Figure 12. Ellipsoid particles
Figure 13. Box-shaped particles
Figure 14. Spherocylindrical particles
OVITO can visualize particles with ellipsoid and box shapes as shown in the pictures on the right.
In addition, particles with cylindrical and spherocylindrical (capsule) shape can be visualized.
While the size of standard spherical and cubic particles is controlled by the Radius
particle property,
the size and shape of non-spherical and non-cubic particles is determined by the Aspherical Shape
property.
For OVITO to display non-spherical particles, this property must be defined and the
desired type of shape must be selected in the Particle display parameters panels.
The Aspherical Shape
particle property consists of three components X
, Y
, and Z
which specify the size (radius) of ellipsoidal or box particles along the three principal axes.
Particles for which all three components of the Aspherical Shape
property are zero, are rendered
as standard spheres (or cubes). In this case their size is controlled by the Radius
property, as if the Aspherical Shape
property was not defined.
The size of cylindrical and spherocylindrical particles is also determined by the Aspherical Shape
property.
Here, the X
component specifies the radius of the cylinder and the Z
component specifies its length
(along the local Z axis). The Y
component is ignored.
The orientation of aspherical particles is controlled by the Orientation
particle property,
which has four components X
, Y
, Z
, W
that form
a quaternion. If the Orientation
property is not defined, or if the four components do not form a unit quaternion,
no rotation is applied to an aspherical particle and it remains aligned with the coordinate axes.
Both the Aspherical Shape
and the Orientation
properties are typically
read from simulation files. The LAMMPS (or LIGGGHTS) simulation code can output this information to dump files using the following LAMMPS script commands:
compute orient all property/atom quati quatj quatk quatw compute shape all property/atom shapex shapey shapez dump 1 all custom 100 ellipsoid.dump id type x y z & c_orient[1] c_orient[2] c_orient[3] c_orient[4] & c_shape[1] c_shape[2] c_shape[3]
The quati
, quatj
, quatj
, and quatw
atom properties of LAMMPS need to be mapped to the Orientation.X
, Orientation.Y
,
Orientation.Z
, and Orientation.W
properties of OVITO when importing
the dump file. Similarily, the shapex
, shapey
, and shapez
columns
need to be mapped to Aspherical Shape.X
, Aspherical Shape.Y
, and Aspherical Shape.Z
in OVITO. Since these properties are output as c_orient*
and c_shape*
by the
dump command above, OVITO cannot set up this mapping automatically. You have to do it manually by using the
button in the file import panel after loading the dump file.