Visualizing a spherocylinder

Hello,

I want to visualize a spherocylinder (radius r and height L) centred at (x0,y0,z0) and oriented along the unit vector (ux,uy,uz). I am a bit confused to specify the parameters (quatw quati quatj quatk) in the file to be supplied to OVITO. From the documentation, I could understand that shapex = r and shapez = L? Please check the details below and kindly help me to calculate these parameters.

ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
1
ITEM: BOX BOUNDS pp pp pp
-10 10
-10 10
-10 10
ITEM: ATOMS id type x y z quatw quati quatj quatk shapex shapey shapez

Thanks,
Vinay

Hi,

Yes, that’s correct. Spherocylindrical particles require the same input properties as cylindrical particles, as described here:
https://www.ovito.org/docs/current/advanced_topics/aspherical_particles.html#howto-aspherical-particles-cylinders

Furthermore, here is a more detailed description of how to specify the Orientation particle property in the form of a quaternion and how to include that information in a LAMMPS dump file: Non-spherical particle shapes — OVITO User Manual 3.10.6 documentation. The Orientation property describes a coordinate transformation from the Particles system into the global simulation coordinate system. In other words, it describes how a spherocylinder’s axis shall be rotated away from the z-axis of the global coordinate system.