System Class Reference

This class represents a molecular system. More...

#include <System.h>

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.
void	setVirtualSite (int index, VirtualSite *virtualSite)
	Set a particle to be a virtual site.
bool	isVirtualSite (int index) const
	Get whether a particle is a VirtualSite.
const VirtualSite &	getVirtualSite (int index) const
	Get VirtualSite object for 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	getDefaultPeriodicBoxVectors (Vec3 &a, Vec3 &b, Vec3 &c) const
	Get the default values of the vectors defining the axes of the periodic box (measured in nm).
void	setDefaultPeriodicBoxVectors (const Vec3 &a, const Vec3 &b, const Vec3 &c)
	Set the default values of the vectors defining 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:

1. The set of particles in the system
2. The forces acting on them
3. Pairs of particles whose separation should be constrained to a fixed value
4. 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.

In addition, particles may be designated as "virtual sites". These are particles whose positions are computed automatically based on the positions of other particles. To define a virtual site, call setVirtualSite(), passing in a VirtualSite object that defines the rules for computing its position.

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.

Particles whose mass is 0 cannot participate in constraints.

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.

If the mass is 0, Integrators will ignore the particle and not modify its position or velocity. This is most often used for virtual sites, but can also be used as a way to prevent a particle from moving.

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

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

Get the default values of the vectors defining the axes of the periodic box (measured in nm).

Any newly created Context will have its box vectors set to these. They 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

const Force& getForce

(

int

index

)

const

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

Parameters

index

the index of the Force to get

Force& getForce

(

int

index

)

Get a writable 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

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

If the mass is 0, Integrators will ignore the particle and not modify its position or velocity. This is most often used for virtual sites, but can also be used as a way to prevent a particle from moving.

Parameters

index

the index of the particle for which to get the mass

const VirtualSite& getVirtualSite

(

int

index

)

const

Get VirtualSite object for a particle.

If the particle is not a virtual site, this throws an exception.

Parameters

index

the index of the particle to get

bool isVirtualSite ( int  index ) const

inline

Get whether a particle is a VirtualSite.

Parameters

index

the index of the particle to check

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

Set the parameters defining a distance constraint.

Particles whose mass is 0 cannot participate in constraints.

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 setDefaultPeriodicBoxVectors	(	const Vec3 &	a,
		const Vec3 &	b,
		const Vec3 &	c
	)

Set the default values of the vectors defining the axes of the periodic box (measured in nm).

Any newly created Context will have its box vectors set to these. They 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

void setParticleMass	(	int	index,
		double	mass
	)

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

If the mass is 0, Integrators will ignore the particle and not modify its position or velocity. This is most often used for virtual sites, but can also be used as a way to prevent a particle from moving.

Parameters

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

void setVirtualSite	(	int	index,
		VirtualSite *	virtualSite
	)

Set a particle to be a virtual site.

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

Parameters

index	the index of the particle that should be treated as a virtual site
virtualSite	a pointer to the VirtualSite object describing it

---

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

• System.h