md.methods.thermostats#

Overview

`Berendsen`	The Berendsen thermostat.
`Bussi`	The Bussi-Donadio-Parrinello thermostat.
`MTTK`	The Nosé-Hoover thermostat.
`Thermostat`	Base thermostat object class.

Details

Provide classes for thermostatting simulations.

Classes are for use with hoomd.md.methods.ConstantVolume and hoomd.md.methods.ConstantPressure.

Important

Ensure that your initial condition includes non-zero particle velocities and angular momenta (when appropriate). The coupling between the thermostat and the velocities / angular momenta occurs via multiplication, so the thermostat cannot convert a zero velocity into a non-zero one except through particle collisions.

class hoomd.md.methods.thermostats.Berendsen(kT, tau)#

The Berendsen thermostat.

Parameters:

kT (hoomd.variant.variant_like) – Temperature of the simulation. \([\mathrm{energy}]\)
tau (float) – Thermostat time constant. \([\mathrm{time}]\)

Berendsen rescales the velocities of all particles on each time step. The rescaling is performed so that the difference in the current temperature from the set point decays exponentially:

\[\frac{dT_\mathrm{cur}}{dt} = \frac{T - T_\mathrm{cur}}{\tau}\]

Attention

Berendsen does not yield a proper canonical ensemble

See also

Berendsen et. al. 1984.

Example:

# NVT integration using Berendsen thermostat
dt = 0.005
berendsen = hoomd.md.methods.thermostats.Berendsen(kT=1.0, tau=dt*100)
nvt = hoomd.md.methods.ConstantVolume(filter=hoomd.filter.All(),
                                    thermostat=berendsen)
integrator = hoomd.md.Integrator(dt=dt, methods=[nvt])

kT#

Temperature of the simulation. \([energy]\)

Type:: hoomd.variant.variant_like

tau#

Time constant of thermostat. \([time]\)

Type:: float

class hoomd.md.methods.thermostats.Bussi(kT)#

The Bussi-Donadio-Parrinello thermostat.

Parameters:: kT (hoomd.variant.variant_like) – Temperature set point for the thermostat \([\mathrm{energy}]\).

Provides temperature control by rescaling the velocity by a factor taken from the canonical velocity distribution. On each timestep, velocities are rescaled by a factor \(\alpha=\sqrt{K_t / K}\), where \(K\) is the current kinetic energy, and \(K_t\) is chosen randomly from the distribution

\[P(K_t) \propto K_t^{N_f/2 - 1} \exp(-K_t / kT)\]

where \(N_f\) is the number of degrees of freedom thermalized.

See also

Bussi et. al. 2007.

Example:

# NVT integration using Bussi thermostat
bussi = hoomd.md.methods.thermostats.Bussi(kT=1.0)
nvt = hoomd.md.methods.ConstantVolume(filter=hoomd.filter.All(),
                                    thermostat=bussi)
integrator = hoomd.md.Integrator(dt=0.005, methods=[nvt])

kT#

Temperature set point for the thermostat \([\mathrm{energy}]\).

Type:: hoomd.variant.variant_like

class hoomd.md.methods.thermostats.MTTK(kT, tau)#

The Nosé-Hoover thermostat.

Produces temperature control through a Nosé-Hoover thermostat.

Parameters:

kT (hoomd.variant.variant_like) – Temperature set point for the thermostat \([\mathrm{energy}]\).
tau (float) – Coupling constant for the thermostat \([\mathrm{time}]\)

The translational thermostat has a momentum \(\xi\) and position \(\eta\). The rotational thermostat has momentum \(\xi_{\mathrm{rot}}\) and position \(\eta_\mathrm{rot}\). Access these quantities using translational_dof and rotational_dof.

Note

The coupling constant tau should be set within a reasonable range to avoid abrupt fluctuations in the kinetic temperature and to avoid long time to equilibration. The recommended value for most systems is \(\tau = 100 \delta t\).

Example:

# NVT integration using MTTK Nose-Hoover thermostat
dt = 0.005
MTTK = hoomd.md.methods.thermostats.Berendsen(kT=1.0, tau=dt*100)
nvt = hoomd.md.methods.ConstantVolume(filter=hoomd.filter.All(),
                                    thermostat=MTTK)
integrator = hoomd.md.Integrator(dt=dt, methods=[nvt])

kT#

Temperature set point for the thermostat \([\mathrm{energy}]\).

Type:: hoomd.variant.variant_like

tau#

Coupling constant for the thermostat \([\mathrm{time}]\)

Type:: float

translational_dof#

Additional degrees of freedom for the translational thermostat (\(\xi\), \(\eta\))

Type:: tuple[float, float]

rotational_dof#

Additional degrees of freedom for the rotational thermostat (\(\xi_\mathrm{rot}\), \(\eta_\mathrm{rot}\))

Type:: tuple[float, float]

property energy#

Energy the thermostat contributes to the Hamiltonian \([\mathrm{energy}]\).

(Loggable: category=”scalar”)

thermalize_dof()#

Set the thermostat momenta to random values.

thermalize_dof sets a random value for the momentum \(\xi\). When Integrator.integrate_rotational_dof is True, it also sets a random value for the rotational thermostat momentum \(\xi_{\mathrm{rot}}\). Call thermalize_dof to set a new random state for the thermostat.

Important

You must call Simulation.run before thermalize_dof. Call run(steps=0) to prepare a newly created hoomd.Simulation.

See also

State.thermalize_particle_momenta

class hoomd.md.methods.thermostats.Thermostat(kT)#: Base thermostat object class.

Note

Users should use the subclasses and not instantiate Thermostat directly.