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Hoomd 2-D Ellipsoid


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.


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


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:

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.



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!