This Integrator simulates systems that include Drude particles. More...

#include <DrudeLangevinIntegrator.h>

Inheritance diagram for DrudeLangevinIntegrator:

Public Member Functions
	DrudeLangevinIntegrator (double temperature, double frictionCoeff, double drudeTemperature, double drudeFrictionCoeff, double stepSize)
	Create a DrudeLangevinIntegrator. More...

double	getTemperature () const
	Get the temperature of the main heat bath (in Kelvin). More...

void	setTemperature (double temp)
	Set the temperature of the main heat bath (in Kelvin). More...

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

void	setFriction (double coeff)
	Set the friction coefficient which determines how strongly the system is coupled to the main heat bath (in inverse ps). More...

double	getDrudeTemperature () const
	Get the temperature of the heat bath applied to internal coordinates of Drude particles (in Kelvin). More...

void	setDrudeTemperature (double temp)
	Set the temperature of the heat bath applied to internal coordinates of Drude particles (in Kelvin). More...

double	getDrudeFriction () const
	Get the friction coefficient which determines how strongly the internal coordinates of Drude particles are coupled to the heat bath (in inverse ps). More...

void	setDrudeFriction (double coeff)
	Set the friction coefficient which determines how strongly the internal coordinates of Drude particles are 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...

void	stateChanged (State::DataType changed)
	When the user modifies the state, we need to mark that the forces need to be recalculated. 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...

Additional Inherited Members
Protected Attributes inherited from Integrator
ContextImpl *	context

Context *	owner

Detailed Description

This Integrator simulates systems that include Drude particles.

It applies two different Langevin thermostats to different parts of the system. The first is applied to ordinary particles (ones that are not part of a Drude particle pair), as well as to the center of mass of each Drude particle pair. A second thermostat, typically with a much lower temperature, is applied to the relative internal displacement of each pair.

This Integrator requires the System to include a DrudeForce, which it uses to identify the Drude particles.

Constructor & Destructor Documentation

DrudeLangevinIntegrator	(	double	temperature,
		double	frictionCoeff,
		double	drudeTemperature,
		double	drudeFrictionCoeff,
		double	stepSize
	)

Create a DrudeLangevinIntegrator.

Parameters

temperature	the temperature of the main heat bath (in Kelvin)
frictionCoeff	the friction coefficient which couples the system to the main heat bath (in inverse picoseconds)
drudeTemperature	the temperature of the heat bath applied to internal coordinates of Drude particles (in Kelvin)
drudeFrictionCoeff	the friction coefficient which couples the system to the heat bath applied to internal coordinates of Drude particles (in inverse picoseconds)
stepSize	the step size with which to integrator 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 getDrudeFriction ( ) const

inline

Get the friction coefficient which determines how strongly the internal coordinates of Drude particles are coupled to the heat bath (in inverse ps).

Returns: the friction coefficient, measured in 1/ps

double getDrudeTemperature ( ) const

inline

Get the temperature of the heat bath applied to internal coordinates of Drude particles (in Kelvin).

Returns: the temperature of the heat bath, measured in Kelvin

double getFriction ( ) const

inline

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

Returns: the temperature of the heat bath, measured 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 setDrudeFriction ( double coeff )

inline

Set the friction coefficient which determines how strongly the internal coordinates of Drude particles are coupled to the heat bath (in inverse ps).

Parameters

coeff the friction coefficient, measured in 1/ps

void setDrudeTemperature ( double temp )

inline

Set the temperature of the heat bath applied to internal coordinates of Drude particles (in Kelvin).

Parameters

temp	the temperature of the heat bath, measured in Kelvin

void setFriction ( double coeff )

inline

Set the friction coefficient which determines how strongly the system is coupled to the main 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.

void setTemperature ( double temp )

inline

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

Parameters

temp	the temperature of the heat bath, measured in Kelvin

void stateChanged ( State::DataType changed )

protectedvirtual

When the user modifies the state, we need to mark that the forces need to be recalculated.

Reimplemented from Integrator.

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.

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

DrudeLangevinIntegrator.h

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation