BoxResize

class hoomd.update.BoxResize(trigger, box, filter=hoomd._hoomd.ParticleFilter)

Bases: Updater

Vary the simulation box size as a function of time.

Parameters:

• trigger (hoomd.trigger.trigger_like) – The trigger to activate this updater.

• filter (hoomd.filter.filter_like) – The subset of particle positions to update (defaults to hoomd.filter.All).

• box (hoomd.variant.box.BoxVariant) – Box as a function of time.

BoxResize resizes the simulation box as a function of time. For each particle $i$ matched by filter, BoxResize scales the particle to fit in the new box:

$$\vec{r}_i \leftarrow s_x \vec{a}_1' + s_y \vec{a}_2' + s_z \vec{a}_3' - \frac{\vec{a}_1' + \vec{a}_2' + \vec{a}_3'}{2}$$

where $\vec{a}_k'$ are the new box vectors determined by box evaluated at the current time step and the scale factors are determined by the current particle position $\vec{r}_i$ and the previous box vectors $\vec{a}_k$:

$$\vec{r}_i = s_x \vec{a}_1 + s_y \vec{a}_2 + s_z \vec{a}_3 - \frac{\vec{a}_1 + \vec{a}_2 + \vec{a}_3}{2}$$

After scaling particles that match the filter, BoxResize wraps all particles $j$ back into the new box:

$$\vec{r_j} \leftarrow \mathrm{minimum\_image}_{\vec{a}_k}' (\vec{r}_j)$$

Warning

Rescaling particles in HPMC simulations with hard particles may introduce overlaps.

Note

When using rigid bodies, ensure that the BoxResize updater is last in the operations updater list. Immediately after the BoxResize updater triggers, rigid bodies (hoomd.md.constrain.Rigid) will be temporarily deformed. hoomd.md.Integrator will run after the last updater and resets the constituent particle positions before computing forces.

Example:

box_resize = hoomd.update.BoxResize(
    trigger=hoomd.trigger.Periodic(10),
    box=inverse_volume_ramp,
)
simulation.operations.updaters.append(box_resize)

Members inherited from AutotunedObject:

property kernel_parameters

Kernel parameters. Read more...

property is_tuning_complete

Check if kernel parameter tuning is complete. Read more...

tune_kernel_parameters()

Start tuning kernel parameters. Read more...

Members inherited from TriggeredOperation:

trigger

The trigger to activate this operation. Read more...

Members defined in BoxResize:

box

The box as a function of time.

Example:

box_resize.box = inverse_volume_ramp

Type:

hoomd.variant.box.BoxVariant

filter

The subset of particles to update.

Example:

filter_ = box_resize.filter

Type:

hoomd.filter.filter_like

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

Example:

box = box_resize.get_box(1_000_000)

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 (hoomd.box.box_like) – New box.

• filter (hoomd.filter.filter_like) – The subset of particles to update (defaults to hoomd.filter.All).

Example:

hoomd.update.BoxResize.update(state=simulation.state, box=box)