OpenMD 3.0
Molecular Dynamics in the Open
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OpenMD::MoleculeStamp Class Reference
+ Inheritance diagram for OpenMD::MoleculeStamp:

Public Member Functions

bool addAtomStamp (AtomStamp *atom)
 
bool addBondStamp (BondStamp *bond)
 
bool addBendStamp (BendStamp *bend)
 
bool addTorsionStamp (TorsionStamp *torsion)
 
bool addInversionStamp (InversionStamp *inversion)
 
bool addRigidBodyStamp (RigidBodyStamp *rigidbody)
 
bool addCutoffGroupStamp (CutoffGroupStamp *cutoffgroup)
 
bool addFragmentStamp (FragmentStamp *fragment)
 
bool addConstraintStamp (ConstraintStamp *constraint)
 
void setRegion (int r)
 
int getRegion ()
 
std::size_t getNAtoms ()
 
std::size_t getNBonds ()
 
std::size_t getNBends ()
 
std::size_t getNTorsions ()
 
std::size_t getNInversions ()
 
std::size_t getNRigidBodies ()
 
std::size_t getNCutoffGroups ()
 
std::size_t getNConstraints ()
 
int getNIntegrable ()
 
std::size_t getNFreeAtoms ()
 
virtual void validate ()
 
AtomStampgetAtomStamp (int index)
 
BondStampgetBondStamp (int index)
 
BendStampgetBendStamp (int index)
 
TorsionStampgetTorsionStamp (int index)
 
InversionStampgetInversionStamp (int index)
 
RigidBodyStampgetRigidBodyStamp (int index)
 
CutoffGroupStampgetCutoffGroupStamp (int index)
 
FragmentStampgetFragmentStamp (int index)
 
ConstraintStampgetConstraintStamp (int index)
 
bool isBondInSameRigidBody (BondStamp *bond)
 
bool isAtomInRigidBody (int atomIndex)
 
bool isAtomInRigidBody (int atomIndex, int &whichRigidBody, int &consAtomIndex)
 
std::vector< std::pair< int, int > > getJointAtoms (int rb1, int rb2)
 
- Public Member Functions inherited from OpenMD::DataHolder
template<class T >
void assign (const std::string &keyword, T val)
 

Additional Inherited Members

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

Detailed Description

Definition at line 62 of file MoleculeStamp.hpp.

Constructor & Destructor Documentation

◆ MoleculeStamp()

OpenMD::MoleculeStamp::MoleculeStamp ( )

Definition at line 66 of file MoleculeStamp.cpp.

◆ ~MoleculeStamp()

OpenMD::MoleculeStamp::~MoleculeStamp ( )
virtual

Definition at line 79 of file MoleculeStamp.cpp.

Member Function Documentation

◆ addAtomStamp()

bool OpenMD::MoleculeStamp::addAtomStamp ( AtomStamp * atom)

Definition at line 91 of file MoleculeStamp.cpp.

◆ addBendStamp()

bool OpenMD::MoleculeStamp::addBendStamp ( BendStamp * bend)

Definition at line 108 of file MoleculeStamp.cpp.

◆ addBondStamp()

bool OpenMD::MoleculeStamp::addBondStamp ( BondStamp * bond)

Definition at line 103 of file MoleculeStamp.cpp.

◆ addConstraintStamp()

bool OpenMD::MoleculeStamp::addConstraintStamp ( ConstraintStamp * constraint)

Definition at line 144 of file MoleculeStamp.cpp.

◆ addCutoffGroupStamp()

bool OpenMD::MoleculeStamp::addCutoffGroupStamp ( CutoffGroupStamp * cutoffgroup)

Definition at line 135 of file MoleculeStamp.cpp.

◆ addFragmentStamp()

bool OpenMD::MoleculeStamp::addFragmentStamp ( FragmentStamp * fragment)

Definition at line 140 of file MoleculeStamp.cpp.

◆ addInversionStamp()

bool OpenMD::MoleculeStamp::addInversionStamp ( InversionStamp * inversion)

Definition at line 118 of file MoleculeStamp.cpp.

◆ addRigidBodyStamp()

bool OpenMD::MoleculeStamp::addRigidBodyStamp ( RigidBodyStamp * rigidbody)

Definition at line 123 of file MoleculeStamp.cpp.

◆ addTorsionStamp()

bool OpenMD::MoleculeStamp::addTorsionStamp ( TorsionStamp * torsion)

Definition at line 113 of file MoleculeStamp.cpp.

◆ getAtomStamp()

AtomStamp * OpenMD::MoleculeStamp::getAtomStamp ( int index)
inline

Definition at line 94 of file MoleculeStamp.hpp.

◆ getBendStamp()

BendStamp * OpenMD::MoleculeStamp::getBendStamp ( int index)
inline

Definition at line 96 of file MoleculeStamp.hpp.

◆ getBondStamp()

BondStamp * OpenMD::MoleculeStamp::getBondStamp ( int index)
inline

Definition at line 95 of file MoleculeStamp.hpp.

◆ getConstraintStamp()

ConstraintStamp * OpenMD::MoleculeStamp::getConstraintStamp ( int index)
inline

Definition at line 110 of file MoleculeStamp.hpp.

◆ getCutoffGroupStamp()

CutoffGroupStamp * OpenMD::MoleculeStamp::getCutoffGroupStamp ( int index)
inline

Definition at line 104 of file MoleculeStamp.hpp.

◆ getFragmentStamp()

FragmentStamp * OpenMD::MoleculeStamp::getFragmentStamp ( int index)
inline

Definition at line 107 of file MoleculeStamp.hpp.

◆ getInversionStamp()

InversionStamp * OpenMD::MoleculeStamp::getInversionStamp ( int index)
inline

Definition at line 98 of file MoleculeStamp.hpp.

◆ getJointAtoms()

std::vector< std::pair< int, int > > OpenMD::MoleculeStamp::getJointAtoms ( int rb1,
int rb2 )

Definition at line 893 of file MoleculeStamp.cpp.

◆ getNAtoms()

std::size_t OpenMD::MoleculeStamp::getNAtoms ( )
inline

Definition at line 82 of file MoleculeStamp.hpp.

◆ getNBends()

std::size_t OpenMD::MoleculeStamp::getNBends ( )
inline

Definition at line 84 of file MoleculeStamp.hpp.

◆ getNBonds()

std::size_t OpenMD::MoleculeStamp::getNBonds ( )
inline

Definition at line 83 of file MoleculeStamp.hpp.

◆ getNConstraints()

std::size_t OpenMD::MoleculeStamp::getNConstraints ( )
inline

Definition at line 89 of file MoleculeStamp.hpp.

◆ getNCutoffGroups()

std::size_t OpenMD::MoleculeStamp::getNCutoffGroups ( )
inline

Definition at line 88 of file MoleculeStamp.hpp.

◆ getNFreeAtoms()

std::size_t OpenMD::MoleculeStamp::getNFreeAtoms ( )
inline

Definition at line 91 of file MoleculeStamp.hpp.

◆ getNIntegrable()

int OpenMD::MoleculeStamp::getNIntegrable ( )
inline

Definition at line 90 of file MoleculeStamp.hpp.

◆ getNInversions()

std::size_t OpenMD::MoleculeStamp::getNInversions ( )
inline

Definition at line 86 of file MoleculeStamp.hpp.

◆ getNRigidBodies()

std::size_t OpenMD::MoleculeStamp::getNRigidBodies ( )
inline

Definition at line 87 of file MoleculeStamp.hpp.

◆ getNTorsions()

std::size_t OpenMD::MoleculeStamp::getNTorsions ( )
inline

Definition at line 85 of file MoleculeStamp.hpp.

◆ getRegion()

int OpenMD::MoleculeStamp::getRegion ( )
inline

Definition at line 81 of file MoleculeStamp.hpp.

◆ getRigidBodyStamp()

RigidBodyStamp * OpenMD::MoleculeStamp::getRigidBodyStamp ( int index)
inline

Definition at line 101 of file MoleculeStamp.hpp.

◆ getTorsionStamp()

TorsionStamp * OpenMD::MoleculeStamp::getTorsionStamp ( int index)
inline

Definition at line 97 of file MoleculeStamp.hpp.

◆ isAtomInRigidBody() [1/2]

bool OpenMD::MoleculeStamp::isAtomInRigidBody ( int atomIndex)

Definition at line 857 of file MoleculeStamp.cpp.

◆ isAtomInRigidBody() [2/2]

bool OpenMD::MoleculeStamp::isAtomInRigidBody ( int atomIndex,
int & whichRigidBody,
int & consAtomIndex )

Definition at line 868 of file MoleculeStamp.cpp.

◆ isBondInSameRigidBody()

bool OpenMD::MoleculeStamp::isBondInSameRigidBody ( BondStamp * bond)

Definition at line 838 of file MoleculeStamp.cpp.

◆ setRegion()

void OpenMD::MoleculeStamp::setRegion ( int r)
inline

Definition at line 80 of file MoleculeStamp.hpp.

◆ validate()

void OpenMD::MoleculeStamp::validate ( )
virtual

Reimplemented from OpenMD::DataHolder.

Definition at line 149 of file MoleculeStamp.cpp.


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