McMd::SystemInterface Class Reference

Detailed Description

An interface to a System.

A SystemInterface is an interface for a system that is intended to be used as a protected or private base class for classes that evaluate properties of a system. It provides functions to directly access:

• an ArraySet of Molecule objects of each Species.
• a Boundary.

Definition at line 43 of file SystemInterface.h.

#include <SystemInterface.h>

Inheritance diagram for McMd::SystemInterface:

Public Member Functions
	SystemInterface (System &parent)
	Constructor. More...
virtual	~SystemInterface ()
	Destructor. More...
System &	system () const
	Get the parent System by reference. More...

Protected Member Functions
Accessors (Miscellaneous)
Boundary &	boundary () const
	Get the Boundary by reference. More...
Simulation &	simulation () const
	Get the parent Simulation by reference. More...
Molecule Set Accessors
int	nMolecule (int speciesId) const
	Get the number of molecules of one Species in this SystemInterface. More...
int	nAtom () const
	Return the total number of atoms in this SystemInterface. More...
bool	isEmpty () const
	Is this an empty SystemInterface (i.e., one with no molecules) ? More...
void	begin (int speciesId, System::MoleculeIterator &iterator)
	Initialize an iterator for molecules of one species in this SystemInterface. More...
void	begin (int speciesId, System::ConstMoleculeIterator &iterator) const
	Initialize a const iterator for molecules of one species in this SystemInterface. More...
Potential Energy Queries
bool	hasBonds () const
	Does a bond potential exist? More...
bool	hasAngles () const
	Does an angle potential exist? More...
bool	hasDihedrals () const
	Does a dihedral potential exist? More...
bool	hasLinks () const
	Does a link potential exist? More...
bool	hasExternal () const
	Does an external potential exist? More...

Constructor & Destructor Documentation

McMd::SystemInterface::SystemInterface

(

System &

parent

)

Constructor.

Parameters

parent

parent System

Definition at line 24 of file SystemInterface.cpp.

McMd::SystemInterface::~SystemInterface ( )

virtual

Destructor.

Definition at line 52 of file SystemInterface.cpp.

Member Function Documentation

System & McMd::SystemInterface::system ( ) const

inline

Get the parent System by reference.

Definition at line 215 of file SystemInterface.h.

Referenced by McMd::DeformCommand::execute(), and McMd::ExternalPotentialImpl< Interaction >::readParameters().

Boundary & McMd::SystemInterface::boundary ( ) const

inlineprotected

Get the Boundary by reference.

Definition at line 224 of file SystemInterface.h.

Referenced by McMd::LinkPotentialImpl< Interaction >::addForces(), McMd::BondPotentialImpl< Interaction >::addForces(), McMd::MdEwaldPairPotentialImpl< Interaction >::addForces(), McMd::MdPairPotentialImpl< Interaction >::addForces(), McMd::DihedralPotentialImpl< Interaction >::addForces(), McMd::AnglePotentialImpl< Interaction >::addForces(), McMd::LinkPotentialImpl< Interaction >::atomEnergy(), McMd::BondPotentialImpl< Interaction >::atomEnergy(), McMd::McPairPotentialImpl< Interaction >::atomEnergy(), McMd::DihedralPotentialImpl< Interaction >::atomEnergy(), McMd::AnglePotentialImpl< Interaction >::atomEnergy(), McMd::McPairPotential::buildCellList(), McMd::MdPairPotential::buildPairList(), McMd::LinkPotentialImpl< Interaction >::computeEnergy(), McMd::BondPotentialImpl< Interaction >::computeEnergy(), McMd::McPairPotentialImpl< Interaction >::computeEnergy(), McMd::MdEwaldPairPotentialImpl< Interaction >::computeEnergy(), McMd::MdPairPotentialImpl< Interaction >::computeEnergy(), McMd::DihedralPotentialImpl< Interaction >::computeEnergy(), McMd::AnglePotentialImpl< Interaction >::computeEnergy(), McMd::MdEwaldPairPotentialImpl< Interaction >::computeStress(), McMd::DeformCommand::execute(), McMd::MdPairPotential::isPairListCurrent(), McMd::McPairPotentialImpl< Interaction >::moleculeEnergy(), and McMd::ExternalPotentialImpl< Interaction >::readParameters().

Simulation & McMd::SystemInterface::simulation ( ) const

inlineprotected

Get the parent Simulation by reference.

Definition at line 206 of file SystemInterface.h.

Referenced by McMd::ExternalPotentialImpl< Interaction >::addForces(), McMd::BondPotentialImpl< Interaction >::addForces(), McMd::DihedralPotentialImpl< Interaction >::addForces(), McMd::AnglePotentialImpl< Interaction >::addForces(), McMd::McPairPotential::buildCellList(), McMd::MdPairPotential::buildPairList(), McMd::ExternalPotentialImpl< Interaction >::computeEnergy(), McMd::BondPotentialImpl< Interaction >::computeEnergy(), McMd::DihedralPotentialImpl< Interaction >::computeEnergy(), McMd::AnglePotentialImpl< Interaction >::computeEnergy(), McMd::DeformCommand::execute(), isEmpty(), McMd::McPairPotentialImpl< Interaction >::loadParameters(), McMd::BondPotentialImpl< Interaction >::loadParameters(), McMd::AnglePotentialImpl< Interaction >::loadParameters(), McMd::ExternalPotentialImpl< Interaction >::loadParameters(), McMd::DihedralPotentialImpl< Interaction >::loadParameters(), McMd::MdEwaldPairPotentialImpl< Interaction >::loadParameters(), McMd::MdPairPotentialImpl< Interaction >::loadParameters(), nAtom(), McMd::McPairPotentialImpl< Interaction >::readParameters(), McMd::BondPotentialImpl< Interaction >::readParameters(), McMd::AnglePotentialImpl< Interaction >::readParameters(), McMd::ExternalPotentialImpl< Interaction >::readParameters(), McMd::DihedralPotentialImpl< Interaction >::readParameters(), McMd::LinkPotentialImpl< Interaction >::readParameters(), McMd::MdEwaldPairPotentialImpl< Interaction >::readParameters(), and McMd::MdPairPotentialImpl< Interaction >::readParameters().

int McMd::SystemInterface::nMolecule ( int  speciesId ) const

inlineprotected

Get the number of molecules of one Species in this SystemInterface.

Parameters

speciesId

integer Id for a Species.

Returns

number of molecules of specified Species in this SystemInterface.

Definition at line 233 of file SystemInterface.h.

Referenced by isEmpty(), and nAtom().

int McMd::SystemInterface::nAtom ( ) const

protected

Return the total number of atoms in this SystemInterface.

Definition at line 69 of file SystemInterface.cpp.

References Simp::Species::nAtom(), nMolecule(), McMd::Simulation::nSpecies(), simulation(), and McMd::Simulation::species().

bool McMd::SystemInterface::isEmpty ( ) const

protected

Is this an empty SystemInterface (i.e., one with no molecules) ?

Definition at line 58 of file SystemInterface.cpp.

References nMolecule(), McMd::Simulation::nSpecies(), and simulation().

void McMd::SystemInterface::begin ( int  speciesId, System::MoleculeIterator &  iterator  )

inlineprotected

Initialize an iterator for molecules of one species in this SystemInterface.

Parameters

speciesId	integer Id for the desired Species (input)
iterator	molecule iterator (output)

Definition at line 243 of file SystemInterface.h.

Referenced by McMd::ExternalPotentialImpl< Interaction >::addForces(), McMd::BondPotentialImpl< Interaction >::addForces(), McMd::DihedralPotentialImpl< Interaction >::addForces(), McMd::AnglePotentialImpl< Interaction >::addForces(), McMd::McPairPotential::buildCellList(), McMd::MdPairPotential::buildPairList(), McMd::ExternalPotentialImpl< Interaction >::computeEnergy(), McMd::BondPotentialImpl< Interaction >::computeEnergy(), McMd::DihedralPotentialImpl< Interaction >::computeEnergy(), McMd::AnglePotentialImpl< Interaction >::computeEnergy(), and McMd::DeformCommand::execute().

void McMd::SystemInterface::begin ( int  speciesId, System::ConstMoleculeIterator &  iterator  ) const

inlineprotected

Initialize a const iterator for molecules of one species in this SystemInterface.

Parameters

speciesId	integer Id for the desired Species (input)
iterator	molecule iterator (output)

Definition at line 253 of file SystemInterface.h.

bool McMd::SystemInterface::hasBonds ( ) const

inlineprotected

Does a bond potential exist?

Definition at line 263 of file SystemInterface.h.

Referenced by McMd::McSystemInterface::McSystemInterface(), and McMd::MdSystemInterface::MdSystemInterface().

bool McMd::SystemInterface::hasAngles ( ) const

inlineprotected

Does an angle potential exist?

Definition at line 271 of file SystemInterface.h.

References hasDihedrals(), hasExternal(), and hasLinks().

Referenced by McMd::McSystemInterface::McSystemInterface(), and McMd::MdSystemInterface::MdSystemInterface().

bool McMd::SystemInterface::hasDihedrals ( ) const

inlineprotected

Does a dihedral potential exist?

Definition at line 277 of file SystemInterface.h.

Referenced by hasAngles(), McMd::McSystemInterface::McSystemInterface(), and McMd::MdSystemInterface::MdSystemInterface().

bool McMd::SystemInterface::hasLinks ( ) const

inlineprotected

Does a link potential exist?

Definition at line 283 of file SystemInterface.h.

Referenced by hasAngles().

bool McMd::SystemInterface::hasExternal ( ) const

inlineprotected

Does an external potential exist?

Definition at line 289 of file SystemInterface.h.

Referenced by hasAngles(), McMd::McSystemInterface::McSystemInterface(), and McMd::MdSystemInterface::MdSystemInterface().

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

• SystemInterface.h
• SystemInterface.cpp