Unit cell not in sync with electron density

[olabe123]

When including the unit cell visualization during the visualization of the electron density, the unit cell is displaced compared to the electron density.

[rartino]

Do you know if this is always the case? Or just for certain inputs? Might help to track down the issue.

[olabe123]

I'm not sure. It didn't work for these two HDF5-files at least.

OneDrive_1_2020-06-01.zip

[jjeessppeer]

I had a similar problem working on this 2019. Something goes wrong with the origin coordinates for atom positions with some HDF5 files so that they get offset. The problem only arised on some HDF5 files.

This could be fixed by disabling the fullMesh property for the StructureMesh processor.
This was originally set in UnitcellNetworkHandler.py.

The problem with disabling fullMesh was that the HDF5 files that worked previously now were offset incorrectly, some files seemed to work with it enabled and some with it disabled. Also the sphere radius cannot be adjusted individually with this property disabled.

I was never sure where this problem originated from. I mainly suspected a bug in the StructureMesh-processor caused it, but it could also be the parser or some VASP setting.

[rartino]

@petersteneteg Just a thought: do you know if there is anything with the StructureMesh processor in Inviwo that is easy to miss with regards to the global offset of the coordinates, and which is affected by the 'fullMesh' property?

[jjeessppeer]

The StructureMesh processor is part of the ENVISIoN project. It is a part of the crystalvisualization module and is not native to Inviwo.

[rartino]

@jjeessppeer Thanks for the clarification; Oh, I see, so it is on our side. The code for that module really isn't so long, so this seems something we should be able to figure out.

I wrote an email to you today on your student email on another rather urgent matter related to ENVISIoN. (Let me know if you no longer use your student email)

[petersteneteg]

Let me know if I can help out somehow