Detailed Description

A physical molecule (a set of covalently bonded Atoms).

Definition at line 42 of file mcMd/chemistry/Molecule.h.

#include <Molecule.h>

Public Types
typedef ArrayIterator< Atom >	AtomIterator
	Iterator for Atoms within a Molecule. More...

typedef ConstArrayIterator< Atom >	ConstAtomIterator
	Iterator for const Atoms within a Molecule. More...

typedef ArrayIterator< Bond >	BondIterator
	Iterator for Bonds within a Molecule. More...

typedef ConstArrayIterator< Bond >	ConstBondIterator
	Iterator for const Bonds within a Molecule. More...

typedef ArrayIterator< Angle >	AngleIterator
	Iterator for Angles within a Molecule. More...

typedef ConstArrayIterator< Angle >	ConstAngleIterator
	Iterator for const Angles within a Molecule. More...

typedef ArrayIterator< Dihedral >	DihedralIterator
	Iterator for Dihedrals within a Molecule. More...

typedef ConstArrayIterator< Dihedral >	ConstDihedralIterator
	Iterator for const Dihedrals within a Molecule. More...

Public Member Functions
	Molecule ()
	Constructor. More...

Mutators
void	setSpecies (Species &species)
	Set the parent Species. More...

void	setSystem (System &system)
	Set the parent System. More...

void	unsetSystem ()
	Set the parent System pointer to null (no System). More...

void	setId (int id)
	Set the integer index for this molecule. More...

void	setFirstAtom (Atom &atom)
	Set the first Atom. More...

void	setNAtom (int nAtom)
	Set the number of Atoms per molecule. More...

void	setFirstBond (Bond &bond)
	Set the first Bond. More...

void	setNBond (int nBond)
	Set the number of Bonds per molecule. More...

void	setFirstAngle (Angle &angle)
	Set the first Angle. More...

void	setNAngle (int nAngle)
	Set the number of Angles per molecule. More...

void	setFirstDihedral (Dihedral &dihedral)
	Set the first Dihedral. More...

void	setNDihedral (int nDihedral)
	Set the number of Dihedrals per molecule. More...

Accessors
Species &	species () const
	Get the molecular Species by reference. More...

System &	system () const
	Get the parent System. More...

int	id () const
	Get the index for this Molecule (unique in species). More...

int	nAtom () const
	Get the number of Atoms in this Molecule. More...

int	nBond () const
	Get the number of Bonds in this Molecule. More...

int	nAngle () const
	Get the number of Angles in this Molecule. More...

int	nDihedral () const
	Get the number of Dihedrals in this Molecule. More...

const Atom &	atom (int localId) const
	Get a specific Atom in this Molecule. More...

Atom &	atom (int localId)
	Get a specific Atom in this Molecule. More...

Bond &	bond (int localId)
	Get a specific Bond in this Molecule by non-const reference. More...

const Bond &	bond (int localId) const
	Get a specific Bond in this Molecule by const reference. More...

Angle &	angle (int localId)
	Get a specific Angle in this Molecule by non-const reference. More...

const Angle &	angle (int localId) const
	Get a specific Angle in this Molecule by const reference. More...

Dihedral &	dihedral (int localId)
	Get a specific Dihedral in this Molecule by reference. More...

const Dihedral &	dihedral (int localId) const
	Get a specific Dihedral in this Molecule by const reference. More...

Iterator Interface
void	begin (AtomIterator &iterator)
	Set an Molecule::AtomIterator to first Atom in this Molecule. More...

void	begin (ConstAtomIterator &iterator) const
	Set an Molecule::ConstAtomIterator to first Atom in this Molecule. More...

void	begin (BondIterator &iterator)
	Set a Molecule::BondIterator to first Bond in this Molecule. More...

void	begin (ConstBondIterator &iterator) const
	Set a Molecule::ConstBondIterator to first Bond in this Molecule. More...

void	begin (AngleIterator &iterator)
	Set a Molecule::AngleIterator to first Angle in this Molecule. More...

void	begin (ConstAngleIterator &iterator) const
	Set a Molecule::ConstAngleIterator to first Angle in this Molecule. More...

void	begin (DihedralIterator &iterator)
	Set a Molecule::DihedralIterator to first Dihedral in this Molecule. More...

void	begin (ConstDihedralIterator &iterator) const
	Set a Molecule::ConstDihedralIterator to first Dihedral in this Molecule. More...

Static Public Attributes
static const int	NullIndex = -1
	Null value for molecule id. More...

Member Typedef Documentation

typedef ArrayIterator<Atom> McMd::Molecule::AtomIterator

Iterator for Atoms within a Molecule.

Definition at line 50 of file mcMd/chemistry/Molecule.h.

typedef ConstArrayIterator<Atom> McMd::Molecule::ConstAtomIterator

Iterator for const Atoms within a Molecule.

Definition at line 53 of file mcMd/chemistry/Molecule.h.

typedef ArrayIterator<Bond> McMd::Molecule::BondIterator

Iterator for Bonds within a Molecule.

Definition at line 57 of file mcMd/chemistry/Molecule.h.

typedef ConstArrayIterator<Bond> McMd::Molecule::ConstBondIterator

Iterator for const Bonds within a Molecule.

Definition at line 60 of file mcMd/chemistry/Molecule.h.

typedef ArrayIterator<Angle> McMd::Molecule::AngleIterator

Iterator for Angles within a Molecule.

Definition at line 65 of file mcMd/chemistry/Molecule.h.

typedef ConstArrayIterator<Angle> McMd::Molecule::ConstAngleIterator

Iterator for const Angles within a Molecule.

Definition at line 68 of file mcMd/chemistry/Molecule.h.

typedef ArrayIterator<Dihedral> McMd::Molecule::DihedralIterator

Iterator for Dihedrals within a Molecule.

Definition at line 73 of file mcMd/chemistry/Molecule.h.

typedef ConstArrayIterator<Dihedral> McMd::Molecule::ConstDihedralIterator

Iterator for const Dihedrals within a Molecule.

Definition at line 76 of file mcMd/chemistry/Molecule.h.

Constructor & Destructor Documentation

McMd::Molecule::Molecule ( )

Constructor.

Definition at line 21 of file mcMd/chemistry/Molecule.cpp.

Member Function Documentation

void McMd::Molecule::setSpecies ( Species & species )

inline

Set the parent Species.

Parameters

species parent Species object.

Definition at line 660 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Simulation::save().

void McMd::Molecule::setSystem ( System & system )

inline

Set the parent System.

Parameters

system parent System object.

Definition at line 666 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::System::addMolecule().

void McMd::Molecule::unsetSystem ( )

inline

Set the parent System pointer to null (no System).

Definition at line 672 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::System::removeMolecule().

void McMd::Molecule::setId ( int id )

inline

Set the integer index for this molecule.

Parameters

id	integer array index.

Definition at line 732 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Simulation::save().

void McMd::Molecule::setFirstAtom ( Atom & atom )

inline

Set the first Atom.

Parameters

atom	first Atom in molecule.

Definition at line 678 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Simulation::save().

void McMd::Molecule::setNAtom ( int nAtom )

inline

Set the number of Atoms per molecule.

Parameters

nAtom number of Atoms in the molecule.

Definition at line 684 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Simulation::save().

void McMd::Molecule::setFirstBond ( Bond & bond )

inline

Set the first Bond.

Parameters

bond	first Bond in molecule.

Definition at line 691 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Simulation::save().

void McMd::Molecule::setNBond ( int nBond )

inline

Set the number of Bonds per molecule.

Parameters

nBond number of Bonds in the molecule.

Definition at line 697 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Simulation::save().

void McMd::Molecule::setFirstAngle ( Angle & angle )

inline

Set the first Angle.

Parameters

angle first Angle in molecule.

Definition at line 705 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Simulation::save().

void McMd::Molecule::setNAngle ( int nAngle )

inline

Set the number of Angles per molecule.

Parameters

nAngle number of Angles in molecule.

Definition at line 711 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Simulation::save().

void McMd::Molecule::setFirstDihedral ( Dihedral & dihedral )

inline

Set the first Dihedral.

Parameters

dihedral first Dihedral in molecule.

Definition at line 719 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Simulation::save().

void McMd::Molecule::setNDihedral ( int nDihedral )

inline

Set the number of Dihedrals per molecule.

Parameters

nDihedral number of Dihedrals in molecule.

Definition at line 725 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Simulation::save().

Species & McMd::Molecule::species ( ) const

inline

Get the molecular Species by reference.

Definition at line 418 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::CfbLinear::addAtom(), McMd::System::addMolecule(), McMd::Activate::deactivate(), McMd::getAtomAngles(), McMd::getAtomBonds(), McMd::getAtomDihedrals(), McMd::Simulation::isValid(), McMd::System::moleculeId(), McMd::Activate::reactivate(), McMd::System::removeMolecule(), McMd::Simulation::returnMolecule(), McMd::MdPairEnergyCoefficients::sample(), McMd::RingOctaRebridgeMove::scanBridge(), and McMd::McMdConfigIo::write().

System & McMd::Molecule::system ( ) const

inline

Get the parent System.

Definition at line 427 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::System::isValid(), and McMd::System::removeMolecule().

int McMd::Molecule::id ( ) const

inline

Get the index for this Molecule (unique in species).

Definition at line 560 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::ClusterIdentifier::initialize(), McMd::Simulation::isValid(), McMd::SpeciesMutator::moleculeStateId(), McMd::CfbReptationMove::move(), McMd::CfbReptateMove::move(), McMd::ClusterHistogram::sample(), McMd::MdPairEnergyCoefficients::sample(), McMd::RingOctaRebridgeMove::scanBridge(), and McMd::SpeciesMutator::setMoleculeStateId().

int McMd::Molecule::nAtom ( ) const

inline

Get the number of Atoms in this Molecule.

Definition at line 436 of file mcMd/chemistry/Molecule.h.

int McMd::Molecule::nBond ( ) const

inline

Get the number of Bonds in this Molecule.

Definition at line 443 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Activate::activate(), McMd::getAtomBonds(), and McMd::Simulation::isValid().

int McMd::Molecule::nAngle ( ) const

inline

Get the number of Angles in this Molecule.

Definition at line 451 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Activate::activate(), McMd::getAtomAngles(), and McMd::Simulation::isValid().

int McMd::Molecule::nDihedral ( ) const

inline

Get the number of Dihedrals in this Molecule.

Definition at line 459 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Activate::activate(), McMd::getAtomDihedrals(), and McMd::Simulation::isValid().

const Atom & McMd::Molecule::atom ( int localId ) const

inline

Get a specific Atom in this Molecule.

Returns the atom with local integer index 0 <= localId < nAtom.

Parameters

localId local index of desired atom within this Molecule.

Definition at line 477 of file mcMd/chemistry/Molecule.h.

Atom & McMd::Molecule::atom ( int localId )

inline

Get a specific Atom in this Molecule.

Returns the atom with local integer index 0 <= localId < nAtom.

Parameters

localId local index of desired atom within this Molecule.

Definition at line 466 of file mcMd/chemistry/Molecule.h.

Bond & McMd::Molecule::bond ( int localId )

inline

Get a specific Bond in this Molecule by non-const reference.

Returns the bond with local integer index 0 <= localId < nBond.

Parameters

localId local index of desired bond within this Molecule.

Definition at line 489 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Activate::activate(), McMd::CfbLinear::addAtom(), McMd::Activate::deactivate(), McMd::CfbLinear::deleteAtom(), McMd::getAtomBonds(), McMd::Simulation::isValid(), McMd::McNVTChemicalPotential::load(), McMd::RingTetraRebridgeMove::move(), McMd::CfbDoubleRebridgeMove::move(), McMd::CfbEndMove::move(), McMd::CfbRebridgeMove::move(), McMd::CfbRingRebridgeMove::move(), McMd::Activate::reactivate(), and McMd::McNVTChemicalPotential::sample().

const Bond & McMd::Molecule::bond ( int localId ) const

inline

Get a specific Bond in this Molecule by const reference.

Returns the bond with local integer index 0 <= localId < nBond.

Parameters

localId local index of desired bond within this Molecule.

Definition at line 500 of file mcMd/chemistry/Molecule.h.

Angle & McMd::Molecule::angle ( int localId )

inline

Get a specific Angle in this Molecule by non-const reference.

Returns the angle with local integer index 0 <= localId < nAngle.

Parameters

localId local index of desired angle within this Molecule.

Definition at line 513 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Activate::activate(), McMd::Activate::deactivate(), McMd::getAtomAngles(), McMd::Simulation::isValid(), McMd::McNVTChemicalPotential::load(), McMd::Activate::reactivate(), and McMd::McNVTChemicalPotential::sample().

const Angle & McMd::Molecule::angle ( int localId ) const

inline

Get a specific Angle in this Molecule by const reference.

Returns the angle with local integer index 0 <= localId < nAngle.

Parameters

localId local index of desired angle within this Molecule.

Definition at line 524 of file mcMd/chemistry/Molecule.h.

Dihedral & McMd::Molecule::dihedral ( int localId )

inline

Get a specific Dihedral in this Molecule by reference.

Returns the dihedral with local integer index 0 <= localId < nDihedral.

Parameters

localId local index of desired dihedral within this Molecule.

Definition at line 537 of file mcMd/chemistry/Molecule.h.

Referenced by McMd::Activate::activate(), McMd::Activate::deactivate(), McMd::getAtomDihedrals(), McMd::Simulation::isValid(), McMd::McNVTChemicalPotential::load(), and McMd::Activate::reactivate().

const Dihedral & McMd::Molecule::dihedral ( int localId ) const

inline

Get a specific Dihedral in this Molecule by const reference.

Returns the dihedral with local integer index 0 <= localId < nDihedral.

Parameters

localId local index of desired dihedral within this Molecule.

Definition at line 548 of file mcMd/chemistry/Molecule.h.

void McMd::Molecule::begin ( AtomIterator & iterator )

inline

Set an Molecule::AtomIterator to first Atom in this Molecule.

Parameters

iterator on output, points to first Atom.

Definition at line 566 of file mcMd/chemistry/Molecule.h.

References Util::ArrayIterator< Data >::setCurrent(), and Util::ArrayIterator< Data >::setEnd().

Referenced by McMd::Cluster::clusterCOM(), McMd::ClusterIdentifier::initialize(), McMd::System::loadConfig(), McMd::Cluster::momentTensor(), McMd::McMdConfigIo::read(), McMd::SmpConfigIo::read(), McMd::DdMdConfigIo::read(), McMd::LammpsConfigIo::read(), McMd::LammpsDumpReader::readFrame(), McMd::DdMdTrajectoryReader::readFrame(), and McMd::DCDTrajectoryReader::readFrame().

void McMd::Molecule::begin ( ConstAtomIterator & iterator ) const

inline

Set an Molecule::ConstAtomIterator to first Atom in this Molecule.

Parameters

iterator on output, points to first Atom.

Definition at line 577 of file mcMd/chemistry/Molecule.h.

References Util::ConstArrayIterator< Data >::setCurrent(), and Util::ConstArrayIterator< Data >::setEnd().

void McMd::Molecule::begin ( BondIterator & iterator )

inline

Set a Molecule::BondIterator to first Bond in this Molecule.

Parameters

iterator on output, points to first Bond.

Definition at line 589 of file mcMd/chemistry/Molecule.h.

References Util::ArrayIterator< Data >::setCurrent(), and Util::ArrayIterator< Data >::setEnd().

void McMd::Molecule::begin ( ConstBondIterator & iterator ) const

inline

Set a Molecule::ConstBondIterator to first Bond in this Molecule.

Parameters

iterator on output, points to first Bond.

Definition at line 600 of file mcMd/chemistry/Molecule.h.

References Util::ConstArrayIterator< Data >::setCurrent(), and Util::ConstArrayIterator< Data >::setEnd().

void McMd::Molecule::begin ( AngleIterator & iterator )

inline

Set a Molecule::AngleIterator to first Angle in this Molecule.

Parameters

iterator on output, points to first Angle.

Definition at line 613 of file mcMd/chemistry/Molecule.h.

References Util::ArrayIterator< Data >::setCurrent(), and Util::ArrayIterator< Data >::setEnd().

void McMd::Molecule::begin ( ConstAngleIterator & iterator ) const

inline

Set a Molecule::ConstAngleIterator to first Angle in this Molecule.

Parameters

iterator on output, points to first Angle.

Definition at line 624 of file mcMd/chemistry/Molecule.h.

References Util::ConstArrayIterator< Data >::setCurrent(), and Util::ConstArrayIterator< Data >::setEnd().

void McMd::Molecule::begin ( DihedralIterator & iterator )

inline

Set a Molecule::DihedralIterator to first Dihedral in this Molecule.

Parameters

iterator on output, points to first Dihedral.

Definition at line 637 of file mcMd/chemistry/Molecule.h.

References Util::ArrayIterator< Data >::setCurrent(), and Util::ArrayIterator< Data >::setEnd().

void McMd::Molecule::begin ( ConstDihedralIterator & iterator ) const

inline

Set a Molecule::ConstDihedralIterator to first Dihedral in this Molecule.

Parameters

iterator on output, points to first Dihedral.

Definition at line 648 of file mcMd/chemistry/Molecule.h.

References Util::ConstArrayIterator< Data >::setCurrent(), and Util::ConstArrayIterator< Data >::setEnd().

Member Data Documentation

const int McMd::Molecule::NullIndex = -1

static

Null value for molecule id.

Definition at line 80 of file mcMd/chemistry/Molecule.h.

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

Detailed Description

Public Types

Public Member Functions

Static Public Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation