Detailed Description

template<int NAtom>
class McMd::Group< NAtom >

A sequence of NAtom covalently interacting atoms.

An ordered group of atoms that interact via a permanent (covalent) NAtom atom potential energy. A Group<NAtom> object has an array of pointers to Atoms in the group. Specializations of Group<NAtom> with NAtom=2, 3, and 4 are used to represent covalent bond, angle and dihedral interaction groups, respectively. The Bond, Angle, and Dihedral typedefs are aliases for these template specializations.

A Group<NAtom> object also has an integer type id. Different parameters may be used in the corresponding covalent potential for groups with different type Ids.

Definition at line 37 of file mcMd/chemistry/Group.h.

#include <Group.h>

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

Initialization
void	setAtom (int i, Atom &atom)
	Add an atom to this group. More...

void	setTypeId (int typeId)
	Set the group type id for this group. More...

Accessors
Atom &	atom (int i)
	Get a specific Atom in the Group by reference. More...

const Atom &	atom (int i) const
	Get a specific Atom in the Group by const reference. More...

int	typeId () const
	Get the typeId for this covalent group. More...

bool	isActive () const
	Is this group active? More...

int	nInActive () const
	Return number of inactive atoms. More...

bool	checkInactive () const
	Check consistency of number of inactive atoms. More...

Constructor & Destructor Documentation

template<int NAtom>

McMd::Group< NAtom >::Group ( )

Constructor.

Definition at line 149 of file mcMd/chemistry/Group.h.

Member Function Documentation

template<int NAtom>

void McMd::Group< NAtom >::setAtom	(	int	i,
		Atom &	atom
	)

inline

Add an atom to this group.

Parameters

i	index of atom within group.
atom	atom to be added.

Definition at line 162 of file mcMd/chemistry/Group.h.

References McMd::Group< NAtom >::atom().

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

template<int NAtom>

void McMd::Group< NAtom >::setTypeId ( int typeId )

inline

Set the group type id for this group.

Parameters

typeId value of covalent group typeId

Definition at line 169 of file mcMd/chemistry/Group.h.

References McMd::Group< NAtom >::typeId().

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

template<int NAtom>

Atom & McMd::Group< NAtom >::atom ( int i )

inline

Get a specific Atom in the Group by reference.

Parameters

i	index within group (0,...,N-1)

Definition at line 178 of file mcMd/chemistry/Group.h.

Referenced by McMd::CfbEndBase::addEndAtom(), McMd::BondPotentialImpl< Interaction >::atomEnergy(), McMd::DihedralPotentialImpl< Interaction >::atomEnergy(), McMd::AnglePotentialImpl< Interaction >::atomEnergy(), McMd::CfbEndBase::deleteEndAtom(), McMd::Simulation::isValid(), McMd::Group< NAtom >::setAtom(), and McMd::GroupRebridgeBase::tetraEnergy().

template<int NAtom>

const Atom & McMd::Group< NAtom >::atom ( int i ) const

inline

Get a specific Atom in the Group by const reference.

Parameters

i	index within group (0,...,N-1)

Definition at line 188 of file mcMd/chemistry/Group.h.

template<int NAtom>

int McMd::Group< NAtom >::typeId ( ) const

inline

Get the typeId for this covalent group.

Definition at line 198 of file mcMd/chemistry/Group.h.

Referenced by McMd::CfbLinear::addAtom(), McMd::CfbEndBase::addEndAtom(), McMd::BondPotentialImpl< Interaction >::atomEnergy(), McMd::DihedralPotentialImpl< Interaction >::atomEnergy(), McMd::AnglePotentialImpl< Interaction >::atomEnergy(), McMd::CfbLinear::deleteAtom(), McMd::CfbEndBase::deleteEndAtom(), McMd::Simulation::isValid(), McMd::McNVTChemicalPotential::load(), McMd::RingTetraRebridgeMove::move(), McMd::CfbDoubleRebridgeMove::move(), McMd::CfbEndMove::move(), McMd::CfbRebridgeMove::move(), McMd::CfbRingRebridgeMove::move(), McMd::McNVTChemicalPotential::sample(), and McMd::Group< NAtom >::setTypeId().

template<int NAtom>

bool McMd::Group< NAtom >::isActive ( ) const

inline

Is this group active?

A group is active iff all associated atoms are active. Atoms can be temporarily de-activated during some Monte Carlo moves that remove and regrow parts of a molecule.

Definition at line 205 of file mcMd/chemistry/Group.h.

Referenced by McMd::Group< NAtom >::checkInactive(), and McMd::Simulation::isValid().

template<int NAtom>

int McMd::Group< NAtom >::nInActive ( ) const

inline

Return number of inactive atoms.

Definition at line 212 of file mcMd/chemistry/Group.h.

template<int NAtom>

bool McMd::Group< NAtom >::checkInactive ( ) const

Check consistency of number of inactive atoms.

Returns true if consistent, or throws Exception.

Definition at line 219 of file mcMd/chemistry/Group.h.