BALL::AmberNonBonded Class Reference
[AMBER Force Field.]

#include <BALL/MOLMEC/AMBER/amberNonBonded.h>

Inheritance diagram for BALL::AmberNonBonded:

Public Member Functions
Constructors and Destructors

	AmberNonBonded ()
	AmberNonBonded (ForceField &force_field)
	AmberNonBonded (const AmberNonBonded &amber_non_bonded)
virtual	~AmberNonBonded ()


const AmberNonBonded &	operator= (const AmberNonBonded &anb)
virtual void	clear ()


bool	operator== (const AmberNonBonded &anb)
Setup Methods

virtual bool	setup () throw (Exception::TooManyErrors)
Accessors

virtual double	updateEnergy ()
virtual void	updateForces ()
virtual void	update () throw (Exception::TooManyErrors)
virtual double	getElectrostaticEnergy () const
virtual double	getVdwEnergy () const
Neighbourhood and Parameter calculations

virtual MolmecSupport::PairListAlgorithmType	determineMethodOfAtomPairGeneration ()
virtual void	buildVectorOfNonBondedAtomPairs (const std::vector< std::pair< Atom , Atom > > &atom_vector, const LennardJones &lennard_jones, const Potential1210 &hydrogen_bond) throw (Exception::TooManyErrors)
Protected Attributes
double	electrostatic_energy_
double	vdw_energy_
Private Attributes
vector< LennardJones::Data >	non_bonded_
vector< char >	is_hydrogen_bond_
Size	number_of_1_4_
Size	number_of_h_bonds_
double	cut_off_
double	cut_off_vdw_
double	cut_on_vdw_
double	cut_off_electrostatic_
double	cut_on_electrostatic_
double	inverse_distance_off_on_vdw_3_
double	inverse_distance_off_on_electrostatic_3_
double	scaling_vdw_1_4_
double	scaling_electrostatic_1_4_
bool	use_dist_depend_dielectric_
MolmecSupport::PairListAlgorithmType	algorithm_type_
LennardJones	van_der_waals_
Potential1210	hydrogen_bond_

Detailed Description

Amber NonBonded (VdW + Electrostatic) component

Definition at line 36 of file amberNonBonded.h.

Constructor & Destructor Documentation

BALL::AmberNonBonded::AmberNonBonded ( )

Default constructor.

BALL::AmberNonBonded::AmberNonBonded ( ForceField & force_field )

Constructor.

BALL::AmberNonBonded::AmberNonBonded ( const AmberNonBonded & amber_non_bonded )

Copy constructor

virtual BALL::AmberNonBonded::~AmberNonBonded ( ) [virtual]

Destructor.

Member Function Documentation

virtual void BALL::AmberNonBonded::buildVectorOfNonBondedAtomPairs	(	const std::vector< std::pair< Atom , Atom > > &	atom_vector,
		const LennardJones &	lennard_jones,
		const Potential1210 &	hydrogen_bond
	)			throw (Exception::TooManyErrors) `[virtual]`

Build a vector of non-bonded atom pairs with the vdw parameters

virtual void BALL::AmberNonBonded::clear ( ) [virtual]

Clear method

virtual MolmecSupport::PairListAlgorithmType BALL::AmberNonBonded::determineMethodOfAtomPairGeneration ( ) [virtual]

Computes the most efficient way to calculate the non-bonded atom pairs

virtual double BALL::AmberNonBonded::getElectrostaticEnergy ( ) const [virtual]

Return the electrostatic energy.

virtual double BALL::AmberNonBonded::getVdwEnergy ( ) const [virtual]

Return the Van-der-Waals energy.

const AmberNonBonded& BALL::AmberNonBonded::operator= ( const AmberNonBonded & anb )

Assignment Assignment operator

bool BALL::AmberNonBonded::operator== ( const AmberNonBonded & anb )

Predicates Equality operator

virtual bool BALL::AmberNonBonded::setup ( ) throw (Exception::TooManyErrors) [virtual]

Setup method.

Reimplemented from BALL::ForceFieldComponent.

virtual void BALL::AmberNonBonded::update ( ) throw (Exception::TooManyErrors) [virtual]

Update the pair list. This method is called by the force field whenever ForceField::update is called. It is used to recalculate the nonbonded pair list.

Reimplemented from BALL::ForceFieldComponent.

virtual double BALL::AmberNonBonded::updateEnergy ( ) [virtual]

Calculates and returns the component's energy.

Reimplemented from BALL::ForceFieldComponent.

virtual void BALL::AmberNonBonded::updateForces ( ) [virtual]

Calculates and returns the component's forces.

Reimplemented from BALL::ForceFieldComponent.