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

#include <AtomStamp.hpp>

Inheritance diagram for OpenMD::AtomStamp:
OpenMD::DataHolder

Public Types

typedef std::set< int >::iterator AtomIter
 
typedef std::vector< int >::iterator BondIter
 

Public Member Functions

 AtomStamp (int index)
 
bool setPosition (const std::vector< RealType > &pos)
 
bool setOrientation (const std::vector< RealType > &ort)
 
bool havePosition ()
 
bool haveOrientation ()
 
RealType getPosX ()
 
RealType getPosY ()
 
RealType getPosZ ()
 
RealType getEulerPhi ()
 
RealType getEulerTheta ()
 
RealType getEulerPsi ()
 
int getIndex ()
 
virtual void validate ()
 
int getFirstBondedAtom (AtomIter &ai)
 
int getNextBondedAtom (AtomIter &ai)
 
int getFirstBond (BondIter &bi)
 
int getNextBond (BondIter &bi)
 
void addBond (int bondIndex)
 
void addBondedAtom (int atomIndex)
 
int getBondCount ()
 
void overrideCharge (RealType c)
 
bool hasOverride ()
 
- Public Member Functions inherited from OpenMD::DataHolder
 DataHolder ()
 
virtual ~DataHolder ()
 
template<class T >
void assign (const std::string &keyword, T val)
 

Private Member Functions

 DeclareParameter (Type, std::string)
 

Private Attributes

Vector3d position_
 
Vector3d orientation_
 
RealType orCharge_
 
bool havePos_
 
bool haveOrt_
 
bool hasOverride_
 
int index_
 
std::vector< int > bonds_
 
std::set< int > bondedAtoms_
 

Additional Inherited Members

- Protected Types inherited from OpenMD::DataHolder
typedef std::map< std::string, ParameterBase * > ParamMap
 
- Protected Attributes inherited from OpenMD::DataHolder
ParamMap parameters_
 
std::set< std::string > deprecatedKeywords_
 

Detailed Description

Definition at line 52 of file AtomStamp.hpp.

Member Typedef Documentation

◆ AtomIter

typedef std::set<int>::iterator OpenMD::AtomStamp::AtomIter

Definition at line 70 of file AtomStamp.hpp.

◆ BondIter

typedef std::vector<int>::iterator OpenMD::AtomStamp::BondIter

Definition at line 71 of file AtomStamp.hpp.

Constructor & Destructor Documentation

◆ AtomStamp()

OpenMD::AtomStamp::AtomStamp ( int  index)

Definition at line 51 of file AtomStamp.cpp.

References DefineParameter.

Member Function Documentation

◆ addBond()

void OpenMD::AtomStamp::addBond ( int  bondIndex)
inline

Definition at line 88 of file AtomStamp.hpp.

References bonds_.

Referenced by OpenMD::MoleculeStamp::fillBondInfo().

◆ addBondedAtom()

void OpenMD::AtomStamp::addBondedAtom ( int  atomIndex)
inline

Definition at line 89 of file AtomStamp.hpp.

References bondedAtoms_.

Referenced by OpenMD::MoleculeStamp::fillBondInfo().

◆ DeclareParameter()

OpenMD::AtomStamp::DeclareParameter ( Type  ,
std::string   
)
private

◆ getBondCount()

int OpenMD::AtomStamp::getBondCount ( )
inline

Definition at line 90 of file AtomStamp.hpp.

References bonds_.

Referenced by OpenMD::MoleculeStamp::checkInversions().

◆ getEulerPhi()

RealType OpenMD::AtomStamp::getEulerPhi ( )
inline

Definition at line 65 of file AtomStamp.hpp.

References orientation_.

Referenced by OpenMD::RigidBody::addAtom().

◆ getEulerPsi()

RealType OpenMD::AtomStamp::getEulerPsi ( )
inline

Definition at line 67 of file AtomStamp.hpp.

References orientation_.

Referenced by OpenMD::RigidBody::addAtom().

◆ getEulerTheta()

RealType OpenMD::AtomStamp::getEulerTheta ( )
inline

Definition at line 66 of file AtomStamp.hpp.

References orientation_.

Referenced by OpenMD::RigidBody::addAtom().

◆ getFirstBond()

int OpenMD::AtomStamp::getFirstBond ( BondIter bi)
inline

Definition at line 80 of file AtomStamp.hpp.

References bonds_.

◆ getFirstBondedAtom()

int OpenMD::AtomStamp::getFirstBondedAtom ( AtomIter ai)
inline

◆ getIndex()

int OpenMD::AtomStamp::getIndex ( )
inline

Definition at line 68 of file AtomStamp.hpp.

References index_, and validate().

Referenced by OpenMD::MoleculeStamp::addAtomStamp(), and OpenMD::MoleculeStamp::checkInversions().

◆ getNextBond()

int OpenMD::AtomStamp::getNextBond ( BondIter bi)
inline

Definition at line 84 of file AtomStamp.hpp.

References bonds_.

◆ getNextBondedAtom()

int OpenMD::AtomStamp::getNextBondedAtom ( AtomIter ai)
inline

◆ getPosX()

RealType OpenMD::AtomStamp::getPosX ( )
inline

Definition at line 62 of file AtomStamp.hpp.

References position_.

Referenced by OpenMD::RigidBody::addAtom(), and OpenMD::MoLocator::calcRef().

◆ getPosY()

RealType OpenMD::AtomStamp::getPosY ( )
inline

Definition at line 63 of file AtomStamp.hpp.

References position_.

Referenced by OpenMD::RigidBody::addAtom(), and OpenMD::MoLocator::calcRef().

◆ getPosZ()

RealType OpenMD::AtomStamp::getPosZ ( )
inline

Definition at line 64 of file AtomStamp.hpp.

References position_.

Referenced by OpenMD::RigidBody::addAtom(), and OpenMD::MoLocator::calcRef().

◆ hasOverride()

bool OpenMD::AtomStamp::hasOverride ( )
inline

Definition at line 96 of file AtomStamp.hpp.

References hasOverride_.

◆ haveOrientation()

bool OpenMD::AtomStamp::haveOrientation ( )
inline

Definition at line 61 of file AtomStamp.hpp.

References haveOrt_.

Referenced by OpenMD::RigidBody::addAtom(), and OpenMD::MoleculeStamp::checkBends().

◆ havePosition()

bool OpenMD::AtomStamp::havePosition ( )
inline

Definition at line 60 of file AtomStamp.hpp.

References havePos_.

Referenced by OpenMD::RigidBody::addAtom(), and OpenMD::MoLocator::calcRef().

◆ overrideCharge()

void OpenMD::AtomStamp::overrideCharge ( RealType  c)
inline

Definition at line 91 of file AtomStamp.hpp.

References hasOverride_, and orCharge_.

Referenced by MDTreeParser::atomstatement().

◆ setOrientation()

bool OpenMD::AtomStamp::setOrientation ( const std::vector< RealType > &  ort)

Definition at line 71 of file AtomStamp.cpp.

References OpenMD::containerToString(), haveOrt_, and orientation_.

Referenced by MDTreeParser::atomstatement().

◆ setPosition()

bool OpenMD::AtomStamp::setPosition ( const std::vector< RealType > &  pos)

Definition at line 56 of file AtomStamp.cpp.

References OpenMD::containerToString(), havePos_, and position_.

Referenced by MDTreeParser::atomstatement().

◆ validate()

void OpenMD::AtomStamp::validate ( )
virtual

Reimplemented from OpenMD::DataHolder.

Definition at line 87 of file AtomStamp.cpp.

References CheckParameter, OpenMD::isNotEmpty(), and OpenMD::DataHolder::validate().

Referenced by getIndex().

Member Data Documentation

◆ bondedAtoms_

std::set<int> OpenMD::AtomStamp::bondedAtoms_
private

Definition at line 106 of file AtomStamp.hpp.

Referenced by addBondedAtom(), getFirstBondedAtom(), and getNextBondedAtom().

◆ bonds_

std::vector<int> OpenMD::AtomStamp::bonds_
private

Definition at line 105 of file AtomStamp.hpp.

Referenced by addBond(), getBondCount(), getFirstBond(), and getNextBond().

◆ hasOverride_

bool OpenMD::AtomStamp::hasOverride_
private

Definition at line 103 of file AtomStamp.hpp.

Referenced by hasOverride(), and overrideCharge().

◆ haveOrt_

bool OpenMD::AtomStamp::haveOrt_
private

Definition at line 102 of file AtomStamp.hpp.

Referenced by haveOrientation(), and setOrientation().

◆ havePos_

bool OpenMD::AtomStamp::havePos_
private

Definition at line 101 of file AtomStamp.hpp.

Referenced by havePosition(), and setPosition().

◆ index_

int OpenMD::AtomStamp::index_
private

Definition at line 104 of file AtomStamp.hpp.

Referenced by getIndex().

◆ orCharge_

RealType OpenMD::AtomStamp::orCharge_
private

Definition at line 100 of file AtomStamp.hpp.

Referenced by overrideCharge().

◆ orientation_

Vector3d OpenMD::AtomStamp::orientation_
private

Definition at line 99 of file AtomStamp.hpp.

Referenced by getEulerPhi(), getEulerPsi(), getEulerTheta(), and setOrientation().

◆ position_

Vector3d OpenMD::AtomStamp::position_
private

Definition at line 98 of file AtomStamp.hpp.

Referenced by getPosX(), getPosY(), getPosZ(), and setPosition().


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