Classes
struct	HBondDonor

Public Types
using	AtomIterator = std::vector<Atom*>::iterator
using	BondIterator = std::vector<Bond*>::iterator
using	BendIterator = std::vector<Bend*>::iterator
using	TorsionIterator = std::vector<Torsion*>::iterator
using	InversionIterator = std::vector<Inversion*>::iterator
using	RigidBodyIterator = std::vector<RigidBody*>::iterator
using	CutoffGroupIterator = std::vector<CutoffGroup*>::iterator
using	IntegrableObjectIterator = std::vector<StuntDouble*>::iterator
using	ConstraintPairIterator = std::vector<ConstraintPair*>::iterator
using	ConstraintElemIterator = std::vector<ConstraintElem*>::iterator
using	FluctuatingChargeIterator = std::vector<Atom*>::iterator
using	HBondDonorIterator = std::vector<HBondDonor*>::iterator
using	HBondAcceptorIterator = std::vector<Atom*>::iterator

Public Member Functions
	Molecule (int globalIndex, MoleculeStamp *molStamp)
int	getGlobalIndex ()
	Returns the global index of this molecule.
int	getStampId ()
	Returns the stamp id of this molecule.
int	getRegion ()
MoleculeStamp *	getMolStamp () const
std::string	getType ()
	Returns the name of the molecule.
void	setGlobalIndex (int index)
	Sets the global index of this molecule.
void	setConstrainTotalCharge (bool ctc)
bool	constrainTotalCharge ()
void	addAtom (Atom *atom)
	add an atom into this molecule
void	addBond (Bond *bond)
	add a bond into this molecule
void	addBend (Bend *bend)
	add a bend into this molecule
void	addTorsion (Torsion *torsion)
	add a torsion into this molecule
void	addInversion (Inversion *inversion)
	add an improper torsion into this molecule
void	addRigidBody (RigidBody *rb)
	add a rigidbody into this molecule
void	addCutoffGroup (CutoffGroup *cp)
	add a cutoff group into this molecule
void	addConstraintPair (ConstraintPair *consPair)
void	addConstraintElem (ConstraintElem *consElem)
void	complete ()
size_t	getNAtoms ()
	Returns the total number of atoms in this molecule.
size_t	getNBonds ()
	Returns the total number of bonds in this molecule.
size_t	getNBends ()
	Returns the total number of bends in this molecule.
size_t	getNTorsions ()
	Returns the total number of torsions in this molecule.
size_t	getNInversions ()
	Returns the total number of improper torsions in this molecule.
size_t	getNRigidBodies ()
	Returns the total number of rigid bodies in this molecule.
size_t	getNIntegrableObjects ()
	Returns the total number of integrable objects in this molecule.
size_t	getNCutoffGroups ()
	Returns the total number of cutoff groups in this molecule.
size_t	getNConstraintPairs ()
	Returns the total number of constraints in this molecule.
size_t	getNFluctuatingCharges ()
	Returns the total number of fluctuating charges in this molecule.
size_t	getNHBondDonors ()
	Returns the total number of Hydrogen Bond donors in this molecule.
size_t	getNHBondAcceptors ()
	Returns the total number of Hydrogen Bond acceptors in this molecule.
Atom *	getAtomAt (unsigned int i)
RigidBody *	getRigidBodyAt (unsigned int i)
Atom *	beginAtom (std::vector< Atom * >::iterator &i)
Atom *	nextAtom (std::vector< Atom * >::iterator &i)
Bond *	beginBond (std::vector< Bond * >::iterator &i)
Bond *	nextBond (std::vector< Bond * >::iterator &i)
Bend *	beginBend (std::vector< Bend * >::iterator &i)
Bend *	nextBend (std::vector< Bend * >::iterator &i)
Torsion *	beginTorsion (std::vector< Torsion * >::iterator &i)
Torsion *	nextTorsion (std::vector< Torsion * >::iterator &i)
Inversion *	beginInversion (std::vector< Inversion * >::iterator &i)
Inversion *	nextInversion (std::vector< Inversion * >::iterator &i)
RigidBody *	beginRigidBody (std::vector< RigidBody * >::iterator &i)
RigidBody *	nextRigidBody (std::vector< RigidBody * >::iterator &i)
StuntDouble *	beginIntegrableObject (std::vector< StuntDouble * >::iterator &i)
StuntDouble *	nextIntegrableObject (std::vector< StuntDouble * >::iterator &i)
CutoffGroup *	beginCutoffGroup (std::vector< CutoffGroup * >::iterator &i)
CutoffGroup *	nextCutoffGroup (std::vector< CutoffGroup * >::iterator &i)
ConstraintPair *	beginConstraintPair (std::vector< ConstraintPair * >::iterator &i)
ConstraintPair *	nextConstraintPair (std::vector< ConstraintPair * >::iterator &i)
ConstraintElem *	beginConstraintElem (std::vector< ConstraintElem * >::iterator &i)
ConstraintElem *	nextConstraintElem (std::vector< ConstraintElem * >::iterator &i)
Atom *	beginFluctuatingCharge (std::vector< Atom * >::iterator &i)
Atom *	nextFluctuatingCharge (std::vector< Atom * >::iterator &i)
HBondDonor *	beginHBondDonor (std::vector< HBondDonor * >::iterator &i)
HBondDonor *	nextHBondDonor (std::vector< HBondDonor * >::iterator &i)
Atom *	beginHBondAcceptor (std::vector< Atom * >::iterator &i)
Atom *	nextHBondAcceptor (std::vector< Atom * >::iterator &i)
RealType	getPotential ()
	Returns the total potential energy of short range interaction of this molecule.
RealType	getMass ()
	get total mass of this molecule
RealType	getFixedCharge ()
	get total fixed charge of this molecule
Vector3d	getPrevCom ()
	Returns the center of mass position of this molecule in the previous snapshot.
Vector3d	getCom ()
	Returns the current center of mass position of this molecule.
Vector3d	getCom (int snapshotNo)
	Returns the center of mass position of this molecule in specified snapshot.
void	setCom (const Vector3d &newCom)
	Sets the center of this molecule.
void	moveCom (const Vector3d &delta)
	Moves the center of this molecule.
Vector3d	getComVel ()
	Returns the velocity of center of mass of this molecule.
void	addProperty (std::shared_ptr< GenericData > genData)
	Adds property into property map.
void	removeProperty (const std::string &propName)
	Removes property from PropertyMap by name.
std::vector< std::string >	getPropertyNames ()
	Returns all names of properties.
std::vector< std::shared_ptr< GenericData > >	getProperties ()
	Returns all of the properties in PropertyMap.
std::shared_ptr< GenericData >	getPropertyByName (const std::string &propName)
	Returns property.

Friends
std::ostream &	operator<< (std::ostream &o, Molecule &mol)

Detailed Description

Definition at line 81 of file Molecule.hpp.

Member Typedef Documentation

◆ AtomIterator

using OpenMD::Molecule::AtomIterator = std::vector<Atom*>::iterator

Definition at line 88 of file Molecule.hpp.

◆ BendIterator

using OpenMD::Molecule::BendIterator = std::vector<Bend*>::iterator

Definition at line 90 of file Molecule.hpp.

◆ BondIterator

using OpenMD::Molecule::BondIterator = std::vector<Bond*>::iterator

Definition at line 89 of file Molecule.hpp.

◆ ConstraintElemIterator

using OpenMD::Molecule::ConstraintElemIterator = std::vector<ConstraintElem*>::iterator

Definition at line 97 of file Molecule.hpp.

◆ ConstraintPairIterator

using OpenMD::Molecule::ConstraintPairIterator = std::vector<ConstraintPair*>::iterator

Definition at line 96 of file Molecule.hpp.

◆ CutoffGroupIterator

using OpenMD::Molecule::CutoffGroupIterator = std::vector<CutoffGroup*>::iterator

Definition at line 94 of file Molecule.hpp.

◆ FluctuatingChargeIterator

using OpenMD::Molecule::FluctuatingChargeIterator = std::vector<Atom*>::iterator

Definition at line 98 of file Molecule.hpp.

◆ HBondAcceptorIterator

using OpenMD::Molecule::HBondAcceptorIterator = std::vector<Atom*>::iterator

Definition at line 100 of file Molecule.hpp.

◆ HBondDonorIterator

using OpenMD::Molecule::HBondDonorIterator = std::vector<HBondDonor*>::iterator

Definition at line 99 of file Molecule.hpp.

◆ IntegrableObjectIterator

using OpenMD::Molecule::IntegrableObjectIterator = std::vector<StuntDouble*>::iterator

Definition at line 95 of file Molecule.hpp.

◆ InversionIterator

using OpenMD::Molecule::InversionIterator = std::vector<Inversion*>::iterator

Definition at line 92 of file Molecule.hpp.

◆ RigidBodyIterator

using OpenMD::Molecule::RigidBodyIterator = std::vector<RigidBody*>::iterator

Definition at line 93 of file Molecule.hpp.

◆ TorsionIterator

using OpenMD::Molecule::TorsionIterator = std::vector<Torsion*>::iterator

Definition at line 91 of file Molecule.hpp.

Constructor & Destructor Documentation

◆ Molecule()

OpenMD::Molecule::Molecule	(	int	globalIndex,
		MoleculeStamp *	molStamp )

Definition at line 67 of file Molecule.cpp.

◆ ~Molecule()

OpenMD::Molecule::~Molecule ( )

virtual

Definition at line 71 of file Molecule.cpp.

Member Function Documentation

◆ addAtom()

void OpenMD::Molecule::addAtom ( Atom * atom )

add an atom into this molecule

Definition at line 88 of file Molecule.cpp.

References addAtom().

Referenced by addAtom().

◆ addBend()

void OpenMD::Molecule::addBend ( Bend * bend )

add a bend into this molecule

Definition at line 100 of file Molecule.cpp.

References addBend().

Referenced by addBend().

◆ addBond()

void OpenMD::Molecule::addBond ( Bond * bond )

add a bond into this molecule

Definition at line 94 of file Molecule.cpp.

References addBond().

Referenced by addBond().

◆ addConstraintElem()

void OpenMD::Molecule::addConstraintElem ( ConstraintElem * consElem )

Definition at line 141 of file Molecule.cpp.

◆ addConstraintPair()

void OpenMD::Molecule::addConstraintPair ( ConstraintPair * consPair )

Definition at line 134 of file Molecule.cpp.

◆ addCutoffGroup()

void OpenMD::Molecule::addCutoffGroup ( CutoffGroup * cp )

add a cutoff group into this molecule

Definition at line 127 of file Molecule.cpp.

References addCutoffGroup().

Referenced by addCutoffGroup().

◆ addInversion()

void OpenMD::Molecule::addInversion ( Inversion * inversion )

add an improper torsion into this molecule

Definition at line 113 of file Molecule.cpp.

References addInversion().

Referenced by addInversion().

◆ addProperty()

void OpenMD::Molecule::addProperty ( std::shared_ptr< GenericData > genData )

Adds property into property map.

Parameters

genData GenericData to be added into PropertyMap

Definition at line 421 of file Molecule.cpp.

References addProperty().

Referenced by addProperty().

◆ addRigidBody()

void OpenMD::Molecule::addRigidBody ( RigidBody * rb )

add a rigidbody into this molecule

Definition at line 120 of file Molecule.cpp.

References addRigidBody().

Referenced by addRigidBody().

◆ addTorsion()

void OpenMD::Molecule::addTorsion ( Torsion * torsion )

add a torsion into this molecule

Definition at line 106 of file Molecule.cpp.

References addTorsion().

Referenced by addTorsion().

◆ beginAtom()

Atom * OpenMD::Molecule::beginAtom ( std::vector< Atom * >::iterator & i )

inline

Definition at line 209 of file Molecule.hpp.

◆ beginBend()

Bend * OpenMD::Molecule::beginBend ( std::vector< Bend * >::iterator & i )

inline

Definition at line 229 of file Molecule.hpp.

◆ beginBond()

Bond * OpenMD::Molecule::beginBond ( std::vector< Bond * >::iterator & i )

inline

Definition at line 219 of file Molecule.hpp.

◆ beginConstraintElem()

ConstraintElem * OpenMD::Molecule::beginConstraintElem ( std::vector< ConstraintElem * >::iterator & i )

inline

Definition at line 301 of file Molecule.hpp.

◆ beginConstraintPair()

ConstraintPair * OpenMD::Molecule::beginConstraintPair ( std::vector< ConstraintPair * >::iterator & i )

inline

Definition at line 289 of file Molecule.hpp.

◆ beginCutoffGroup()

CutoffGroup * OpenMD::Molecule::beginCutoffGroup ( std::vector< CutoffGroup * >::iterator & i )

inline

Definition at line 279 of file Molecule.hpp.

◆ beginFluctuatingCharge()

Atom * OpenMD::Molecule::beginFluctuatingCharge ( std::vector< Atom * >::iterator & i )

inline

Definition at line 313 of file Molecule.hpp.

◆ beginHBondAcceptor()

Atom * OpenMD::Molecule::beginHBondAcceptor ( std::vector< Atom * >::iterator & i )

inline

Definition at line 333 of file Molecule.hpp.

◆ beginHBondDonor()

HBondDonor * OpenMD::Molecule::beginHBondDonor ( std::vector< HBondDonor * >::iterator & i )

inline

Definition at line 323 of file Molecule.hpp.

◆ beginIntegrableObject()

StuntDouble * OpenMD::Molecule::beginIntegrableObject ( std::vector< StuntDouble * >::iterator & i )

inline

Definition at line 269 of file Molecule.hpp.

◆ beginInversion()

Inversion * OpenMD::Molecule::beginInversion ( std::vector< Inversion * >::iterator & i )

inline

Definition at line 249 of file Molecule.hpp.

◆ beginRigidBody()

RigidBody * OpenMD::Molecule::beginRigidBody ( std::vector< RigidBody * >::iterator & i )

inline

Definition at line 259 of file Molecule.hpp.

◆ beginTorsion()

Torsion * OpenMD::Molecule::beginTorsion ( std::vector< Torsion * >::iterator & i )

inline

Definition at line 239 of file Molecule.hpp.

◆ complete()

void OpenMD::Molecule::complete ( )

Definition at line 148 of file Molecule.cpp.

◆ constrainTotalCharge()

bool OpenMD::Molecule::constrainTotalCharge ( )

inline

Definition at line 134 of file Molecule.hpp.

◆ getAtomAt()

Atom * OpenMD::Molecule::getAtomAt ( unsigned int i )

inline

Definition at line 199 of file Molecule.hpp.

◆ getCom() [1/2]

Vector3d OpenMD::Molecule::getCom ( )

Returns the current center of mass position of this molecule.

Returns: the center of mass position of this molecule.

Definition at line 315 of file Molecule.cpp.

References getCom(), OpenMD::StuntDouble::getMass(), and OpenMD::StuntDouble::getPos().

Referenced by OpenMD::Thermo::getAngularMomentum(), getCom(), getCom(), OpenMD::Thermo::getCom(), OpenMD::Thermo::getComAll(), OpenMD::Thermo::getComVel(), and setCom().

◆ getCom() [2/2]

Vector3d OpenMD::Molecule::getCom ( int snapshotNo )

Returns the center of mass position of this molecule in specified snapshot.

Returns: the center of mass position of this molecule

Parameters

snapshotNo

Definition at line 334 of file Molecule.cpp.

References getCom(), OpenMD::StuntDouble::getMass(), and OpenMD::StuntDouble::getPos().

◆ getComVel()

Vector3d OpenMD::Molecule::getComVel ( )

Returns the velocity of center of mass of this molecule.

Definition at line 368 of file Molecule.cpp.

References getComVel(), OpenMD::StuntDouble::getMass(), and OpenMD::StuntDouble::getVel().

Referenced by OpenMD::Thermo::getAngularMomentum(), OpenMD::Thermo::getComAll(), getComVel(), and OpenMD::Thermo::getComVel().

◆ getFixedCharge()

RealType OpenMD::Molecule::getFixedCharge ( )

get total fixed charge of this molecule

Definition at line 281 of file Molecule.cpp.

References OpenMD::Atom::getAtomType(), and getFixedCharge().

Referenced by getFixedCharge().

◆ getGlobalIndex()

int OpenMD::Molecule::getGlobalIndex ( )

inline

Returns the global index of this molecule.

Returns: the global index of this molecule

Definition at line 109 of file Molecule.hpp.

Referenced by OpenMD::SimInfo::addMolecule(), and OpenMD::SimInfo::removeMolecule().

◆ getMass()

RealType OpenMD::Molecule::getMass ( )

get total mass of this molecule

Definition at line 268 of file Molecule.cpp.

References getMass(), and OpenMD::StuntDouble::getMass().

Referenced by OpenMD::Thermo::getAngularMomentum(), OpenMD::Thermo::getCom(), OpenMD::Thermo::getComAll(), OpenMD::Thermo::getComVel(), and getMass().

◆ getMolStamp()

MoleculeStamp * OpenMD::Molecule::getMolStamp ( ) const

inline

Definition at line 121 of file Molecule.hpp.

◆ getNAtoms()

size_t OpenMD::Molecule::getNAtoms ( )

inline

Returns the total number of atoms in this molecule.

Definition at line 165 of file Molecule.hpp.

Referenced by OpenMD::SimInfo::addMolecule(), and OpenMD::SimInfo::removeMolecule().

◆ getNBends()

size_t OpenMD::Molecule::getNBends ( )

inline

Returns the total number of bends in this molecule.

Definition at line 171 of file Molecule.hpp.

Referenced by OpenMD::SimInfo::addMolecule(), and OpenMD::SimInfo::removeMolecule().

◆ getNBonds()

size_t OpenMD::Molecule::getNBonds ( )

inline

Returns the total number of bonds in this molecule.

Definition at line 168 of file Molecule.hpp.

Referenced by OpenMD::SimInfo::addMolecule(), and OpenMD::SimInfo::removeMolecule().

◆ getNConstraintPairs()

size_t OpenMD::Molecule::getNConstraintPairs ( )

inline

Returns the total number of constraints in this molecule.

Definition at line 189 of file Molecule.hpp.

Referenced by OpenMD::SimInfo::addMolecule(), and OpenMD::SimInfo::removeMolecule().

◆ getNCutoffGroups()

size_t OpenMD::Molecule::getNCutoffGroups ( )

inline

Returns the total number of cutoff groups in this molecule.

Definition at line 186 of file Molecule.hpp.

Referenced by OpenMD::SimInfo::addMolecule(), and OpenMD::SimInfo::removeMolecule().

◆ getNFluctuatingCharges()

size_t OpenMD::Molecule::getNFluctuatingCharges ( )

inline

Returns the total number of fluctuating charges in this molecule.

Definition at line 192 of file Molecule.hpp.

◆ getNHBondAcceptors()

size_t OpenMD::Molecule::getNHBondAcceptors ( )

inline

Returns the total number of Hydrogen Bond acceptors in this molecule.

Definition at line 197 of file Molecule.hpp.

◆ getNHBondDonors()

size_t OpenMD::Molecule::getNHBondDonors ( )

inline

Returns the total number of Hydrogen Bond donors in this molecule.

Definition at line 194 of file Molecule.hpp.

◆ getNIntegrableObjects()

size_t OpenMD::Molecule::getNIntegrableObjects ( )

inline

Returns the total number of integrable objects in this molecule.

Definition at line 183 of file Molecule.hpp.

Referenced by OpenMD::SimInfo::addMolecule(), and OpenMD::SimInfo::removeMolecule().

◆ getNInversions()

size_t OpenMD::Molecule::getNInversions ( )

inline

Returns the total number of improper torsions in this molecule.

Definition at line 177 of file Molecule.hpp.

Referenced by OpenMD::SimInfo::addMolecule(), and OpenMD::SimInfo::removeMolecule().

◆ getNRigidBodies()

size_t OpenMD::Molecule::getNRigidBodies ( )

inline

Returns the total number of rigid bodies in this molecule.

Definition at line 180 of file Molecule.hpp.

Referenced by OpenMD::SimInfo::addMolecule(), and OpenMD::SimInfo::removeMolecule().

◆ getNTorsions()

size_t OpenMD::Molecule::getNTorsions ( )

inline

Returns the total number of torsions in this molecule.

Definition at line 174 of file Molecule.hpp.

Referenced by OpenMD::SimInfo::addMolecule(), and OpenMD::SimInfo::removeMolecule().

◆ getPotential()

RealType OpenMD::Molecule::getPotential ( )

Returns the total potential energy of short range interaction of this molecule.

Definition at line 387 of file Molecule.cpp.

References getPotential().

Referenced by getPotential().

◆ getPrevCom()

Vector3d OpenMD::Molecule::getPrevCom ( )

Returns the center of mass position of this molecule in the previous snapshot.

Returns: the center of mass position of this molecule.

Definition at line 296 of file Molecule.cpp.

References OpenMD::StuntDouble::getMass(), getPrevCom(), and OpenMD::StuntDouble::getPrevPos().

Referenced by getPrevCom().

◆ getProperties()

std::vector< std::shared_ptr< GenericData > > OpenMD::Molecule::getProperties ( )

Returns all of the properties in PropertyMap.

Returns: all of the properties in PropertyMap

Definition at line 433 of file Molecule.cpp.

References getProperties().

Referenced by getProperties().

◆ getPropertyByName()

std::shared_ptr< GenericData > OpenMD::Molecule::getPropertyByName ( const std::string & propName )

Returns property.

Parameters

propName name of property

Returns: a pointer point to property with propName. If no property named propName exists, return NULL

Definition at line 437 of file Molecule.cpp.

References getPropertyByName().

Referenced by getPropertyByName().

◆ getPropertyNames()

std::vector< std::string > OpenMD::Molecule::getPropertyNames ( )

Returns all names of properties.

Returns: all names of properties

Definition at line 429 of file Molecule.cpp.

References getPropertyNames().

Referenced by getPropertyNames().

◆ getRegion()

int OpenMD::Molecule::getRegion ( )

inline

Definition at line 119 of file Molecule.hpp.

◆ getRigidBodyAt()

RigidBody * OpenMD::Molecule::getRigidBodyAt ( unsigned int i )

inline

Definition at line 204 of file Molecule.hpp.

◆ getStampId()

int OpenMD::Molecule::getStampId ( )

inline

Returns the stamp id of this molecule.

Note: Ideally, every molecule should keep a pointer of its molecule stamp instead of its stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.

Definition at line 118 of file Molecule.hpp.

◆ getType()

std::string OpenMD::Molecule::getType ( )

inline

Returns the name of the molecule.

Definition at line 124 of file Molecule.hpp.

◆ moveCom()

void OpenMD::Molecule::moveCom ( const Vector3d & delta )

Moves the center of this molecule.

Definition at line 358 of file Molecule.cpp.

References OpenMD::StuntDouble::getPos(), moveCom(), and OpenMD::StuntDouble::setPos().

Referenced by moveCom(), and setCom().

◆ nextAtom()

Atom * OpenMD::Molecule::nextAtom ( std::vector< Atom * >::iterator & i )

inline

Definition at line 214 of file Molecule.hpp.

◆ nextBend()

Bend * OpenMD::Molecule::nextBend ( std::vector< Bend * >::iterator & i )

inline

Definition at line 234 of file Molecule.hpp.

◆ nextBond()

Bond * OpenMD::Molecule::nextBond ( std::vector< Bond * >::iterator & i )

inline

Definition at line 224 of file Molecule.hpp.

◆ nextConstraintElem()

ConstraintElem * OpenMD::Molecule::nextConstraintElem ( std::vector< ConstraintElem * >::iterator & i )

inline

Definition at line 307 of file Molecule.hpp.

◆ nextConstraintPair()

ConstraintPair * OpenMD::Molecule::nextConstraintPair ( std::vector< ConstraintPair * >::iterator & i )

inline

Definition at line 295 of file Molecule.hpp.

◆ nextCutoffGroup()

CutoffGroup * OpenMD::Molecule::nextCutoffGroup ( std::vector< CutoffGroup * >::iterator & i )

inline

Definition at line 284 of file Molecule.hpp.

◆ nextFluctuatingCharge()

Atom * OpenMD::Molecule::nextFluctuatingCharge ( std::vector< Atom * >::iterator & i )

inline

Definition at line 318 of file Molecule.hpp.

◆ nextHBondAcceptor()

Atom * OpenMD::Molecule::nextHBondAcceptor ( std::vector< Atom * >::iterator & i )

inline

Definition at line 338 of file Molecule.hpp.

◆ nextHBondDonor()

HBondDonor * OpenMD::Molecule::nextHBondDonor ( std::vector< HBondDonor * >::iterator & i )

inline

Definition at line 328 of file Molecule.hpp.

◆ nextIntegrableObject()

StuntDouble * OpenMD::Molecule::nextIntegrableObject ( std::vector< StuntDouble * >::iterator & i )

inline

Definition at line 274 of file Molecule.hpp.

◆ nextInversion()

Inversion * OpenMD::Molecule::nextInversion ( std::vector< Inversion * >::iterator & i )

inline

Definition at line 254 of file Molecule.hpp.

◆ nextRigidBody()

RigidBody * OpenMD::Molecule::nextRigidBody ( std::vector< RigidBody * >::iterator & i )

inline

Definition at line 264 of file Molecule.hpp.

◆ nextTorsion()

Torsion * OpenMD::Molecule::nextTorsion ( std::vector< Torsion * >::iterator & i )

inline

Definition at line 244 of file Molecule.hpp.

◆ removeProperty()

void OpenMD::Molecule::removeProperty ( const std::string & propName )

Removes property from PropertyMap by name.

Parameters

propName the name of property to be removed

Definition at line 425 of file Molecule.cpp.

References removeProperty().

Referenced by removeProperty().

◆ setCom()

void OpenMD::Molecule::setCom ( const Vector3d & newCom )

Sets the center of this molecule.

Definition at line 353 of file Molecule.cpp.

References getCom(), moveCom(), and setCom().

Referenced by setCom().

◆ setConstrainTotalCharge()

void OpenMD::Molecule::setConstrainTotalCharge ( bool ctc )

inline

Definition at line 132 of file Molecule.hpp.

◆ setGlobalIndex()

void OpenMD::Molecule::setGlobalIndex ( int index )

inline

Sets the global index of this molecule.

Parameters

index new global index to be set

Definition at line 130 of file Molecule.hpp.

◆ operator<<

std::ostream & operator<<	(	std::ostream &	o,
		Molecule &	mol )

friend

Definition at line 442 of file Molecule.cpp.

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

primitives/Molecule.hpp
primitives/Molecule.cpp

Classes

Public Types

Public Member Functions

Friends

Detailed Description

Member Typedef Documentation

◆ AtomIterator

◆ BendIterator

◆ BondIterator

◆ ConstraintElemIterator

◆ ConstraintPairIterator

◆ CutoffGroupIterator

◆ FluctuatingChargeIterator

◆ HBondAcceptorIterator

◆ HBondDonorIterator

◆ IntegrableObjectIterator

◆ InversionIterator

◆ RigidBodyIterator

◆ TorsionIterator

Constructor & Destructor Documentation

◆ Molecule()

◆ ~Molecule()

Member Function Documentation

◆ addAtom()

◆ addBend()

◆ addBond()

◆ addConstraintElem()

◆ addConstraintPair()

◆ addCutoffGroup()

◆ addInversion()

◆ addProperty()

◆ addRigidBody()

◆ addTorsion()

◆ beginAtom()

◆ beginBend()

◆ beginBond()

◆ beginConstraintElem()

◆ beginConstraintPair()

◆ beginCutoffGroup()

◆ beginFluctuatingCharge()

◆ beginHBondAcceptor()

◆ beginHBondDonor()

◆ beginIntegrableObject()

◆ beginInversion()

◆ beginRigidBody()

◆ beginTorsion()

◆ complete()

◆ constrainTotalCharge()

◆ getAtomAt()

◆ getCom() [1/2]

◆ getCom() [2/2]

◆ getComVel()

◆ getFixedCharge()

◆ getGlobalIndex()

◆ getMass()

◆ getMolStamp()

◆ getNAtoms()

◆ getNBends()

◆ getNBonds()

◆ getNConstraintPairs()

◆ getNCutoffGroups()

◆ getNFluctuatingCharges()

◆ getNHBondAcceptors()

◆ getNHBondDonors()

◆ getNIntegrableObjects()

◆ getNInversions()

◆ getNRigidBodies()

◆ getNTorsions()

◆ getPotential()

◆ getPrevCom()

◆ getProperties()

◆ getPropertyByName()

◆ getPropertyNames()

◆ getRegion()

◆ getRigidBodyAt()

◆ getStampId()

◆ getType()

◆ moveCom()

◆ nextAtom()

◆ nextBend()