BALL::PeriodicBoundary Class Reference
[General Force Field Classes.]

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

List of all members.

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.
void	disable ()
	Disable periodic boundary conditions.
SimpleBox3	getBox () const
void	setBox (const SimpleBox3 &box)
Size	addSolvent (const String &filename) const
Size	removeSolvent () const
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_

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Detailed Description

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

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Member Typedef Documentation

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

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

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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.

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Member Function Documentation

Size BALL::PeriodicBoundary::addSolvent

(

const String &

filename

)

const

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.

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

(

)

const

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.

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Member Data Documentation

SimpleBox3 BALL::PeriodicBoundary::box_ [private]

bool BALL::PeriodicBoundary::enabled_ [private]

ForceField* BALL::PeriodicBoundary::force_field_ [private]

AtomIndexArray BALL::PeriodicBoundary::molecules_ [private]

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.