hoomd.update

Overview

`BoxResize`	Resizes the box between an initial and final box.
`CustomUpdater`	User-defined updater.
`FilterUpdater`	Update sets of particles associated with a filter.
`RemoveDrift`	Remove the average drift from a system restrained on a lattice.

Details

Updaters.

class hoomd.update.BoxResize(trigger, box1, box2, variant, filter=hoomd._hoomd.ParticleFilter)

Resizes the box between an initial and final box.

When part of a hoomd.Simulation updater list, this object will resize the box between the initial and final boxes passed. The behavior is a linear interpolation between the initial and final boxes where the minimum of the variant is tagged to box1 and the maximum is tagged to box2. All values between the minimum and maximum result in a box that is the interpolation of the three lengths and tilt factors of the initial and final boxes.

Note

The passed Variant must be bounded (i.e. it must have a true minimum and maximum) or the behavior of the updater is undefined.

Note

Currently for MPI simulations the rescaling of particles does not work properly in HPMC.

Parameters

trigger (hoomd.trigger.Trigger) – The trigger to activate this updater.
box1 (hoomd.Box) – The box associated with the minimum of the passed variant.
box2 (hoomd.Box) – The box associated with the maximum of the passed variant.
variant (hoomd.variant.Variant) – A variant used to interpolate between the two boxes.
filter (hoomd.filter.ParticleFilter) – The subset of particle positions to update.

box1

The box associated with the minimum of the passed variant.

Type: hoomd.Box

box2

The box associated with the maximum of the passed variant.

Type: hoomd.Box

variant

A variant used to interpolate between the two boxes.

Type: hoomd.variant.Variant

trigger

The trigger to activate this updater.

Type: hoomd.trigger.Trigger

filter

The subset of particles to update.

Type: hoomd.filter.ParticleFilter

get_box(timestep)

Get the box for a given timestep.

Parameters: timestep (int) – The timestep to use for determining the resized box.
Returns: The box used at the given timestep. None before the first call to Simulation.run.
Return type: Box

static update(state, box, filter=hoomd._hoomd.ParticleFilter)

Immediately scale the particle in the system state to the given box.

Parameters

state (State) – System state to scale.
box (Box) – New box.
filter (hoomd.filter.ParticleFilter) – The subset of particles to update.

class hoomd.update.CustomUpdater(trigger, action)

User-defined updater.

Parameters

action (hoomd.custom.Action) – The action to call.
trigger (hoomd.trigger.Trigger) – Select the timesteps to call the action.

CustomUpdater is a hoomd.operation.Updater that wraps a user-defined hoomd.custom.Action object so the action can be added to a hoomd.Operations instance for use with hoomd.Simulation objects.

Updaters modify the system state.

See also

The base class hoomd.custom.CustomOperation.

hoomd.tune.CustomTuner

hoomd.write.CustomWriter

class hoomd.update.FilterUpdater(trigger, filters)

Update sets of particles associated with a filter.

HOOMD caches the particles selected by hoomd.filter.ParticleFilter instances to avoid the cost of re-running the filter on every time step. This means that unless the particles selected by a filter are recomputed the set of particles an operation works on is static. This class provides a mechanism to update the cached list of particles periodically. For example, use it to update the particles operated on by an MD integration method so that the integration method applies to particles in a given region of space.

Note

If needed to improve performance, use a hoomd.trigger.Trigger subclass, to update only when there is a known change to the particles that a filter would select.

Note

Some actions automatically recompute all filter particles such as adding or removing particles.

Parameters

trigger (hoomd.trigger.Trigger or int) – A trigger to use for determining when to update particles associated with a filter.
filters (list[hoomd.filter.ParticleFilter]) – A list of hoomd.filter.ParticleFilter instances to update.

trigger

The trigger associated with the updater.

Type: hoomd.trigger.Trigger

__eq__(other): Return whether two objects are equivalent.

property filters

filters to update select particles.

Type: list[hoomd.filter.ParticleFilter]

class hoomd.update.RemoveDrift(reference_positions, trigger=1)

Remove the average drift from a system restrained on a lattice.

Parameters

reference_positions ((N_particles, 3) numpy.ndarray of float) – the reference positions of the lattice \([\mathrm{length}]\).
trigger (hoomd.trigger.Trigger) – Select the timesteps to remove drift.

During the time steps specified by trigger, the mean drift \(\Delta\vec{r}\) from the reference_positions (\(\vec{r}_{ref, i}\)) is substracted from the current particle positions (\(\vec{r}_i\)). The drift is then given is given by:

\[\Delta\vec{r} = \frac{1}{\mathrm{N_{particles}}} \sum_{i=1}^\mathrm{N_{particles}} \mathrm{min\_image}(\vec{r}_i - \vec{r}_{ref,i})\]