BrownianIntegrator Class Reference

This is an Integrator which simulates a System using Brownian dynamics. More...

#include <BrownianIntegrator.h>

Inheritance diagram for BrownianIntegrator:

Public Member Functions
	BrownianIntegrator (double temperature, double frictionCoeff, double stepSize)
	Create a BrownianIntegrator. More...
double	getTemperature () const
	Get the temperature of the heat bath (in Kelvin). More...
void	setTemperature (double temp)
	Set the temperature of the heat bath (in Kelvin). More...
double	getFriction () const
	Get the friction coefficient which determines how strongly the system is coupled to the heat bath (in inverse ps). More...
void	setFriction (double coeff)
	Set the friction coefficient which determines how strongly the system is coupled to the heat bath (in inverse ps). More...
int	getRandomNumberSeed () const
	Get the random number seed. More...
void	setRandomNumberSeed (int seed)
	Set the random number seed. More...
void	step (int steps)
	Advance a simulation through time by taking a series of time steps. More...
Public Member Functions inherited from Integrator
	Integrator ()
virtual	~Integrator ()
double	getStepSize () const
	Get the size of each time step, in picoseconds. More...
void	setStepSize (double size)
	Set the size of each time step, in picoseconds. More...
double	getConstraintTolerance () const
	Get the distance tolerance within which constraints are maintained, as a fraction of the constrained distance. More...
void	setConstraintTolerance (double tol)
	Set the distance tolerance within which constraints are maintained, as a fraction of the constrained distance. More...

Protected Member Functions
void	initialize (ContextImpl &context)
	This will be called by the Context when it is created. More...
void	cleanup ()
	This will be called by the Context when it is destroyed to let the Integrator do any necessary cleanup. More...
std::vector< std::string >	getKernelNames ()
	Get the names of all Kernels used by this Integrator. More...
double	computeKineticEnergy ()
	Compute the kinetic energy of the system at the current time. More...
Protected Member Functions inherited from Integrator
virtual void	stateChanged (State::DataType changed)
	This will be called by the Context when the user modifies aspects of the context state, such as positions, velocities, or parameters. More...

Additional Inherited Members
Protected Attributes inherited from Integrator
ContextImpl *	context
Context *	owner

Detailed Description

This is an Integrator which simulates a System using Brownian dynamics.

Constructor & Destructor Documentation

BrownianIntegrator	(	double	temperature,
		double	frictionCoeff,
		double	stepSize
	)

Create a BrownianIntegrator.

Parameters

temperature	the temperature of the heat bath (in Kelvin)
frictionCoeff	the friction coefficient which couples the system to the heat bath, measured in 1/ps
stepSize	the step size with which to integrate the system (in picoseconds)

Member Function Documentation

void cleanup ( )

protectedvirtual

This will be called by the Context when it is destroyed to let the Integrator do any necessary cleanup.

It will also get called again if the application calls reinitialize() on the Context.

Reimplemented from Integrator.

double computeKineticEnergy ( )

protectedvirtual

Compute the kinetic energy of the system at the current time.

Implements Integrator.

double getFriction ( ) const

inline

Get the friction coefficient which determines how strongly the system is coupled to the heat bath (in inverse ps).

Returns

the friction coefficient, measured in 1/ps

std::vector<std::string> getKernelNames ( )

protectedvirtual

Get the names of all Kernels used by this Integrator.

Implements Integrator.

int getRandomNumberSeed ( ) const

inline

Get the random number seed.

See setRandomNumberSeed() for details.

double getTemperature ( ) const

inline

Get the temperature of the heat bath (in Kelvin).

Returns

the temperature of the heat bath (in Kelvin).

void initialize ( ContextImpl &  context )

protectedvirtual

This will be called by the Context when it is created.

It informs the Integrator of what context it will be integrating, and gives it a chance to do any necessary initialization. It will also get called again if the application calls reinitialize() on the Context.

Implements Integrator.

void setFriction ( double  coeff )

inline

Set the friction coefficient which determines how strongly the system is coupled to the heat bath (in inverse ps).

Parameters

coeff

the friction coefficient, measured in 1/ps

void setRandomNumberSeed ( int  seed )

inline

Set the random number seed.

The precise meaning of this parameter is undefined, and is left up to each Platform to interpret in an appropriate way. It is guaranteed that if two simulations are run with different random number seeds, the sequence of random forces will be different. On the other hand, no guarantees are made about the behavior of simulations that use the same seed. In particular, Platforms are permitted to use non-deterministic algorithms which produce different results on successive runs, even if those runs were initialized identically.

If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context is created from this Force. This is done to ensure that each Context receives unique random seeds without you needing to set them explicitly.

void setTemperature ( double  temp )

inline

Set the temperature of the heat bath (in Kelvin).

Parameters

temp	the temperature of the heat bath, measured in Kelvin.

void step ( int  steps )

virtual

Advance a simulation through time by taking a series of time steps.

Parameters

steps

the number of time steps to take

Implements Integrator.

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

• BrownianIntegrator.h