QuantumATK Forum

QuantumATK => Scripts, Tutorials and Applications => Topic started by: Anders Blom on March 22, 2012, 17:58

Title: Plugin for wrapping tubes in VNL
Post by: Anders Blom on March 22, 2012, 17:58

Ok - ready?

• Start VNL and open the "AddOn Manager". Sort by name, and scroll down until you find the "TubeWrapper". Install it.
• Open the Builder, and click "Coordinate Tools" to make sure you have the "Tube Wrapper" installed. If not - it's a bug in the beta-version, and I can suggest another (a bit more complicated) way to install the plugin.
• Now, click "Add">"Add from Database" and locate molybdenite. Add it.
• Use the mouse selection to delete the 3 atoms to the right in the cell. This leaves a single layer of MoS2, in the hexagonal cell.
• Use the "Supercell" (Bulk Tools) plugin with A'=2A+B to get an orthorhombic cell.
• Open the "Repeat" (Bulk Tools) plugin. You now have two choices: repeat in A or B - this will give either zigzag (B) or armchair (A) tubes. Repeat some decent number, like 20.
• If you repeated in A, open the "Swap Axes" (Bulk Tools) plugin and click "A<>B" then "X<>Y".
• In "Swap Axes", click "A<>C" then "X<>Z" (both for A and B repeat).
• Open "Lattice Parameters" (Bulk Tools) and select "Cartesian" coordinates. Then change the first cell vector A so that the size of the cell in X is at least as large as in Y.
• Open "Center" (Coordinate Tools) and center the system, only in A.
• Open the new plugin, "Tube Wrapper" (Coordinate Tools) and wrap the tube! You can use 360 directly to get a tube, or perhaps 180 :)
• Finally, adjust the cell size (it's a bit big) and then center the system in A and B.

Now you can perform calculations on MoS2 nanotubes. Note that the article uses DFTB, this model is also available in ATK, and you can as academic request the Mo/S parameters from http://www.dftb.org for free, and run ATK with those. How to install DFTB parameters is described in a tutorial (http://quantumwise.com/documents/tutorials/latest/DFTB/).

Have fun!

PS: The recipe above looks complicated perhaps, but compare it to trying to make it yourself ;) Besides, all operations have a point: we need to go from hexagonal to ortho, we need to repeat, and to extend the unit cell to fit the tube. The only non-obvious thing is perhaps the Swap Axes operations. These are there because the Tube Wrapper assumes a certain orientation of the system. The alternative would have been to allow selection of axes in the plugin, but that also comes with some logical complications.

PS2: As you can guess, you can of course also use the same method to make carbon nanotubes. There is of course existing functionality in VNL for that, but you could use this plugin to make "open" or partially wrapped nanotubes!

Title: Re: Plugin for wrapping tubes in VNL
Post by: ramkrishna on March 30, 2012, 09:11

Dear Sir,
         TubeWrapper is not coming in the AddOn Manager in beta version. How can I add this one in the beta version? In the alpha version (or final version), will it be fixed?

Regards
Ramkrishna 

Title: Re: Plugin for wrapping tubes in VNL
Post by: Anders Blom on March 30, 2012, 10:21

Many things are not correct in the beta-version, and the new release will fix all of them, even if it's not a final release (it will be called a "release candidate"). And the TubeWrapper will be downloadable with that version (which will be available later today).

Note for the future that "alpha" is even earlier than beta, it's a preview version with some missing functionality, whereas "beta" mean all (or most) functionality is in place but has known bugs. In this particular release (12.2) we have added functionality also after the beta-version was released, hope nobody minds :)

Title: Re: Plugin for wrapping tubes in VNL
Post by: ramkrishna on July 26, 2012, 18:25

Dear Sir,
         I am using 12.2.2 version but TubeWrapper is not coming in the AddOn Manager. How can I add this one? Please help.

Regards
Ramkrishna
         

Title: Re: Plugin for wrapping tubes in VNL
Post by: Anders Blom on July 27, 2012, 01:33

It's there... Try hitting "Refresh" and make sure you are online, and have the packages sorted by name so you can find it easier.

Title: Re: Plugin for wrapping tubes in VNL
Post by: ramkrishna on July 27, 2012, 08:46

Dear Sir,
         It shows an error when I am hitting "Refresh" and it does not update the page. Please check the attached picture.

Regards
Ramkrishna

Title: Re: Plugin for wrapping tubes in VNL
Post by: Anders Blom on July 27, 2012, 09:06

As far as I can tell this indicates a network problem on you side, or that the connection to our server from your machine is too slow. You can download the plugin directly instead, I have attached it, and then use "Local Install" in the AddOn Manager.

Title: Re: Plugin for wrapping tubes in VNL
Post by: Serghere on May 11, 2013, 11:51

Anders thanks for awesome plugin , I use it and I really like it .

Title: Re: Plugin for wrapping tubes in VNL
Post by: Anders Blom on May 11, 2013, 21:50

Please note that an update for 12.8 was published a few days ago, version 1.1 of the TubeWrapper. You can install it via the AddOn Manager in VNL 12.8. It doesn't contain any new functionality but has a few minor bug fixes.