md.update

Overview

ActiveRotationalDiffusion

Updater to introduce rotational diffusion with an active force.

ReversePerturbationFlow

Reverse Perturbation (Müller-Plathe) method to establish shear flow.

ZeroMomentum

Zeroes system momentum.

Details

Update particle properties.

When an updater is specified, it acts on the particle system each time step it is triggered to change its state.

class hoomd.md.update.ActiveRotationalDiffusion(trigger, active_force, rotational_diffusion)

Updater to introduce rotational diffusion with an active force.

Parameters

This updater works directly with an hoomd.md.force.Active or hoomd.md.force.ActiveOnManifold instance to update rotational diffusion for simulations with active forces.

The diffusion of the updater follows \(\delta \theta / \delta t = \sqrt{2 D_r / \delta t} \Gamma\), where \(D_r\) is the rotational diffusion constant, and the gamma function is a unit-variance random variable, whose components are uncorrelated in time, space, and between particles. In 3D, \(\hat{p}_i\) is a unit vector in 3D space, and diffusion follows \(\delta \hat{p}_i / \delta t = \sqrt{2 D_r / \delta t} \Gamma (\hat{p}_i (\cos \theta - 1) + \hat{p}_r \sin \theta)\), where \(\hat{p}_r\) is an uncorrelated random unit vector. The persistence length of an active particle’s path is \(v_0 / D_r\). The rotational diffusion is applied to the orientation quaternion of each particle. When used with hoomd.md.force.ActiveOnManifold, rotational diffusion is performed in the tangent plane of the manifold.

trigger

Select the timesteps to update rotational diffusion.

Type

hoomd.trigger.Trigger

active_force

The active force associated with the updater. This is not settable after construction.

Type

hoomd.md.force.Active

rotational_diffusion

The rotational diffusion as a function of time.

Type

hoomd.variant.Variant

class hoomd.md.update.ReversePerturbationFlow(filter, flow_target, slab_direction, flow_direction, n_slabs, max_slab=- 1, min_slab=- 1)

Reverse Perturbation (Müller-Plathe) method to establish shear flow.

“Florian Mueller-Plathe. Reversing the perturbation in nonequilibrium molecular dynamics: An easy way to calculate the shear viscosity of fluids. Phys. Rev. E, 59:4894-4898, May 1999.”

The simulation box is divided in a number of slabs. Two distinct slabs of those are chosen. The “max” slab searches for the maximum velocity component in flow direction while the “min” slab searches for the minimum velocity component. Afterward, both velocity components are swapped.

This introduces a momentum flow, which drives the flow. The strength of this flow is set through the flow_target argument, which defines a target value for the time-integrated momentum flux. The searching and swapping is repeated until the target is reached. Depending on the target sign, the “max” and “min” slab might be swapped.

Parameters
  • filter (hoomd.filter.ParticleFilter) – Subset of particles on which to apply this updater.

  • flow_target (hoomd.variant.Variant) – Target value of the time-integrated momentum flux. \([\delta t \cdot \mathrm{mass} \cdot \mathrm{length} \cdot \mathrm{time}^{-1}]\) - where \(\delta t\) is the integrator step size.

  • slab_direction (str) – Direction perpendicular to the slabs. Can be “x”, “y”, or “z”

  • flow_direction (str) – Direction of the flow. Can be “x”, “y”, or “z”

  • n_slabs (int) – Number of slabs used to divide the simulation box along the shear gradient. Using too few slabs will lead to a larger volume being disturbed by the momentum exchange, while using too many slabs may mean that there are not enough particles to exchange the target momentum.

  • max_slab (int) – Id < n_slabs where the max velocity component is search for. If set < 0 the value is set to its default n_slabs/2.

  • min_slab (int) – Id < n_slabs where the min velocity component is search for. If set < 0 the value is set to its default 0.

Attention

  • This updater uses hoomd.trigger.Periodic(1) as a trigger, meaning it is applied every timestep.

  • This updater works currently only with orthorhombic boxes.

Note

The attributes of this updater are immutable once the updater is attached to a simulation.

Examples:

# const integrated flow with 0.1 slope for max 1e8 timesteps
ramp = hoomd.variant.Ramp(0.0, 0.1e8, 0, int(1e8))
# velocity gradient in z direction and shear flow in x direction.
mpf = hoomd.md.update.ReversePerturbationFlow(filter=hoomd.filter.All(),
                                              flow_target=ramp,
                                              slab_direction="Z",
                                              flow_direction="X",
                                              n_slabs=20)
filter

Subset of particles on which to apply this updater.

Type

hoomd.filter.ParticleFilter

flow_target

Target value of the time-integrated momentum flux.

Type

hoomd.variant.Variant

slab_direction

Direction perpendicular to the slabs.

Type

str

flow_direction

Direction of the flow.

Type

str

n_slabs

Number of slabs.

Type

int

max_slab

Id < n_slabs where the max velocity component is searched for.

Type

int

min_slab

Id < n_slabs where the min velocity component is searched for.

Type

int

property summed_exchanged_momentum

Returned the summed up exchanged velocity of the full simulation.

(Loggable: category=”scalar”)

class hoomd.md.update.ZeroMomentum(trigger)

Zeroes system momentum.

Parameters

trigger (hoomd.trigger.Trigger) – Select the timesteps to zero momentum.

During the time steps specified by trigger, particle velocities are modified such that the total linear momentum of the system is set to zero.

Examples:

zeroer = hoomd.md.update.ZeroMomentum(hoomd.trigger.Periodic(100))