PeriodicBoundary Class Reference
[General Force Field Classes.]

Periodic boundary class for force field simulations. More...

#include <periodicBoundary.h>

List of all members.

Public Types
Type definitions
typedef std::pair< Size, Size >	AtomIndexPair
typedef std::vector< AtomIndexPair >	AtomIndexArray
Public Member Functions
Constructors and Destructors
	PeriodicBoundary ()
	Default constructor.
	PeriodicBoundary (const ForceField &force_field)
	Constructor.
	PeriodicBoundary (const PeriodicBoundary &periodic_boundary)
	Copy constructor.
virtual	~PeriodicBoundary ()
	Destructor.
Assignment
PeriodicBoundary &	operator= (const PeriodicBoundary &periodic_boundary)
	Assignment operator.
virtual void	clear () throw ()
	Clear method.
Setup Methods
bool	setup ()
	Sets up the periodic box.
Size	generateMoleculesVector ()
	Generate the vector of molecules of the system.
Accessors
void	enable ()
	Enable periodic boundary conditions.
void	disable ()
	Disable periodic boundary conditions.
SimpleBox3	getBox () const
	Retrieve the box dimensions.
void	setBox (const SimpleBox3 &box)
	Set the box dimensions.
Size	addSolvent (const String &filename) const
	Fill the defined box with a solvent.
Size	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.
Predicates
bool	isEnabled () const
	Returns true if the periodic boundary is enabled.
Periodic boundary methods
void	updateMolecules ()
	Checks which molecules are inside the box.
Public Attributes
Variables
Options *	options
	Periodic Boundary options.

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Detailed Description

Periodic boundary class for force field simulations.

Molecular Mechanics: class representing periodic boundary conditions.

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Constructor & Destructor Documentation

PeriodicBoundary::PeriodicBoundary (   )

Default constructor.

PeriodicBoundary::PeriodicBoundary (  const ForceField &  force_field  )

Constructor.

virtual PeriodicBoundary::~PeriodicBoundary (   )  [virtual]

Destructor.

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Member Function Documentation

Size 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

SimpleBox3 PeriodicBoundary::getBox (   )  const

Retrieve the box dimensions.

bool PeriodicBoundary::isEnabled (   )  const

Returns true if the periodic boundary is enabled. See also: enable disable

PeriodicBoundary& PeriodicBoundary::operator= (  const PeriodicBoundary &  periodic_boundary  )

Assignment operator.

Size 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 PeriodicBoundary::setBox (  const SimpleBox3 &  box  )

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

void 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

Options* PeriodicBoundary::options

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