About nanotube builder in Avogadro

General Discussion
1

Dear everyone,

Hi, I’m Hyun-seok Kim a graduate student at Seoul National University in
South Korea.

While using the ‘nanotube builder’ included in Avogadro I’ve noticed that
(n,m) specification of nanotube is restricted maximum up to 9.

Is there a particular reason?

Furthermore, it will be nice to know how can I draw a nanotube with (n,m)
indexes over 9.

Such as (12, 0) or (12,1).

Thank you.

Best regards

Hyun-seok Kim

Hyun-Seok Kim,

Ph. D. Candidate,
Creative Research Initiatives Center for Bridging-Scaled Isogemetric Optimal
Design.,
and Department of Naval Architecture and Ocean Engineering,
College of Engineering, Seoul National University, Seoul, South Korea

(Tel.) +82- 2-880-8496
(Fax) +82- 2-883-8496
(E-mail) mailto:[email protected] [email protected]

2

On Thu, Aug 8, 2013 at 12:48 PM, Hyun-seok Kim [email protected] wrote:

Hi, I’m Hyun-seok Kim a graduate student at Seoul National University in
South Korea.

While using the ‘nanotube builder’ included in Avogadro I’ve noticed that
(n,m) specification of nanotube is restricted maximum up to 9.

Is there a particular reason?

The nanotube builder uses the TubeGen code to generate the nanotube
geometry, and the algorithm used can be very slow for large chirality
indices. We’ve clamped the values to produce structures that can be
built in a reasonable amount of time.

Why 9? Probably because it’s the largest single digit number :slight_smile:

We could increase the limit if people are regularly working with larger tubes.

Furthermore, it will be nice to know how can I draw a nanotube with (n,m)
indexes over 9.

Such as (12, 0) or (12,1).

At this time, you’d need to modify the Avogadro source code and
recompile the executable, but that is a complicated task unless you’re
familiar with software development.

For now, I’d recommend just using TubeGen through the author’s web interface:

http://turin.nss.udel.edu/research/tubegenonline.html

IIRC, it will produce a .xyz file that can be opened in Avogadro.

Hope this helps,
Dave

3

Dear Avogadro Developers

I wonder if I can build a MoS2 (or generally TX2) nanotube using Avogadro

Best wishes

4

At the moment, no. We’re working on new interfaces with materials generation tools for Avogadro 2 as part of the new plugin system.

I would think this possible using Python and ASE:
https://wiki.fysik.dtu.dk/ase/ase/build/build.html#ase.build.nanotube

5

There’s also the Python Scikit-Nano package that looks interesting:
https://docs.scikit-nano.org/scripts.nanogen.html#module-sknano.scripts.nanogen

6

Dear Hutchison

Thank you. I will try it.

I’m staying tuned for its implementation in Avogadro2

Best wishes