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Hoomd 2-D Ellipsoid

Hello!

I am trying to visualize an ellipsoid trajectory but get an error message when attempting an to open the files. It claims I have a "Missing or invalid 'c' field in 'Ellipsoid' particle shape definition in GSD file" and I am wondering if Ovito knows how to handle 2-D ellipsoid trajectories or this is a Hoomd problem? I seemed to get data but was unable to visualize it. I am unable to attach an example of the GSD file but I attached my Hoomd script for reference.

Thanks!

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Hi,

Thank you for letting us know, could you please send the GSD file through the official mail support mail@ovito.org? Then we can look into this further.

Kaley,

Can you please clarify what you mean with "2-D ellipsoid trajectories"? Does that mean the ellipsoids are two-dimensional objects (i.e. ellipsis) or is their motion two-dimensional (i.e. particle coordinates z=0)?

OVITO strictly follows the GSD file format specification for ellipsoid particle shapes:

https://gsd.readthedocs.io/en/stable/shapes.html#ellipsoids

That means all principle axes a/b/c of the ellipsoid are expected to be positive, and OVITO's file parser generates an error if they are not.

-Alex

EDIT:

I just looked at your HOOMD script. It seems that the 'c' principle axes is 0 in your case. Would it be correct to simply set 'c' equal to 'b' during import into OVITO? OVITO can only visualise three-dimensional ellipsoids, not two-dimensional ellipses. In other words, all three axes need to be positive. But I could extend the file reader to detect the special case c=0, and then implicitly change its value to c=b.

Just to let you know: I have released a program update today (v3.1.2) containing an update to the GSD file reader. It now accepts ellipsoid shape definitions with principle axes b=0 and/or c=0.

Thank you so much this is so helpful!