Stone Wales defect in GNR

[ams_nanolab]

Could you point me how to make a stone-wales defect in a graphene nanoribbon using ATK builder?

[kstokbro]

check:
http://www.quantumwise.com/documents/manuals/latest/VNLTutorial/index.html/chap.gnr.html

[ams_nanolab]

Say I want to make similar defect in MoS2, would the same methodology apply?

[Anders Blom]

I guess so, provided it makes physical sense...

[ams_nanolab]

Practically with MoS2 I am looking to something like

http://arxiv.org/ftp/arxiv/papers/1304/1304.3701.pdf (Fig. 2, Fig. 3 and Fig. 4)

but cant build these sort of structures in the ATK builder, could you suggest how to?

[Anders Blom]

Looks like one could use mirror symmetry, at least from Fig 2. That is, build the structure up to the line defect plane by using a supercell and then delete the last row of atoms if necessary, then mirror the system in those atoms, and adjust the lattice constant.

[ams_nanolab]

I am trying to build the lattice as you suggested but strangely the S atoms seem to form an in-plane hexagon while using Mirror (+copy). How to get rid of this? Attached is a screenshot.

[Anders Blom]

Without doing the actual work it's hard to say exactly, but the figures in the article had the Mo or S atoms in the mirror plane, it seems your mirror plane is rather at the edge of the unit cell?

[ams_nanolab]

Yes I have corrected the issue about the mirror edge , but the problem occurs in the original cell as soon as we use the copy option. When we give copy the atoms seem to form strange bonds like in the screenshot attached.

[Anders Blom]

That's because you have atoms outside the cell. Make the cell correspondingly bigger and the bonds disappear. Remember that bonds are just for pretty pictures - the only thing which really matters for the calculation are the positions of the atoms.

[ams_nanolab]

Thanks... that solves it 

[ams_nanolab]

While simulating such structures I am getting the error - screenshot attached, can you tell me what is wrong?

[Anders Blom]

As the error message says, you have atoms in equivalent positions. You need to check the atomic configuration.

PS: Always use the latest version of ATK, which currently in 12.8.2. The version you have contains known bugs (although it's not related to the problem you see).