inline

TwoParticleForce * MoleculeSystem::twoParticleForce ( ) const

void MoleculeSystem::updateForces ( )

void MoleculeSystem::updateStatistics ( )

Member Data Documentation

bool MoleculeSystem::m_areCellsSetUp

protected

vector<Atom*> MoleculeSystem::m_atoms

protected

double MoleculeSystem::m_averageDisplacement

protected

double MoleculeSystem::m_averageSquareDisplacement

protected

mat MoleculeSystem::m_boundaries

protected

rowvec MoleculeSystem::m_cellLengths

protected

mat MoleculeSystem::m_cellShiftVectors

protected

vector<MoleculeSystemCell*> MoleculeSystem::m_globalCells

protected

irowvec MoleculeSystem::m_globalCellsPerDimension

protected

Integrator* MoleculeSystem::m_integrator

protected

bool MoleculeSystem::m_isCalculatePotentialEnabled

protected

bool MoleculeSystem::m_isCalculatePressureEnabled

protected

bool MoleculeSystem::m_isCreateSymlinkEnabled

protected

bool MoleculeSystem::m_isFinalTimeStep

protected

bool MoleculeSystem::m_isOutputEnabled

protected

bool MoleculeSystem::m_isPeriodicDimension[3]

protected

bool MoleculeSystem::m_isSaveEnabled

protected

double MoleculeSystem::m_kineticEnergyTotal

protected

vector<Modifier*> MoleculeSystem::m_modifiers

protected

int MoleculeSystem::m_nAtomsTotal

protected

int MoleculeSystem::m_nDimensions

protected

int MoleculeSystem::m_nSimulationSteps

protected

vector<AtomType> MoleculeSystem::m_particleTypes

protected

unordered_map<int,AtomType> MoleculeSystem::m_particleTypesByID

protected

double MoleculeSystem::m_potentialEnergyTotal

protected

double MoleculeSystem::m_pressure

protected

Processor* MoleculeSystem::m_processor

protected

ProgressReporter* MoleculeSystem::m_progressReporter

protected

int MoleculeSystem::m_saveEveryNSteps

protected

vector<SingleParticleForce*> MoleculeSystem::m_singleParticleForces

protected

bool MoleculeSystem::m_skipInitialize

protected

uint MoleculeSystem::m_step

protected

double MoleculeSystem::m_temperature

protected

ThreeParticleForce* MoleculeSystem::m_threeParticleForce

protected

double MoleculeSystem::m_time

protected

TwoParticleForce* MoleculeSystem::m_twoParticleForce

protected

int MoleculeSystem::pow3nDimensions

protected

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

/home/svenni/Dropbox/projects/programming/emdee/emdee/src/libs/moleculesystem.h
/home/svenni/Dropbox/projects/programming/emdee/emdee/src/libs/moleculesystem (hyperon's conflicted copy 2013-11-21).cpp
/home/svenni/Dropbox/projects/programming/emdee/emdee/src/libs/moleculesystem.cpp

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation