BALL::AmberNonBonded Class Reference

#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)
Public Member Functions inherited from BALL::ForceFieldComponent
	ForceFieldComponent ()
	ForceFieldComponent (ForceField &force_field)
	ForceFieldComponent (const ForceFieldComponent &force_field_component)
virtual	~ForceFieldComponent ()
ForceField *	getForceField () const
void	setForceField (ForceField &force_field)
void	setName (const String &name)
String	getName () const
bool	isEnabled () const
void	setEnabled (bool state)
virtual double	getEnergy () const

Protected Attributes
double	electrostatic_energy_
double	vdw_energy_
Protected Attributes inherited from BALL::ForceFieldComponent
ForceField *	force_field_
double	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

)

AssignmentAssignment operator

bool BALL::AmberNonBonded::operator==

(

const AmberNonBonded &

anb

)

PredicatesEquality 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.

Member Data Documentation

MolmecSupport::PairListAlgorithmType BALL::AmberNonBonded::algorithm_type_

private

Definition at line 245 of file amberNonBonded.h.

double BALL::AmberNonBonded::cut_off_

private

Definition at line 200 of file amberNonBonded.h.

double BALL::AmberNonBonded::cut_off_electrostatic_

private

Definition at line 212 of file amberNonBonded.h.

double BALL::AmberNonBonded::cut_off_vdw_

private

Definition at line 204 of file amberNonBonded.h.

double BALL::AmberNonBonded::cut_on_electrostatic_

private

Definition at line 216 of file amberNonBonded.h.

double BALL::AmberNonBonded::cut_on_vdw_

private

Definition at line 208 of file amberNonBonded.h.

double BALL::AmberNonBonded::electrostatic_energy_

protected

Definition at line 167 of file amberNonBonded.h.

Potential1210 BALL::AmberNonBonded::hydrogen_bond_

private

Definition at line 249 of file amberNonBonded.h.

double BALL::AmberNonBonded::inverse_distance_off_on_electrostatic_3_

private

Definition at line 226 of file amberNonBonded.h.

double BALL::AmberNonBonded::inverse_distance_off_on_vdw_3_

private

Definition at line 221 of file amberNonBonded.h.

vector<char> BALL::AmberNonBonded::is_hydrogen_bond_

private

Definition at line 188 of file amberNonBonded.h.

vector<LennardJones::Data> BALL::AmberNonBonded::non_bonded_

private

Definition at line 183 of file amberNonBonded.h.

Size BALL::AmberNonBonded::number_of_1_4_

private

Definition at line 192 of file amberNonBonded.h.

Size BALL::AmberNonBonded::number_of_h_bonds_

private

Definition at line 196 of file amberNonBonded.h.

double BALL::AmberNonBonded::scaling_electrostatic_1_4_

private

Definition at line 234 of file amberNonBonded.h.

double BALL::AmberNonBonded::scaling_vdw_1_4_

private

Definition at line 230 of file amberNonBonded.h.

bool BALL::AmberNonBonded::use_dist_depend_dielectric_

private

Definition at line 239 of file amberNonBonded.h.

LennardJones BALL::AmberNonBonded::van_der_waals_

private

Definition at line 247 of file amberNonBonded.h.

double BALL::AmberNonBonded::vdw_energy_

protected

Definition at line 171 of file amberNonBonded.h.