QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: bfazi on March 31, 2015, 12:16
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Hello every body
In ATK, how can we build a zig-zag and an armchair silicene nanoribbon?
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Check the tutorial:
https://docs.quantumatk.com/tutorials/opening_a_band_gap/opening_a_band_gap.html
i.e. build bilayer graphene armchair or zig-zag,
change C into Si,
relax
Edit: Updated link
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Alternatively you can use the nanoribbon plugin tool:
Open the builder and ”add-> From Plugin->nanoribbon”.
Change the elements to Si instead of C.
Change the bond length to 2.2286 Å.
Choose the desired edge (zigzag or armchair) and width.
Click Build.
The most stable configuration of Silicene is not planar but is buckling – e.g. every other atoms is displaced in the out-of-plane direction.
For small ribbons you can impose the buckling by marking every other atom (All atoms of type A for instance) and use “Coordinate Tools-> Translate” to displace them 0.44 Å in the out-of-plane direction.
Alternatively you can click the rattle tool a few times and perform a relaxation as discussed in the tutorial on bulk silicene:
https://docs.quantumatk.com/tutorials/opening_a_band_gap/opening_a_band_gap.html
Edit: Updated link
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Try Cerda for Si and Muller or Hoffman for H.
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Although I tried Optimizing the geometry of the silicene nanoribbon by following the steps given in the tutorial, however, there was no buckling in the silicene nanoribbon. I built the silicene nanoribbon by using the plugin tool in the software and replaced the carbon atoms with Si atoms. I also chose the bond length of 2.286 for the nanoribbon. After that I clicked on the rattle tool a few times and sent the configuration for optimization. Still there is no buckling in the geometry.
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Did you make sure to optimize with DFT? Forcefields might not get it right.
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Yes, I used DFT for optimization. Still there was no buckling. If you have made it already, can you please share the CIF of the nanoribbons of ZSiNR and ASiNR
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The procedure in the tutorial works perfectly well, I just tried it, it takes just a few minutes to set up and 1 minute to run on a laptop. It's a good exercise. But I didn't optimize the whole nanoribbon, just the 2-atom Silicene "crystal". After you have that you can start building nanoribbons etc.
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Indeed the procedure works fine for building two atom silicene and germanene. However, it is the building of nanoribbons that gives problems. Could you please provide the detailed process of building nanoribbons from buckled (two atom) silicene/germanene.
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Same as making graphene ribbons really.
First, if needed, force the system into hexagonal using the Lattice Parameters tool (keeping the fractional coordinates fixed), since it might be slightly out of the hexagonal configuration after the geometry optimization.
Then create a supercell with A'=A+B and B'=B-A (see screenshot)
Now you have a rectangular building block that you can turn and repeat and terminate as you need for a ribbon.
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By following this procedure would the ribbon formed be zigzag or armchair
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Neither, it's still periodic in both directions in the plane. So it's not a nanoribbon, it's an infinite nanosheet still. The zigzag/armchair depends which direction you cut along, just like for graphene, as shown e.g. in https://www.eurekalert.org/multimedia/pub/79039.php
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would the same method work for building the nanoribbons of other buckled 2D materials like stanene, plumbene etc. as well
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For sure :-)
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Earlier you said, to get a nanoribbon out of a nanosheet I have to cut it into the particular direction. Do I need to perform a swap axes operation to get a zigzag/armchair oriented nanoribbon? If yes, please tell me which swap axes operations to perform for zigzag and armchair nanoribbons respectively.
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Yes you might need to swap axes to align the transport direction, but that will be needed anyway because the C axis (the transport axis in QuantumATK) is perpendicular to the sheet in the original system.
After the supercell operation as indicated above, it's very simple to make armchair and zigzag by noting that the new A direction is along the zigzag direction, and B along armchair, as you can see if you make some repeats (picture below).
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Do I need to add vacuum in one of the directions apart from transport direction (i.e. either X or Y ) to form a nanoribbon after following the above mentioned steps
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That is the definition of a nanoribbon, yes... And hydrogen passivation of the edges
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Do I passivate the edges by using custom passivator with sp2 ?
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It's a bit trickier with the buckled sheet, since the automatic passivation tool does not recognize it as sp2 when it's not flat, but you are absolutely right that the Custom Passivator (should really be called Advanced Passivator...) will manage it when you explicitly select sp2!
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Thanks for your help on Zigzag Silicene Nanoribbons. I wanted to know how can we set up the antiferromagnetic configuration of Zigzag Silicene Nanoribbons which would be later on used for band structure calculations
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Some tips here https://docs.quantumatk.com/tutorials/spin_bloch_gnr/spin_bloch_gnr.html
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thanks for the link. However in this tutorial it is written that "Since the up and down Bloch states are localized on opposite edges, there must be a difference in the total spin up and down electron density. The Mulliken populations is the easiest way to get a first view of this. Under the column “Total”,the two spin-channels are shown on separate lines, and we find that the two edge carbon atoms(numbers 0 and 1) have a surplus population of 0.25 of either spin-up or spin-down". What if one does not obtain any difference that is to say that the spin channels on the separate lines have same values?
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Then there is no net spin polarization across the ribbon