Class Berendsen
java.lang.Object
ffx.algorithms.dynamics.thermostats.Thermostat
ffx.algorithms.dynamics.thermostats.Berendsen
Thermostat a molecular dynamics trajectory to an external bath using the Berendsen weak-coupling
thermostat.
- Author:
- Michael J. Schnieders
- See Also:
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Field Summary
Fields inherited from class ffx.algorithms.dynamics.thermostats.Thermostat
constraints, degreesOfFreedom, kT, name, random, state, type
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Constructor Summary
ConstructorDescriptionBerendsen
(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 TypeMethodDescriptionvoid
fullStep
(double dt) The full-step temperature correction.double
getTau()
Getter for the fieldtau
.void
halfStep
(double dt) The half-step temperature correction.void
setTau
(double tau) Setter for the fieldtau
.toString()
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
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Constructor Details
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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).
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Berendsen
public Berendsen(SystemState state, Potential.VARIABLE_TYPE[] type, double targetTemperature, double tau, List<Constraint> constraints) -
Berendsen
Constructor for Berendsen.- Parameters:
state
- The MDState to operate on.type
- The VARIABLE_TYPE of each variable.targetTemperature
- The target temperatures.
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Method Details
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fullStep
public void fullStep(double dt) The full-step temperature correction.Full step velocity modification.
- Specified by:
fullStep
in classThermostat
- Parameters:
dt
- a double.
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getTau
public double getTau()Getter for the fieldtau
.- Returns:
- a double.
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setTau
public void setTau(double tau) Setter for the fieldtau
.- Parameters:
tau
- a double.
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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 classThermostat
- Parameters:
dt
- a double.
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toThermostatString
Add Thermostat details to the kinetic energy and temperature details.- Returns:
- Description of the thermostat, kinetic energy and temperature.
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toString
- Overrides:
toString
in classThermostat
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