System Class Reference

This class represents a molecular system. More...

#include <System.h>

Classes
class	ConstraintInfo
	This is an internal class used to record information about a constraint.
Public Member Functions
	System ()
	Create a new System.
	~System ()
int	getNumParticles () const
	Get the number of particles in this System.
int	addParticle (double mass)
	Add a particle to the System.
double	getParticleMass (int index) const
	Get the mass (in atomic mass units) of a particle.
void	setParticleMass (int index, double mass)
	Set the mass (in atomic mass units) of a particle.
int	getNumConstraints () const
	Get the number of distance constraints in this System.
int	addConstraint (int particle1, int particle2, double distance)
	Add a constraint to the System.
void	getConstraintParameters (int index, int &particle1, int &particle2, double &distance) const
	Get the parameters defining a distance constraint.
void	setConstraintParameters (int index, int particle1, int particle2, double distance)
	Set the parameters defining a distance constraint.
int	addForce (Force *force)
	Add a Force to the System.
int	getNumForces () const
	Get the number of Force objects that have been added to the System.
const Force &	getForce (int index) const
	Get a const reference to one of the Forces in this System.
Force &	getForce (int index)
	Get a writable reference to one of the Forces in this System.
void	getPeriodicBoxVectors (Vec3 &a, Vec3 &b, Vec3 &c) const
	Get the vectors which define the axes of the periodic box (measured in nm).
void	setPeriodicBoxVectors (Vec3 a, Vec3 b, Vec3 c)
	Set the vectors which define the axes of the periodic box (measured in nm).

Detailed Description

This class represents a molecular system.

The definition of a System involves four elements:

The set of particles in the system
The forces acting on them
Pairs of particles whose separation should be constrained to a fixed value
For periodic systems, the dimensions of the periodic box

The particles and constraints are defined directly by the System object, while forces are defined by objects that extend the Force class. After creating a System, call addParticle() once for each particle, addConstraint() for each constraint, and addForce() for each Force.

Constructor & Destructor Documentation

System ( )

Create a new System.

~System ( )

Member Function Documentation

int addConstraint	(	int	particle1,
		int	particle2,
		double	distance
	)

Add a constraint to the System.

Parameters:

	particle1	the index of the first particle involved in the constraint
	particle2	the index of the second particle involved in the constraint
	distance	the required distance between the two particles, measured in nm

Returns:: the index of the constraint that was added

int addForce ( Force * force ) [inline]

Add a Force to the System.

The Force should have been created on the heap with the "new" operator. The System takes over ownership of it, and deletes the Force when the System itself is deleted.

Parameters:

force

a pointer to the Force object to be added

Returns:: the index within the System of the Force that was added

int addParticle ( double mass ) [inline]

Add a particle to the System.

Parameters:

mass

the mass of the particle (in atomic mass units)

Returns:: the index of the particle that was added

void getConstraintParameters	(	int	index,
		int &	particle1,
		int &	particle2,
		double &	distance
	)			const

Get the parameters defining a distance constraint.

Parameters:

	index	the index of the constraint for which to get parameters
	particle1	the index of the first particle involved in the constraint
	particle2	the index of the second particle involved in the constraint
	distance	the required distance between the two particles, measured in nm

Force& getForce ( int index ) [inline]

Get a writable reference to one of the Forces in this System.

Parameters:

index

the index of the Force to get

const Force& getForce ( int index ) const [inline]

Get a const reference to one of the Forces in this System.

Parameters:

index

the index of the Force to get

int getNumConstraints ( ) const [inline]

Get the number of distance constraints in this System.

int getNumForces ( ) const [inline]

Get the number of Force objects that have been added to the System.

int getNumParticles ( ) const [inline]

Get the number of particles in this System.

double getParticleMass ( int index ) const [inline]

Get the mass (in atomic mass units) of a particle.

Parameters:

index

the index of the particle for which to get the mass

void getPeriodicBoxVectors	(	Vec3 &	a,
		Vec3 &	b,
		Vec3 &	c
	)			const

Get the vectors which define the axes of the periodic box (measured in nm).

These will affect any Force added to the System that uses periodic boundary conditions.

Currently, only rectangular boxes are supported. This means that a, b, and c must be aligned with the x, y, and z axes respectively. Future releases may support arbitrary triclinic boxes.

Parameters:

	a	on exit, this contains the vector defining the first edge of the periodic box
	b	on exit, this contains the vector defining the second edge of the periodic box
	c	on exit, this contains the vector defining the third edge of the periodic box

void setConstraintParameters	(	int	index,
		int	particle1,
		int	particle2,
		double	distance
	)

Set the parameters defining a distance constraint.

Parameters:

	index	the index of the constraint for which to set parameters
	particle1	the index of the first particle involved in the constraint
	particle2	the index of the second particle involved in the constraint
	distance	the required distance between the two particles, measured in nm

void setParticleMass	(	int	index,
		double	mass
	)			`[inline]`

Set the mass (in atomic mass units) of a particle.

Parameters:

	index	the index of the particle for which to set the mass
	mass	the mass of the particle

void setPeriodicBoxVectors	(	Vec3	a,
		Vec3	b,
		Vec3	c
	)

Set the vectors which define the axes of the periodic box (measured in nm).

These will affect any Force added to the System that uses periodic boundary conditions.

Currently, only rectangular boxes are supported. This means that a, b, and c must be aligned with the x, y, and z axes respectively. Future releases may support arbitrary triclinic boxes.

Parameters:

	a	the vector defining the first edge of the periodic box
	b	the vector defining the second edge of the periodic box
	c	the vector defining the third edge of the periodic box

The documentation for this class was generated from the following file:

System.h

System Class Reference

Classes

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation