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.
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!
