Creating a sphere from monoclinic structure in ovito


I’m new to Ovito. I have a monoclinic simulation box filled with 3 different types of atoms obtained from the LAMMPS simulation. I wish to select a particular atom and find the coordinates of all its neighbouring atoms within a user defined radius in 3D.

Also, I wish to add a directional arrow from a particular atom in a specified direction (with known theta and phi in a sphere).

Kindly help.

Thanks in advance.

Hi Deepak,

You could use OVITO’s Expression Selection Modifier in conjunction with the Expand Selection Modifier to select a specific atom and all of its neighbouring atoms within a given cutoff radius, see linked manual entries. To select an atom based on its Particle Identifier you could e.g. use the following expression in the Expression Selection Modifier: ParticleIdentifier == 1283.

As for your second questions, the easiest solution would be to work with a Compute Property Modifier. In the current program version, the modifier does not allow you to create user-defined vector properties. But you could e.g. choose the output property Force and edit the three vector components in the “Expressions” field. This will cause a new object called Forces to appear under Visual Elements. If not already activated, tick the checkbox such that they will be shown in the active viewport.
Since you asked how to do that for one particular atom only, the idea would be to first select that atom (e.g. with another instance of the Expression Selection Modifier described above) and then activate the option “Compute only for selected elements” within the settings of the Compute Property Modifier.