Cylinder

class hoomd.wall.Cylinder(radius, axis, origin=(0.0, 0.0, 0.0), inside=True, open=True)

Bases: WallGeometry

A right circular cylinder.

Parameters:

• radius (float) – The radius of the circle faces of the cylinder $[\mathrm{length}]$.

• axis (tuple [float, float, float]) – A vector perpendicular to the circular faces.

• origin (tuple [float, float, float], optional) – The origin of the cylinder defined as the center of the circle along the cylinder’s axis $[\mathrm{length}]$.

• inside (bool, optional) – Whether positive signed distances are inside or outside the cylinder.

• open (bool, optional) – Whether to include the surface of the cylinder in the space. True means do not include the surface, defaults to True.

Cylinder walls in HOOMD span the simulation box in the direction given by the axis attribute.

The signed distance from the wall surface is

$$d = \left( R - \lvert \left( \vec{r} - \vec{r}_o \right) - \left( \left( \vec{r} - \vec{r}_o \right) \cdot \hat{n} \right) \hat{n} \rvert \right)$$

for inside=True, where $r$ is the particle position, $\vec{r}_o$ is the origin of the cylinder, $\hat{n}$ is the cylinder’s unit axis, and $R$ is the cylinder’s radius. The distance is negated when inside=False.

Warning

When running MD simulations in 2D simulation boxes, set axis=(0,0,1). Otherwise, the wall force will push particles off the xy plane.

Note

Cylinder objects are immutable.

Example:

cylinder = hoomd.wall.Cylinder(radius=10.0, axis=(0, 0, 1))

radius

The radius of the circle faces of the cylinder $[\mathrm{length}]$.

Type:

float

origin

The origin of the cylinder defined as the center of the circle along the cylinder’s axis $[\mathrm{length}]$.

Type:

tuple [float, float, float]

axis

A vector perpendicular to the circular faces.

Type:

tuple [float, float, float]

inside

Whether positive signed distances are inside or outside the cylinder.

Type:

bool

open

Whether to include the surface of the cylinder in the space. True means do not include the surface.

Type:

bool, optional

__repr__()

A string representation of the Cylinder.

__str__()

A string representation of the Cylinder.

to_dict()

Convert the wall geometry to a dictionary defining the cylinder.

Returns:

The geometry in a Python dictionary.

Return type:

dict