QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: carbn9 on June 10, 2012, 08:05

Title: Building graphene shell in VNL
Post by: carbn9 on June 10, 2012, 08:05

Hi,

I need to build the graphene shell shown in the second or the final step of the following image:

(http://origin-ars.sciencedirect.com/content/image/1-s2.0-S0021999111007042-gr11.jpg)

which is from the publication of http://www.sciencedirect.com/science/article/pii/S0021999111007042 (http://www.sciencedirect.com/science/article/pii/S0021999111007042)

I know and I can build a graphene sheet with NanoSheet command and I studied the corresponding tutorial. However could you please help me for connecting upper and lower graphene sheets to form a shell like structure?

Best regards,
Maresh

Title: Re: Building graphene shell in VNL
Post by: Anders Blom on June 10, 2012, 22:21

Well now - that's hardly trivial... :-\

You may be better off starting with a nanotube, and deform it into an ellipsoidal shape by compressing the cell in one direction while keeping the fractional coordinates fixed. Then maybe you can try "Coordinate Tools>Transform by Expression" to squeeze the edge... In a sense you just need a good starting guess, you will need a geometry optimization in the end anyway.

Good luck! :)

Title: Re: Building graphene shell in VNL
Post by: carbn9 on June 11, 2012, 16:16

Thanks Anders Blom.

"deform it into an ellipsoidal shape by compressing the cell in one direction while keeping the fractional coordinates fixed" Sorry but how to do this?  ::)

Best regards and fingers crossed...

Title: Re: Building graphene shell in VNL
Post by: Nordland on June 12, 2012, 00:50

I tried to play around with builder, and you can quite easily build something like this.

It is not perfect, but it is possible to this operation.

Title: Re: Building graphene shell in VNL
Post by: carbn9 on June 12, 2012, 09:19

Thanks Nordland. The structure you built seems really good.

One thing: In the builder, which menu should I use? Or is there a tutorial on this?

Thanks again...

Title: Re: Building graphene shell in VNL
Post by: Nordland on June 15, 2012, 16:23

I have tried it a couple of times and since I made the screenshots I have made it even better,
but the approach is exactly the same. The way I see it, it can be approached as building a graphene box,
and then followed by a relaxation with the Brenner potential.

• Start by making a huge graphene ribbon.
• Clip of a part of each sides - this will effect determine the height of the shell.
• Select one of the flips.
• Rotate it using the move tool to be orthogonal on the sheet.
• Repeat for the other flip.
• Select the long part as shown in picture.
• Rotate this 90 degrees such that it points in the same directions as the flips.
• I connected it to a molecule ( Just for avoid the box around the system )
• Select the top part, and rotate it 90 degrees to put the top down.
• Almost done! :)
• Select the last flip and rotate it 90 degrees. The box is now closed.
• Remove any surplus atoms
• The box is done.
• Using the quick optimizer many many times you get your shell structure :)

Warning heavy image load incoming !
(http://www.quantumwise.com/quantumtester/nanoshell/1.png)
(http://www.quantumwise.com/quantumtester/nanoshell/2.png)
(http://www.quantumwise.com/quantumtester/nanoshell/3.png)
(http://www.quantumwise.com/quantumtester/nanoshell/4.png)
(http://www.quantumwise.com/quantumtester/nanoshell/5.png)
(http://www.quantumwise.com/quantumtester/nanoshell/6.png)
(http://www.quantumwise.com/quantumtester/nanoshell/7.png)
(http://www.quantumwise.com/quantumtester/nanoshell/8.png)
(http://www.quantumwise.com/quantumtester/nanoshell/9.png)
(http://www.quantumwise.com/quantumtester/nanoshell/10.png)
(http://www.quantumwise.com/quantumtester/nanoshell/11.png)
(http://www.quantumwise.com/quantumtester/nanoshell/12.png)
(http://www.quantumwise.com/quantumtester/nanoshell/13.png)
(http://www.quantumwise.com/quantumtester/nanoshell/14.png)