BALL  1.4.1
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BALL::PeriodicBoundary Class Reference

#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, SizeAtomIndexPair
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
PeriodicBoundaryoperator= (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)
Size removeSolvent ()
Predicates
bool isEnabled () const
Periodic boundary methods
void updateMolecules ()

Public Attributes

Variables
Optionsoptions

Private Attributes

ForceFieldforce_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

Definition at line 48 of file periodicBoundary.h.

Definition at line 45 of file periodicBoundary.h.


Constructor & Destructor Documentation

Default constructor.

Constructor.

Copy constructor

Destructor.


Member Function Documentation

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

Disable periodic boundary conditions.

Enable periodic boundary conditions.

Generate the vector of molecules of the system

Retrieve the box dimensions.

Returns true if the periodic boundary is enabled

See also:
enable
disable
PeriodicBoundary& BALL::PeriodicBoundary::operator= ( const PeriodicBoundary periodic_boundary)

Assignment operator.

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

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

Sets up the periodic box

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

Definition at line 264 of file periodicBoundary.h.

Definition at line 261 of file periodicBoundary.h.

Definition at line 258 of file periodicBoundary.h.

Definition at line 267 of file periodicBoundary.h.

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.

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