Non-spherical particle shapes¶
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 shape must be selected in the settings of the Particles visual element.
Aspherical Shape particle property consists of three components
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.
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
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.
Aspherical Shape and the
Orientation properties are typically
read from simulation files. The LAMMPS and LIGGGHTS simulation codes 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 c_orient c_orient c_orient & c_shape c_shape c_shape
atom properties of LAMMPS need to be mapped to the
Orientation.W properties of OVITO when importing
the dump file. Similarly, the
need to be mapped to
Aspherical Shape.Y, and
in OVITO. Since these properties are output as
c_shape* by the
dump command above, OVITO cannot set up this mapping automatically. You have to do it manually by using the
Edit column mapping button in the file import panel after loading the dump file.