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Weird artifacts when displaying gas phase molecules #586

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danielhollas opened this issue Apr 11, 2024 · 2 comments · May be fixed by ispg-group/aiidalab-ispg#230
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Weird artifacts when displaying gas phase molecules #586

danielhollas opened this issue Apr 11, 2024 · 2 comments · May be fixed by ispg-group/aiidalab-ispg#230

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@danielhollas
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Just noticed the following quirk in my app with the latest AWB

image

I suspect this might be due to the bond-drawing code added in 2.1? (I am still on 2.0)
I need to investigate more, since this happens only in certain scenarios, but I want to document this for now.

CC @cpignedoli @yakutovicha @superstar54 in case you saw something like this...
@danielhollas danielhollas added the bug Something isn't working label Apr 11, 2024
@superstar54
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superstar54 commented Apr 11, 2024 •
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It's actually not a bug. I guess you have a small unit cell with the periodic boundary condition (pbc). What's the unit cell of your molecule, I guess these weird bonds will disappear if you use a large unit cell, or switch off the pbc because it's a molecule.

@danielhollas danielhollas mentioned this issue Apr 25, 2024
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@danielhollas danielhollas removed the bug Something isn't working label Apr 29, 2024
@danielhollas
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@superstar54 your were right, thanks. I was a victim of a very strange behaviour of TrajectoryData, where it would by default assume PBC=(True, True,True) when converting to StructureData. I opened an issue here: aiidateam/aiida-core#6376

Here's a fix in my app:
ispg-group/aiidalab-ispg@d26297c

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Bump AWB ispg-group/aiidalab-ispg
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@danielhollas @superstar54