NVT ensemble¶

Overview

Nose Hoover thermostat	`NoseHooverNVT`
Berendsen thermostat	`BerendsenNVT`
Andersen thermostat	`AndersenNVT`
Langevin dynamic thermostat	`LangevinNVT`
NVT for rigid body	`NVTRigid`
Langevin dynamic for rigid body	`LangevinNVTRigid`

Nose Hoover thermostat¶

class NoseHooverNVT(all_info, group, comp_info, T, tauT)¶

The constructor of a NVT NoseHoover thermostat object for a group of particles.

Parameters:

all_info (AllInfo) – The system information.
group (ParticleSet) – The group of particles.
comp_info (ComputeInfo) – The object of calculation of collective information.
T (float) – The temperature.
tauT (float) – The thermostat coupling.

setT(float T)¶: specifies the temperature with a constant value.

setT(Variant vT)¶: specifies the temperature with a defined varying value by time step.

Example:

group = gala.ParticleSet(all_info, 'all')
comp_info = gala.ComputeInfo(all_info, group)
nh = gala.NoseHooverNVT(all_info, group, comp_info, 1.0, 0.5)
app.add(nh)

Berendsen thermostat¶

class BerendsenNVT(all_info, group, comp_info, T, tauT)¶

The constructor of a NVT Berendsen thermostat object for a group of particles.

Parameters:

all_info (AllInfo) – The system information.
group (ParticleSet) – The group of particles.
comp_info (ComputeInfo) – The object of calculation of collective information.
T (float) – The temperature.
tauT (float) – The thermostat coupling parameter.

setT(float T)¶: specifies the temperature with a constant value.

setT(Variant vT)¶: specifies the temperature with a varying value by time steps.

Andersen thermostat¶

class AndersenNVT(all_info, group, T, gamma, seed)¶

The constructor of a NVT Andersen thermostat object for a group of particles.

Parameters:

all_info (AllInfo) – The system information.
group (ParticleSet) – The group of particles.
T (float) – The temperature.
gamma (float) – The collision frequency.
seed (int) – The seed of random number generator.

setT(float T)¶: specifies the temperature with a constant value.

setT(Variant vT)¶: specifies the temperature with a varying value by time steps.

Example:

an = gala.AndersenNVT(all_info,group,1.0,10.0, 12345)
app.add(an)

Langevin dynamic thermostat¶

Description:

The particles are integrated forward in time according to the Langevin equations of motion:

\[ \begin{align}\begin{aligned}m \frac{d\vec{v}}{dt} = \vec{F}_\mathrm{C} - \gamma \cdot \vec{v} + \vec{F}_\mathrm{R}\\\langle \vec{F}_\mathrm{R} \rangle = 0\\\langle |\vec{F}_\mathrm{R}|^2 \rangle = 2 d kT \gamma / \delta t\end{aligned}\end{align} \]

\(\gamma\) - gamma (unitless) - optional: defaults to 1.0

where \(\vec{F}_\mathrm{C}\) is the force on the particle from all potentials and constraint forces, \(\gamma\) is the drag coefficient, \(\vec{v}\) is the particle’s velocity, \(\vec{F}_\mathrm{R}\) is a uniform random force, and \(d\) is the dimensionality of the system (2 or 3). The magnitude of the random force is chosen via the fluctuation-dissipation theorem to be consistent with the specified drag and temperature, \(T\). When \(kT=0\), the random force \(\vec{F}_\mathrm{R}=0\).

class LangevinNVT(all_info, group, T, seed)¶

The constructor of a Langevin NVT thermostat object for a group of particles.

Parameters:

all_info (AllInfo) – The system information.
group (ParticleSet) – The group of particles.
T (float) – The temperature.
seed (int) – The seed of random number generator.

setGamma(float gamma)¶: specifies the gamma with a constant value.

setGamma(string type, float gamma)¶: specifies the gamma of a particle type.

setT(float T)¶: specifies the temperature with a constant value.

setT(Variant vT)¶: specifies the temperature with a varying value by time step.

Example:

group = gala.ParticleSet(all_info, 'all')
lnvt = gala.LangevinNVT(all_info, group, 1.0, 123)
app.add(lnvt)

NVT for rigid body¶

class NVTRigid(AllInfo all_info, ParticleSet group, float T, float tauT)¶

The constructor of a NVT thermostat object for rigid bodies.

Parameters:

all_info (AllInfo) – The system information.
group (ParticleSet) – The group of particles.
T (float) – The temperature.
tauT (float) – The thermostat coupling parameter.

setT(float T)¶: specifies the temperature with a fixed value.

setT(Variant vT)¶: pecifies the temperature with a varying value by time step.

Example:

bgroup = gala.ParticleSet(all_info, 'body')
rigidnvt = gala.NVTRigid(all_info, bgroup, 1.0, 10.0)
app.add(rigidnvt)

Langevin dynamic for rigid body¶

Please see Langevin dynamic thermostat for the theory.

class LangevinNVTRigid(all_info, group, T, seed)¶

The constructor of a Langevin NVT thermostat object for rigid bodies.

Parameters:

all_info (AllInfo) – The system information.
group (ParticleSet) – The group of particles.
T (float) – The temperature.
seed (int) – The seed of random number generator.

setGamma(float gamma)¶: specifies the gamma of Langevin method with a constant value.

setGamma(const std::string & type, float gamma)¶: specifies the gamma of Langevin method of a particle type.

setT(float T)¶: specifies the temperature with a constant value.

setT(Variant vT)¶: specifies the temperature with a varying value by time step.

Example:

bgroup = gala.ParticleSet(all_info, 'body')
lrigidnvt = gala.LangevinNVTRigid(all_info, bgroup, 1.0, 123)
app.add(lrigidnvt)