mpcd.geometry¶

Overview

`Geometry`	Geometry.
`CosineChannel`	Serpentine (sinusoidal) channel.
`CosineExpansionContraction`	Channel with sinusoidal expansion and contraction.
`ParallelPlates`	Parallel-plate channel.
`PlanarPore`	Pore with parallel plate opening.
`Sphere`	Spherical confinement.

Details

MPCD geometries.

A geometry defines solid boundaries that cannot be penetrated. These geometries are used for various operations in the MPCD algorithm including:

Bounce-back streaming for MPCD particles (hoomd.mpcd.stream.BounceBack)
Bounce-back integration for MD particles (hoomd.mpcd.methods.BounceBack)
Virtual particle filling (hoomd.mpcd.fill.GeometryFiller)

Each geometry may put constraints on the size of the simulation and where particles are allowed. These constraints will be documented by each object.

class hoomd.mpcd.geometry.CosineChannel(amplitude, repeat_length, separation, no_slip=True)¶

Bases: Geometry

Serpentine (sinusoidal) channel.

Parameters:

amplitude (float) – Amplitude of cosine.
repeat_length (float) – Repeat length (period) of cosine.
separation (float) – Distance between channel walls.
no_slip (bool) – If True, surfaces have no-slip boundary condition. Otherwise, they have the slip boundary condition.

CosineChannel models a fluid confined in \(y\) between two walls described by a sinusoidal profile with equations

\[y(x) = A \cos\left(\frac{2 \pi x}{L}\right) \pm H\]

where \(A\) is the amplitude, \(L\) is the repeat_length, and \(2H\) is the separation.

Example:

channel = hoomd.mpcd.geometry.CosineChannel(
    amplitude=2.0,
    separation=4.0,
    repeat_length=10.0)
stream = hoomd.mpcd.stream.BounceBack(period=1, geometry=channel)
simulation.operations.integrator.streaming_method = stream

amplitude¶

Amplitude of cosine (read only).

Type:: float

repeat_length¶

Repeat length (period) of cosine. (read only).

Type:: float

separation¶

Distance between walls (read only).

Type:: float

class hoomd.mpcd.geometry.CosineExpansionContraction(expansion_separation, contraction_separation, repeat_length, no_slip=True)¶

Bases: Geometry

Channel with sinusoidal expansion and contraction.

Parameters:

expansion_separation (float) – Maximum distance between channel walls.
contraction_separation (float) – Minimum distance between channel walls.
repeat_length (float) – Repeat length (period) of cosine.
no_slip (bool) – If True, surfaces have no-slip boundary condition. Otherwise, they have the slip boundary condition.

CosineExpansionContraction models a fluid confined in \(y\) between two walls described by a sinusoidal profile with equations

\[y(x) = \pm\left( \frac{H_{\rm e}-H_{\rm c}}{2} \left[1+\cos\left(\frac{2 \pi x}{L}\right)\right] + H_{\rm c} \right)\]

where \(2 H_{\rm e}\) is the expansion_separation, \(2 H_{\rm c}\) is the contraction_separation, and \(L\) is the repeat_length.

Example:

channel = hoomd.mpcd.geometry.CosineExpansionContraction(
    expansion_separation=6.0,
    contraction_separation=3.0,
    repeat_length=10.0)
stream = hoomd.mpcd.stream.BounceBack(period=1, geometry=channel)
simulation.operations.integrator.streaming_method = stream

contraction_separation¶

Distance between channel walls at the minimum contraction (read only).

Type:: float

expansion_separation¶

Distance between channel walls at the maximum expansion (read only).

Type:: float

repeat_length¶

Repeat length (period) of cosine. (read only).

Type:: float

class hoomd.mpcd.geometry.Geometry(no_slip)¶

Bases:

Geometry.

Parameters:: no_slip (bool) – If True, surfaces have a no-slip boundary condition. Otherwise, they have a slip boundary condition.

no_slip¶

If True, plates have a no-slip boundary condition. Otherwise, they have a slip boundary condition (read only).

A no-slip boundary condition means that the average velocity is zero at the surface. A slip boundary condition means that the average normal velocity is zero at the surface, but there is no friction against the tangential velocity.

Type:: bool

class hoomd.mpcd.geometry.ParallelPlates(separation, speed=0.0, no_slip=True)¶

Bases: Geometry

Parallel-plate channel.

Parameters:

separation (float) – Distance between plates.
speed (float) – Wall speed.
no_slip (bool) – If True, surfaces have no-slip boundary condition. Otherwise, they have the slip boundary condition.

ParallelPlates confines particles between two infinite parallel plates centered around the origin. The plates are placed at \(y=-H\) and \(y=+H\), where the total separation is \(2H\). The plates may be put into motion with speed V, having velocity \(-V\) and \(+V\) in the x direction, respectively. If combined with a no-slip boundary condition, this motion can be used to generate simple shear flow.

Examples:

Stationary parallel plates with no-slip boundary condition.

plates = hoomd.mpcd.geometry.ParallelPlates(separation=6.0)
stream = hoomd.mpcd.stream.BounceBack(period=1, geometry=plates)
simulation.operations.integrator.streaming_method = stream

Stationary parallel plates with slip boundary condition.

plates = hoomd.mpcd.geometry.ParallelPlates(
    separation=6.0, no_slip=False)
stream = hoomd.mpcd.stream.BounceBack(period=1, geometry=plates)
simulation.operations.integrator.streaming_method = stream

Moving parallel plates.

plates = hoomd.mpcd.geometry.ParallelPlates(
    separation=6.0, speed=1.0, no_slip=True)
stream = hoomd.mpcd.stream.BounceBack(period=1, geometry=plates)
simulation.operations.integrator.streaming_method = stream

separation¶

Distance between plates (read only).

Type:: float

speed¶

Wall speed (read only).

speed will have no effect if no_slip is False because the slip surface cannot generate shear stress.

Type:: float

class hoomd.mpcd.geometry.PlanarPore(separation, length, no_slip=True)¶

Bases: Geometry

Pore with parallel plate opening.

Parameters:

separation (float) – Distance between pore walls.
length (float) – Pore length.
no_slip (bool) – If True, surfaces have no-slip boundary condition. Otherwise, they have the slip boundary condition.

PlanarPore is a finite-length version of ParallelPlates. The geometry is similar, except that the plates extend from \(x=-L\) to \(x=+L\) (total length 2L). Additional solid walls with normals in x prevent penetration into the regions above / below the plates. The plates are infinite in z. Outside the pore, the simulation box has full periodic boundaries; it is not confined by any walls. This model hence mimics a narrow pore in, e.g., a membrane.

Example:

pore = hoomd.mpcd.geometry.PlanarPore(separation=6.0, length=4.0)
stream = hoomd.mpcd.stream.BounceBack(period=1, geometry=pore)
simulation.operations.integrator.streaming_method = stream

separation¶

Distance between pore walls (read only).

Type:: float

length¶

Pore length (read only).

Type:: float

class hoomd.mpcd.geometry.Sphere(radius, no_slip=True)¶

Bases: Geometry

Spherical confinement.

Parameters:

radius (float) – Radius of sphere.
no_slip (bool) – If True, surfaces have no-slip boundary condition. Otherwise, they have the slip boundary condition.

Sphere confines particles inside a sphere of radius \(R\) centered at the origin.

Examples:

Sphere with no-slip boundary condition.

sphere = hoomd.mpcd.geometry.Sphere(radius=5.0)
stream = hoomd.mpcd.stream.BounceBack(period=1, geometry=sphere)
simulation.operations.integrator.streaming_method = stream

Sphere with slip boundary condition.

sphere = hoomd.mpcd.geometry.Sphere(radius=5.0, no_slip=False)
stream = hoomd.mpcd.stream.BounceBack(period=1, geometry=sphere)
simulation.operations.integrator.streaming_method = stream

radius¶

Radius of sphere (read only).

Type:: float