Package ffx.algorithms.dynamics.thermostats

Class Berendsen

java.lang.Object

ffx.algorithms.dynamics.thermostats.Thermostat

ffx.algorithms.dynamics.thermostats.Berendsen

public class Berendsen
extends Thermostat

Thermostat a molecular dynamics trajectory to an external bath using the Berendsen weak-coupling thermostat.

Author:

Michael J. Schnieders

See Also:

• H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola and J. R. Hauk, "Molecular Dynamics with Coupling to an External Bath", Journal of Chemical Physics, 81, 3684-3690 (1984)

Field Summary

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

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

Constructor Summary

Constructors

Constructor	Description
Berendsen(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature)	Constructor for Berendsen.
Berendsen(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature, double tau)	Constructor for Berendsen.
Berendsen(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	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, setRandomSeed, setRemoveCenterOfMassMotion, setTargetTemperature

Methods inherited from class java.lang.Object

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

Constructor Details

Berendsen

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

Constructor for Berendsen.

Parameters:

type - The VARIABLE_TYPE of each variable.

targetTemperature - The target temperatures.

tau - Berendsen thermostat time constant (psec).

Berendsen

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

Berendsen

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

Constructor for Berendsen.

Parameters:

state - The MDState to operate on.

type - The VARIABLE_TYPE of each variable.

targetTemperature - The target temperatures.

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 Berendsen method at the half-step.

Specified by:

halfStep in class Thermostat

Parameters:

dt - a double.

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