BALL::PeriodicBoundary Class Reference

#include <BALL/MOLMEC/COMMON/periodicBoundary.h>

Classes
struct	Default
	Default values. More...
struct	Option

Public Types
Type definitions
typedef std::pair< Size, Size >	AtomIndexPair
typedef std::vector < AtomIndexPair >	AtomIndexArray

Public Member Functions
Constructors and Destructors
	PeriodicBoundary ()
	PeriodicBoundary (const ForceField &force_field)
	PeriodicBoundary (const PeriodicBoundary &periodic_boundary)
virtual	~PeriodicBoundary ()
Assignment
PeriodicBoundary &	operator= (const PeriodicBoundary &periodic_boundary)
virtual void	clear ()
Setup Methods
bool	setup ()
Size	generateMoleculesVector ()
Accessors
void	enable ()
	Enable periodic boundary conditions. More...
void	disable ()
	Disable periodic boundary conditions. More...
SimpleBox3	getBox () const
void	setBox (const SimpleBox3 &box)
Size	addSolvent (const String &filename)
Size	removeSolvent ()
Predicates
bool	isEnabled () const
Periodic boundary methods
void	updateMolecules ()

Public Attributes
Variables
Options *	options

Private Attributes
ForceField *	force_field_
bool	enabled_
SimpleBox3	box_
AtomIndexArray	molecules_

Detailed Description

Periodic boundary class for force field simulations. Molecular Mechanics: class representing periodic boundary conditions.

Definition at line 34 of file periodicBoundary.h.

Member Typedef Documentation

typedef std::vector<AtomIndexPair> BALL::PeriodicBoundary::AtomIndexArray

Definition at line 48 of file periodicBoundary.h.

typedef std::pair<Size, Size> BALL::PeriodicBoundary::AtomIndexPair

Definition at line 45 of file periodicBoundary.h.

Constructor & Destructor Documentation

BALL::PeriodicBoundary::PeriodicBoundary

(

)

Default constructor.

BALL::PeriodicBoundary::PeriodicBoundary

(

const ForceField &

force_field

)

Constructor.

BALL::PeriodicBoundary::PeriodicBoundary

(

const PeriodicBoundary &

periodic_boundary

)

Copy constructor

virtual BALL::PeriodicBoundary::~PeriodicBoundary ( )

virtual

Destructor.

Member Function Documentation

Size BALL::PeriodicBoundary::addSolvent

(

const String &

filename

)

Fill the defined box with a solvent. This method fills the defined box with solvent molecules. If no box is defined, no solvent is added. The neccessary solvent box template is either taken from the options (solvent_file) or a default is assumed.

This method replicates the solvent box starting at the box origin in all three dimensions and removes all solvent molecules that are within solvent_distance of a solute molecule or outside the periodic box.

To ensure periodicity, our SimpleBox instance might be resized to an integral multiple of the spacing of the periodic solvent box. The method returns the number of inserted solvent molecules. All solvent molecules are marked as such by setting their property Molecule::PROPERTY__PERIODIC_BOX_SOLVENT .

See Also

removeSolvent

virtual void BALL::PeriodicBoundary::clear ( )

virtual

Clear method

void BALL::PeriodicBoundary::disable

(

)

Disable periodic boundary conditions.

void BALL::PeriodicBoundary::enable

(

)

Enable periodic boundary conditions.

Size BALL::PeriodicBoundary::generateMoleculesVector

(

)

Generate the vector of molecules of the system

SimpleBox3 BALL::PeriodicBoundary::getBox

(

)

const

Retrieve the box dimensions.

bool BALL::PeriodicBoundary::isEnabled

(

)

const

Returns true if the periodic boundary is enabled

See Also

enable

disable

PeriodicBoundary& BALL::PeriodicBoundary::operator=

(

const PeriodicBoundary &

periodic_boundary

)

Assignment operator.

Size BALL::PeriodicBoundary::removeSolvent

(

)

Removes all solvent molecules This method removes all molecules that have the property Molecule::PROPERTY__PERIODIC_BOX_SOLVENT set from the force field's system. The number of removed solvent molecules is returned.

See Also

addSolvent

void BALL::PeriodicBoundary::setBox

(

const SimpleBox3 &

box

)

Set the box dimensions. The box dimensions are additionally stored in options using keys lower and upper .

bool BALL::PeriodicBoundary::setup

(

)

Sets up the periodic box

void BALL::PeriodicBoundary::updateMolecules

(

)

Checks which molecules are inside the box. If the center of mass of a molecule leaves the box, it is inserted on the other side.

Member Data Documentation

SimpleBox3 BALL::PeriodicBoundary::box_

private

Definition at line 264 of file periodicBoundary.h.

bool BALL::PeriodicBoundary::enabled_

private

Definition at line 261 of file periodicBoundary.h.

ForceField* BALL::PeriodicBoundary::force_field_

private

Definition at line 258 of file periodicBoundary.h.

AtomIndexArray BALL::PeriodicBoundary::molecules_

private

Definition at line 267 of file periodicBoundary.h.

Options* BALL::PeriodicBoundary::options

Periodic Boundary options. This is usually a pointer to the options of the force field the PeriodicBoundary object is contained in.

Definition at line 245 of file periodicBoundary.h.