OpenMD  2.5
Molecular Dynamics in the Open
OpenMD::Molecule Class Reference

#include "primitives/Molecule.hpp"

Classes

struct  HBondDonor
 

Public Types

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

Public Member Functions

 Molecule (int stampId, int globalIndex, const std::string &molName, int region)
 
virtual ~Molecule ()
 
int getGlobalIndex ()
 
int getStampId ()
 
int getRegion ()
 
std::string getType ()
 
void setGlobalIndex (int index)
 
void setConstrainTotalCharge (bool ctc)
 
bool constrainTotalCharge ()
 
void addAtom (Atom *atom)
 
void addBond (Bond *bond)
 
void addBend (Bend *bend)
 
void addTorsion (Torsion *torsion)
 
void addInversion (Inversion *inversion)
 
void addRigidBody (RigidBody *rb)
 
void addCutoffGroup (CutoffGroup *cp)
 
void addConstraintPair (ConstraintPair *consPair)
 
void addConstraintElem (ConstraintElem *consElem)
 
void complete ()
 
unsigned int getNAtoms ()
 
unsigned int getNBonds ()
 
unsigned int getNBends ()
 
unsigned int getNTorsions ()
 
unsigned int getNInversions ()
 
unsigned int getNRigidBodies ()
 
unsigned int getNIntegrableObjects ()
 
unsigned int getNCutoffGroups ()
 
unsigned int getNConstraintPairs ()
 
unsigned int getNFluctuatingCharges ()
 
unsigned int getNHBondDonors ()
 
unsigned int getNHBondAcceptors ()
 
AtomgetAtomAt (unsigned int i)
 
RigidBodygetRigidBodyAt (unsigned int i)
 
AtombeginAtom (std::vector< Atom *>::iterator &i)
 
AtomnextAtom (std::vector< Atom *>::iterator &i)
 
BondbeginBond (std::vector< Bond *>::iterator &i)
 
BondnextBond (std::vector< Bond *>::iterator &i)
 
BendbeginBend (std::vector< Bend *>::iterator &i)
 
BendnextBend (std::vector< Bend *>::iterator &i)
 
TorsionbeginTorsion (std::vector< Torsion *>::iterator &i)
 
TorsionnextTorsion (std::vector< Torsion *>::iterator &i)
 
InversionbeginInversion (std::vector< Inversion *>::iterator &i)
 
InversionnextInversion (std::vector< Inversion *>::iterator &i)
 
RigidBodybeginRigidBody (std::vector< RigidBody *>::iterator &i)
 
RigidBodynextRigidBody (std::vector< RigidBody *>::iterator &i)
 
StuntDoublebeginIntegrableObject (std::vector< StuntDouble *>::iterator &i)
 
StuntDoublenextIntegrableObject (std::vector< StuntDouble *>::iterator &i)
 
CutoffGroupbeginCutoffGroup (std::vector< CutoffGroup *>::iterator &i)
 
CutoffGroupnextCutoffGroup (std::vector< CutoffGroup *>::iterator &i)
 
ConstraintPairbeginConstraintPair (std::vector< ConstraintPair *>::iterator &i)
 
ConstraintPairnextConstraintPair (std::vector< ConstraintPair *>::iterator &i)
 
ConstraintElembeginConstraintElem (std::vector< ConstraintElem *>::iterator &i)
 
ConstraintElemnextConstraintElem (std::vector< ConstraintElem *>::iterator &i)
 
AtombeginFluctuatingCharge (std::vector< Atom *>::iterator &i)
 
AtomnextFluctuatingCharge (std::vector< Atom *>::iterator &i)
 
HBondDonorbeginHBondDonor (std::vector< HBondDonor *>::iterator &i)
 
HBondDonornextHBondDonor (std::vector< HBondDonor *>::iterator &i)
 
AtombeginHBondAcceptor (std::vector< Atom *>::iterator &i)
 
AtomnextHBondAcceptor (std::vector< Atom *>::iterator &i)
 
RealType getPotential ()
 
RealType getMass ()
 
Vector3d getCom ()
 
Vector3d getCom (int snapshotNo)
 
void moveCom (const Vector3d &delta)
 
Vector3d getComVel ()
 
std::string getMoleculeName ()
 
void addProperty (GenericData *genData)
 
void removeProperty (const std::string &propName)
 
void clearProperties ()
 
std::vector< std::string > getPropertyNames ()
 
std::vector< GenericData * > getProperties ()
 
GenericDatagetPropertyByName (const std::string &propName)
 

Private Attributes

int globalIndex_
 
std::vector< Atom * > atoms_
 
std::vector< Bond * > bonds_
 
std::vector< Bend * > bends_
 
std::vector< Torsion * > torsions_
 
std::vector< Inversion * > inversions_
 
std::vector< RigidBody * > rigidBodies_
 
std::vector< StuntDouble * > integrableObjects_
 
std::vector< CutoffGroup * > cutoffGroups_
 
std::vector< ConstraintPair * > constraintPairs_
 
std::vector< ConstraintElem * > constraintElems_
 
std::vector< Atom * > fluctuatingCharges_
 
std::vector< HBondDonor * > hBondDonors_
 
std::vector< Atom * > hBondAcceptors_
 
int stampId_
 
int region_
 
std::string moleculeName_
 
PropertyMap properties_
 
bool constrainTotalCharge_
 

Friends

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

Detailed Description

Definition at line 75 of file Molecule.hpp.

Member Typedef Documentation

◆ AtomIterator

typedef std::vector<Atom*>::iterator OpenMD::Molecule::AtomIterator

Definition at line 83 of file Molecule.hpp.

◆ BendIterator

typedef std::vector<Bend*>::iterator OpenMD::Molecule::BendIterator

Definition at line 85 of file Molecule.hpp.

◆ BondIterator

typedef std::vector<Bond*>::iterator OpenMD::Molecule::BondIterator

Definition at line 84 of file Molecule.hpp.

◆ ConstraintElemIterator

Definition at line 92 of file Molecule.hpp.

◆ ConstraintPairIterator

Definition at line 91 of file Molecule.hpp.

◆ CutoffGroupIterator

typedef std::vector<CutoffGroup*>::iterator OpenMD::Molecule::CutoffGroupIterator

Definition at line 89 of file Molecule.hpp.

◆ FluctuatingChargeIterator

typedef std::vector<Atom*>::iterator OpenMD::Molecule::FluctuatingChargeIterator

Definition at line 93 of file Molecule.hpp.

◆ HBondAcceptorIterator

typedef std::vector<Atom*>::iterator OpenMD::Molecule::HBondAcceptorIterator

Definition at line 95 of file Molecule.hpp.

◆ HBondDonorIterator

typedef std::vector<HBondDonor*>::iterator OpenMD::Molecule::HBondDonorIterator

Definition at line 94 of file Molecule.hpp.

◆ IntegrableObjectIterator

Definition at line 90 of file Molecule.hpp.

◆ InversionIterator

typedef std::vector<Inversion*>::iterator OpenMD::Molecule::InversionIterator

Definition at line 87 of file Molecule.hpp.

◆ RigidBodyIterator

typedef std::vector<RigidBody*>::iterator OpenMD::Molecule::RigidBodyIterator

Definition at line 88 of file Molecule.hpp.

◆ TorsionIterator

typedef std::vector<Torsion*>::iterator OpenMD::Molecule::TorsionIterator

Definition at line 86 of file Molecule.hpp.

Constructor & Destructor Documentation

◆ Molecule()

OpenMD::Molecule::Molecule ( int  stampId,
int  globalIndex,
const std::string &  molName,
int  region 
)

Definition at line 59 of file Molecule.cpp.

◆ ~Molecule()

Member Function Documentation

◆ addAtom()

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

add an atom into this molecule

Definition at line 86 of file Molecule.cpp.

References atoms_.

Referenced by constrainTotalCharge(), and OpenMD::MoleculeCreator::createMolecule().

◆ addBend()

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

add a bend into this molecule

Definition at line 98 of file Molecule.cpp.

References bends_.

Referenced by constrainTotalCharge(), and OpenMD::MoleculeCreator::createMolecule().

◆ addBond()

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

add a bond into this molecule

Definition at line 92 of file Molecule.cpp.

References bonds_.

Referenced by constrainTotalCharge(), and OpenMD::MoleculeCreator::createMolecule().

◆ addConstraintElem()

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

◆ addConstraintPair()

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

◆ addCutoffGroup()

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

add a cutoff group into this molecule

Definition at line 125 of file Molecule.cpp.

References cutoffGroups_.

Referenced by constrainTotalCharge(), and OpenMD::MoleculeCreator::createMolecule().

◆ addInversion()

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

add an improper torsion into this molecule

Definition at line 111 of file Molecule.cpp.

References inversions_.

Referenced by constrainTotalCharge(), and OpenMD::MoleculeCreator::createMolecule().

◆ addProperty()

void OpenMD::Molecule::addProperty ( GenericData genData)

Adds property into property map

Parameters
genDataGenericData to be added into PropertyMap

Definition at line 389 of file Molecule.cpp.

References OpenMD::PropertyMap::addProperty(), and properties_.

Referenced by getMoleculeName(), and OpenMD::RestraintForceManager::RestraintForceManager().

◆ addRigidBody()

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

add a rigidbody into this molecule

Definition at line 118 of file Molecule.cpp.

References rigidBodies_.

Referenced by constrainTotalCharge(), and OpenMD::MoleculeCreator::createMolecule().

◆ addTorsion()

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

add a torsion into this molecule

Definition at line 104 of file Molecule.cpp.

References torsions_.

Referenced by constrainTotalCharge(), and OpenMD::MoleculeCreator::createMolecule().

◆ beginAtom()

◆ beginBend()

◆ beginBond()

◆ beginConstraintElem()

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

Definition at line 331 of file Molecule.hpp.

References constraintElems_.

Referenced by OpenMD::Shake::doConstraint(), and OpenMD::Rattle::doConstraint().

◆ beginConstraintPair()

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

◆ beginCutoffGroup()

◆ beginFluctuatingCharge()

◆ beginHBondAcceptor()

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

◆ beginHBondDonor()

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

◆ beginIntegrableObject()

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

Definition at line 301 of file Molecule.hpp.

References integrableObjects_.

Referenced by OpenMD::SimInfo::addInteractionPairs(), OpenMD::ThermoIntegrationForceManager::calcForces(), OpenMD::SimInfo::calcNdf(), OpenMD::SimInfo::calcNdfRaw(), OpenMD::ZconstraintForceManager::doHarmonic(), OpenMD::ZconstraintForceManager::doZconstraintForce(), getCom(), getComVel(), OpenMD::PotentialEnergyObjectiveFunction::getGrad(), OpenMD::Thermo::getHeatFlux(), OpenMD::Thermo::getHullVolume(), getMass(), OpenMD::Thermo::getPressureTensor(), OpenMD::Thermo::getRotationalKinetic(), OpenMD::Thermo::getTranslationalKinetic(), OpenMD::HullFinder::HullFinder(), OpenMD::LangevinHullForceManager::LangevinHullForceManager(), OpenMD::LDForceManager::LDForceManager(), main(), OpenMD::LangevinHullDynamics::moveA(), OpenMD::LangevinDynamics::moveA(), OpenMD::NVE::moveA(), OpenMD::NPA::moveA(), OpenMD::NVT::moveA(), OpenMD::NPT::moveA(), OpenMD::LangevinHullDynamics::moveB(), OpenMD::LangevinDynamics::moveB(), OpenMD::NVE::moveB(), OpenMD::NPA::moveB(), OpenMD::NVT::moveB(), OpenMD::NPT::moveB(), moveCom(), OpenMD::MoLocator::placeMol(), OpenMD::LDForceManager::postCalculation(), OpenMD::TetrahedralityParam::process(), OpenMD::RestReader::readReferenceStructure(), OpenMD::Velocitizer::removeAngularDrift(), OpenMD::Velocitizer::removeComDrift(), OpenMD::SimInfo::removeInteractionPairs(), OpenMD::PotentialEnergyObjectiveFunction::setCoor(), OpenMD::SimCreator::setGlobalIndex(), OpenMD::PotentialEnergyObjectiveFunction::setInitialCoords(), OpenMD::Velocitizer::velocitize(), OpenMD::DumpWriter::writeFrame(), and OpenMD::ZconstraintForceManager::zeroVelocity().

◆ beginInversion()

◆ beginRigidBody()

◆ beginTorsion()

◆ clearProperties()

void OpenMD::Molecule::clearProperties ( )

clear all of the properties

Definition at line 397 of file Molecule.cpp.

References OpenMD::PropertyMap::clearProperties(), and properties_.

Referenced by getMoleculeName().

◆ complete()

◆ constrainTotalCharge()

◆ getAtomAt()

◆ getCom() [1/2]

◆ 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 306 of file Molecule.cpp.

References beginIntegrableObject(), OpenMD::StuntDouble::getMass(), OpenMD::StuntDouble::getPos(), and nextIntegrableObject().

◆ getComVel()

◆ getGlobalIndex()

◆ getMass()

◆ getMoleculeName()

std::string OpenMD::Molecule::getMoleculeName ( )
inline

◆ getNAtoms()

unsigned int OpenMD::Molecule::getNAtoms ( )
inline

Returns the total number of atoms in this molecule

Definition at line 172 of file Molecule.hpp.

References atoms_.

Referenced by OpenMD::SimInfo::addMolecule(), OpenMD::NameFinder::matchInternalIndex(), OpenMD::operator<<(), and OpenMD::SimInfo::removeMolecule().

◆ getNBends()

unsigned int OpenMD::Molecule::getNBends ( )
inline

Returns the total number of bends in this molecule

Definition at line 182 of file Molecule.hpp.

References bends_.

Referenced by OpenMD::SimInfo::addMolecule(), OpenMD::MoleculeCreator::createBend(), OpenMD::operator<<(), and OpenMD::SimInfo::removeMolecule().

◆ getNBonds()

unsigned int OpenMD::Molecule::getNBonds ( )
inline

Returns the total number of bonds in this molecule

Definition at line 177 of file Molecule.hpp.

References bonds_.

Referenced by OpenMD::SimInfo::addMolecule(), OpenMD::MoleculeCreator::createBond(), OpenMD::operator<<(), and OpenMD::SimInfo::removeMolecule().

◆ getNConstraintPairs()

unsigned int OpenMD::Molecule::getNConstraintPairs ( )
inline

Returns the total number of constraints in this molecule

Definition at line 212 of file Molecule.hpp.

References constraintPairs_.

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

◆ getNCutoffGroups()

unsigned int OpenMD::Molecule::getNCutoffGroups ( )
inline

Returns the total number of cutoff groups in this molecule

Definition at line 207 of file Molecule.hpp.

References cutoffGroups_.

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

◆ getNFluctuatingCharges()

unsigned int OpenMD::Molecule::getNFluctuatingCharges ( )
inline

Returns the total number of fluctuating charges in this molecule

Definition at line 217 of file Molecule.hpp.

References fluctuatingCharges_.

Referenced by OpenMD::FluctuatingChargeConstraints::applyConstraints(), and OpenMD::operator<<().

◆ getNHBondAcceptors()

unsigned int OpenMD::Molecule::getNHBondAcceptors ( )
inline

Returns the total number of Hydrogen Bond acceptors in this molecule

Definition at line 226 of file Molecule.hpp.

References hBondAcceptors_.

◆ getNHBondDonors()

unsigned int OpenMD::Molecule::getNHBondDonors ( )
inline

Returns the total number of Hydrogen Bond donors in this molecule

Definition at line 221 of file Molecule.hpp.

References hBondDonors_.

◆ getNIntegrableObjects()

unsigned int OpenMD::Molecule::getNIntegrableObjects ( )
inline

Returns the total number of integrable objects in this molecule

Definition at line 202 of file Molecule.hpp.

References integrableObjects_.

Referenced by OpenMD::SimInfo::addMolecule(), OpenMD::operator<<(), OpenMD::MoLocator::placeMol(), OpenMD::SimInfo::removeMolecule(), and OpenMD::SimCreator::setGlobalIndex().

◆ getNInversions()

unsigned int OpenMD::Molecule::getNInversions ( )
inline

Returns the total number of improper torsions in this molecule

Definition at line 192 of file Molecule.hpp.

References inversions_.

Referenced by OpenMD::SimInfo::addMolecule(), OpenMD::MoleculeCreator::createInversion(), OpenMD::operator<<(), and OpenMD::SimInfo::removeMolecule().

◆ getNRigidBodies()

unsigned int OpenMD::Molecule::getNRigidBodies ( )
inline

Returns the total number of rigid bodies in this molecule

Definition at line 197 of file Molecule.hpp.

References rigidBodies_.

Referenced by OpenMD::SimInfo::addMolecule(), OpenMD::MoleculeCreator::createRigidBody(), OpenMD::NameFinder::matchInternalIndex(), OpenMD::operator<<(), and OpenMD::SimInfo::removeMolecule().

◆ getNTorsions()

unsigned int OpenMD::Molecule::getNTorsions ( )
inline

Returns the total number of torsions in this molecule

Definition at line 187 of file Molecule.hpp.

References torsions_.

Referenced by OpenMD::SimInfo::addMolecule(), OpenMD::MoleculeCreator::createTorsion(), OpenMD::operator<<(), and OpenMD::SimInfo::removeMolecule().

◆ getPotential()

RealType OpenMD::Molecule::getPotential ( )

◆ getProperties()

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

Returns all of the properties in PropertyMap

Returns
all of the properties in PropertyMap

Definition at line 405 of file Molecule.cpp.

References OpenMD::PropertyMap::getProperties(), and properties_.

Referenced by getMoleculeName().

◆ getPropertyByName()

GenericData * OpenMD::Molecule::getPropertyByName ( const std::string &  propName)

Returns property

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

Definition at line 409 of file Molecule.cpp.

References OpenMD::PropertyMap::getPropertyByName(), and properties_.

Referenced by getMoleculeName(), and OpenMD::RestReader::readReferenceStructure().

◆ getPropertyNames()

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

Returns all names of properties

Returns
all names of properties

Definition at line 401 of file Molecule.cpp.

References OpenMD::PropertyMap::getPropertyNames(), and properties_.

Referenced by getMoleculeName().

◆ getRegion()

◆ getRigidBodyAt()

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

◆ 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 115 of file Molecule.hpp.

References stampId_.

◆ getType()

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

◆ moveCom()

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

Moves the center of this molecule

Definition at line 325 of file Molecule.cpp.

References beginIntegrableObject(), OpenMD::StuntDouble::getPos(), nextIntegrableObject(), and OpenMD::StuntDouble::setPos().

Referenced by nextHBondAcceptor().

◆ nextAtom()

◆ nextBend()

◆ nextBond()

◆ nextConstraintElem()

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

Definition at line 336 of file Molecule.hpp.

References constraintElems_.

Referenced by OpenMD::Shake::doConstraint(), and OpenMD::Rattle::doConstraint().

◆ nextConstraintPair()

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

◆ nextCutoffGroup()

◆ nextFluctuatingCharge()

◆ nextHBondAcceptor()

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

◆ nextHBondDonor()

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

◆ nextIntegrableObject()

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

Definition at line 306 of file Molecule.hpp.

References integrableObjects_.

Referenced by OpenMD::SimInfo::addInteractionPairs(), OpenMD::ThermoIntegrationForceManager::calcForces(), OpenMD::SimInfo::calcNdf(), OpenMD::SimInfo::calcNdfRaw(), OpenMD::ZconstraintForceManager::doHarmonic(), OpenMD::ZconstraintForceManager::doZconstraintForce(), getCom(), getComVel(), OpenMD::PotentialEnergyObjectiveFunction::getGrad(), OpenMD::Thermo::getHeatFlux(), OpenMD::Thermo::getHullVolume(), getMass(), OpenMD::Thermo::getPressureTensor(), OpenMD::Thermo::getRotationalKinetic(), OpenMD::Thermo::getTranslationalKinetic(), OpenMD::HullFinder::HullFinder(), OpenMD::LangevinHullForceManager::LangevinHullForceManager(), OpenMD::LDForceManager::LDForceManager(), main(), OpenMD::LangevinHullDynamics::moveA(), OpenMD::LangevinDynamics::moveA(), OpenMD::NVE::moveA(), OpenMD::NPA::moveA(), OpenMD::NVT::moveA(), OpenMD::NPT::moveA(), OpenMD::LangevinHullDynamics::moveB(), OpenMD::LangevinDynamics::moveB(), OpenMD::NVE::moveB(), OpenMD::NPA::moveB(), OpenMD::NVT::moveB(), OpenMD::NPT::moveB(), moveCom(), OpenMD::MoLocator::placeMol(), OpenMD::LDForceManager::postCalculation(), OpenMD::TetrahedralityParam::process(), OpenMD::RestReader::readReferenceStructure(), OpenMD::Velocitizer::removeAngularDrift(), OpenMD::Velocitizer::removeComDrift(), OpenMD::SimInfo::removeInteractionPairs(), OpenMD::PotentialEnergyObjectiveFunction::setCoor(), OpenMD::SimCreator::setGlobalIndex(), OpenMD::PotentialEnergyObjectiveFunction::setInitialCoords(), OpenMD::Velocitizer::velocitize(), OpenMD::DumpWriter::writeFrame(), and OpenMD::ZconstraintForceManager::zeroVelocity().

◆ nextInversion()

◆ nextRigidBody()

◆ nextTorsion()

◆ removeProperty()

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

Removes property from PropertyMap by name

Parameters
propNamethe name of property to be removed

Definition at line 393 of file Molecule.cpp.

References properties_, and OpenMD::PropertyMap::removeProperty().

Referenced by getMoleculeName().

◆ setConstrainTotalCharge()

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

Definition at line 135 of file Molecule.hpp.

References constrainTotalCharge_.

Referenced by OpenMD::MoleculeCreator::createMolecule().

◆ setGlobalIndex()

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

Sets the global index of this molecule.

Parameters
indexnew global index to be set

Definition at line 131 of file Molecule.hpp.

References globalIndex_.

Friends And Related Function Documentation

◆ operator<<

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

Definition at line 413 of file Molecule.cpp.

Referenced by getMoleculeName().

Member Data Documentation

◆ atoms_

std::vector<Atom*> OpenMD::Molecule::atoms_
private

Definition at line 452 of file Molecule.hpp.

Referenced by addAtom(), beginAtom(), getAtomAt(), getNAtoms(), nextAtom(), and ~Molecule().

◆ bends_

std::vector<Bend*> OpenMD::Molecule::bends_
private

Definition at line 454 of file Molecule.hpp.

Referenced by addBend(), beginBend(), getNBends(), nextBend(), and ~Molecule().

◆ bonds_

std::vector<Bond*> OpenMD::Molecule::bonds_
private

Definition at line 453 of file Molecule.hpp.

Referenced by addBond(), beginBond(), getNBonds(), nextBond(), and ~Molecule().

◆ constraintElems_

std::vector<ConstraintElem*> OpenMD::Molecule::constraintElems_
private

◆ constrainTotalCharge_

bool OpenMD::Molecule::constrainTotalCharge_
private

Definition at line 470 of file Molecule.hpp.

Referenced by constrainTotalCharge(), and setConstrainTotalCharge().

◆ constraintPairs_

std::vector<ConstraintPair*> OpenMD::Molecule::constraintPairs_
private

◆ cutoffGroups_

std::vector<CutoffGroup*> OpenMD::Molecule::cutoffGroups_
private

◆ fluctuatingCharges_

std::vector<Atom*> OpenMD::Molecule::fluctuatingCharges_
private

◆ globalIndex_

int OpenMD::Molecule::globalIndex_
private

Definition at line 450 of file Molecule.hpp.

Referenced by getGlobalIndex(), and setGlobalIndex().

◆ hBondAcceptors_

std::vector<Atom*> OpenMD::Molecule::hBondAcceptors_
private

Definition at line 464 of file Molecule.hpp.

Referenced by beginHBondAcceptor(), complete(), getNHBondAcceptors(), and nextHBondAcceptor().

◆ hBondDonors_

std::vector<HBondDonor*> OpenMD::Molecule::hBondDonors_
private

Definition at line 463 of file Molecule.hpp.

Referenced by beginHBondDonor(), complete(), getNHBondDonors(), and nextHBondDonor().

◆ integrableObjects_

std::vector<StuntDouble*> OpenMD::Molecule::integrableObjects_
private

◆ inversions_

std::vector<Inversion*> OpenMD::Molecule::inversions_
private

Definition at line 456 of file Molecule.hpp.

Referenced by addInversion(), beginInversion(), getNInversions(), nextInversion(), and ~Molecule().

◆ moleculeName_

std::string OpenMD::Molecule::moleculeName_
private

Definition at line 468 of file Molecule.hpp.

Referenced by getMoleculeName(), and getType().

◆ properties_

PropertyMap OpenMD::Molecule::properties_
private

◆ region_

int OpenMD::Molecule::region_
private

Definition at line 467 of file Molecule.hpp.

Referenced by getRegion().

◆ rigidBodies_

std::vector<RigidBody*> OpenMD::Molecule::rigidBodies_
private

◆ stampId_

int OpenMD::Molecule::stampId_
private

Definition at line 466 of file Molecule.hpp.

Referenced by getStampId().

◆ torsions_

std::vector<Torsion*> OpenMD::Molecule::torsions_
private

Definition at line 455 of file Molecule.hpp.

Referenced by addTorsion(), beginTorsion(), getNTorsions(), nextTorsion(), and ~Molecule().


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