Package ffx.algorithms.dynamics.thermostats

Class Bussi

java.lang.Object

ffx.algorithms.dynamics.thermostats.Thermostat

ffx.algorithms.dynamics.thermostats.Bussi

public class Bussi
extends Thermostat

Thermostat a molecular dynamics trajectory to an external bath using the Bussi, Donadio, and Parrinello method. This method is similar to Berendsen thermostat, but generates a canonical distribution.

Since:

1.0

Author:

Michael J. Schnieders

See Also:

• G. Bussi and M. Parrinello, "Stochastic Thermostats: Comparison of Local and Global Schemes", Computer Physics Communications, 179, 26-29 (2008)

Field Summary

Fields inherited from class ffx.algorithms.dynamics.thermostats.Thermostat

constraints, degreesOfFreedom, kT, name, random, state, type

Constructor Summary

Constructors

Constructor	Description
Bussi(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature)	Constructor for Bussi.
Bussi(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature, double tau)	Constructor for Bussi.
Bussi(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature, double tau, List<Constraint> constraints)

Method Summary

Modifier and Type	Method	Description
void	fullStep(double dt)	The full-step temperature correction.
double	getTau()	Getter for the field tau.
void	halfStep(double dt)	The half-step temperature correction.
void	setRandomSeed(long seed)	The setRandomSeed method is used to initialize the Random number generator to the same starting state, such that separate runs produce the same Maxwell-Boltzmann initial velocities. same
void	setTau(double tau)	Setter for the field tau.
String	toString()
String	toThermostatString()	Add Thermostat details to the kinetic energy and temperature details.

Methods inherited from class ffx.algorithms.dynamics.thermostats.Thermostat

centerOfMassMotion, computeKineticEnergy, getCurrentTemperature, getDegreesOfFreedom, getKineticEnergy, getRemoveCenterOfMassMotion, getTargetTemperature, log, logTemp, maxwell, maxwell, maxwellIndividual, parseThermostat, setQuiet, setRemoveCenterOfMassMotion, setTargetTemperature

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

Bussi

public Bussi(SystemState state,
 Potential.VARIABLE_TYPE[] type,
 double targetTemperature,
 double tau)

Constructor for Bussi.

Parameters:

state - The MDState to operate on.

type - the VARIABLE_TYPE of each variable.

targetTemperature - The target temperature.

tau - Bussi thermostat time constant (psec).

Bussi

public Bussi(SystemState state,
 Potential.VARIABLE_TYPE[] type,
 double targetTemperature,
 double tau,
 List<Constraint> constraints)

Bussi

public Bussi(SystemState state,
 Potential.VARIABLE_TYPE[] type,
 double targetTemperature)

Constructor for Bussi.

Parameters:

state - The MDState to operate on.

type - the VARIABLE_TYPE of each variable.

targetTemperature - a double.

Method Details

fullStep

public void fullStep(double dt)

The full-step temperature correction.

Full step velocity modification.

Specified by:

fullStep in class Thermostat

Parameters:

dt - a double.

getTau

public double getTau()

Getter for the field tau.

Returns:

a double.

setTau

public void setTau(double tau)

Setter for the field tau.

Parameters:

tau - a double.

halfStep

public void halfStep(double dt)

The half-step temperature correction.

No velocity modifications are made by the Bussi method at the half-step.

Specified by:

halfStep in class Thermostat

Parameters:

dt - a double.

setRandomSeed

public void setRandomSeed(long seed)

The setRandomSeed method is used to initialize the Random number generator to the same starting state, such that separate runs produce the same Maxwell-Boltzmann initial velocities. same

Initialize the Random number generator used to apply random forces to the particles.

Overrides:

setRandomSeed in class Thermostat

Parameters:

seed - The seed.

toThermostatString

public String toThermostatString()

Add Thermostat details to the kinetic energy and temperature details.

Returns:

Description of the thermostat, kinetic energy and temperature.

toString

public String toString()

Overrides:

toString in class Thermostat