BALL  1.5.0
Classes | List of all members
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, SizeAtomIndexPair
 
typedef std::vector< AtomIndexPairAtomIndexArray
 

Public Member Functions

Constructors and Destructors <br>
 PeriodicBoundary ()
 
 PeriodicBoundary (const ForceField &force_field)
 
 PeriodicBoundary (const PeriodicBoundary &periodic_boundary)
 
virtual ~PeriodicBoundary ()
 
Assignment
PeriodicBoundaryoperator= (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 <br>
bool isEnabled () const
 
Periodic boundary methods
void updateMolecules ()
 

Variables

Optionsoptions
 

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

◆ AtomIndexArray

Definition at line 48 of file periodicBoundary.h.

◆ AtomIndexPair

Definition at line 45 of file periodicBoundary.h.

Constructor & Destructor Documentation

◆ PeriodicBoundary() [1/3]

BALL::PeriodicBoundary::PeriodicBoundary ( )

Default constructor.

◆ PeriodicBoundary() [2/3]

BALL::PeriodicBoundary::PeriodicBoundary ( const ForceField force_field)

Constructor.

◆ PeriodicBoundary() [3/3]

BALL::PeriodicBoundary::PeriodicBoundary ( const PeriodicBoundary periodic_boundary)

Copy constructor

◆ ~PeriodicBoundary()

virtual BALL::PeriodicBoundary::~PeriodicBoundary ( )
virtual

Destructor.

Member Function Documentation

◆ addSolvent()

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

◆ clear()

virtual void BALL::PeriodicBoundary::clear ( )
virtual

Clear method

◆ disable()

void BALL::PeriodicBoundary::disable ( )

Disable periodic boundary conditions.

◆ enable()

void BALL::PeriodicBoundary::enable ( )

Enable periodic boundary conditions.

◆ generateMoleculesVector()

Size BALL::PeriodicBoundary::generateMoleculesVector ( )

Generate the vector of molecules of the system

◆ getBox()

SimpleBox3 BALL::PeriodicBoundary::getBox ( ) const

Retrieve the box dimensions.

◆ isEnabled()

bool BALL::PeriodicBoundary::isEnabled ( ) const

Returns true if the periodic boundary is enabled

See also
enable
disable

◆ operator=()

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

Assignment operator.

◆ removeSolvent()

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

◆ setBox()

void BALL::PeriodicBoundary::setBox ( const SimpleBox3 box)

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

◆ setup()

bool BALL::PeriodicBoundary::setup ( )

Sets up the periodic box

◆ updateMolecules()

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

◆ options

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.