QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: ams_nanolab on June 27, 2013, 09:05

Title: Stone Wales defect in GNR
Post by: ams_nanolab on June 27, 2013, 09:05

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

Title: Re: Stone Wales defect in GNR
Post by: kstokbro on June 27, 2013, 14:46

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

Title: Re: Stone Wales defect in GNR
Post by: ams_nanolab on July 24, 2013, 10:09

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

Title: Re: Stone Wales defect in GNR
Post by: Anders Blom on July 24, 2013, 21:53

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

Title: Re: Stone Wales defect in GNR
Post by: ams_nanolab on July 29, 2013, 08:30

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?

Title: Re: Stone Wales defect in GNR
Post by: Anders Blom on July 29, 2013, 23:43

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.

Title: Re: Stone Wales defect in GNR
Post by: ams_nanolab on July 30, 2013, 13:09

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.

Title: Re: Stone Wales defect in GNR
Post by: Anders Blom on July 31, 2013, 01:05

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?

Title: Re: Stone Wales defect in GNR
Post by: ams_nanolab on July 31, 2013, 07:57

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.

Title: Re: Stone Wales defect in GNR
Post by: Anders Blom on July 31, 2013, 12:09

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.

Title: Re: Stone Wales defect in GNR
Post by: ams_nanolab on August 1, 2013, 11:49

Thanks... that solves it  ;D

Title: Re: Stone Wales defect in GNR
Post by: ams_nanolab on August 5, 2013, 10:24

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

Title: Re: Stone Wales defect in GNR
Post by: Anders Blom on August 5, 2013, 10:53

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).