QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: qweasel on February 9, 2017, 15:24
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From first look, dragging a zigzag into an armchair and using move->fuse and quick optimizer seems to work. However, when I do hydrogen passivation, several artefacts become apparent (see attach):
- Only part of the edges got passivated.
- Several "normal" sp2 hybridized carbons were unnecessarily passivated.
What is the correct way to make such a device?
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I supposed you intended to build a ribbon, but it's still a periodic structure in the B direction, so there isn't really an edge, and thus it doesn't need/cannot be passivated.
For sp2 vs. sp3, I suggest using the Coordinate Tools>Custom passivator and choose sp2, instead of the passivator button, since it gives more options.
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Good point, thanks!
Now I'm experiencing a related "anomaly": hydrogen from a passivated ribbon edge gets cloned into the electrode (attached).
Why does it happen twice? Is it correct to simply delete it from the electrode regions?
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Can you attach the structure without hydrogens (or, ok, with, I can always delete them). Then we can check
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Attached.
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The correct procedure is to first create the device (Device from bulk) and then passivate, not the other way around, in which case the edges in Z are passivated which they should not be since the device is (semi)infinitely periodic in Z.