QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: James on May 26, 2016, 23:26

Title: Change bond lengths and atoms in half of the system
Post by: James on May 26, 2016, 23:26

Hi, I was constructing a MoS2/MoSe2 monolayer interface. I guess the quickest way is to change half of the MoS2 monolayer into MoSe2 and the corresponding bond lengths as well. Is there any easy way to alter half of the original monolayer?

Also, it would be great if someone could come up with new ideas to build the system.

Thanks in advance!

Title: Re: Change bond lengths and atoms in half of the system
Post by: Daniele Stradi on May 27, 2016, 08:38

Dear James,

in VNL, you can do it in the way you mentioned by using the Periodic Table tool to change the atom type, and the Coordinate Tools -> Transform by expression in the Builder to change the atomic distances.

Alternatively, you can also use the interfface builder (got to Builder -> Interface) to create the interface starting from the bulk structures of the two materials. See also http://docs.quantumwise.com/tutorials/ag_au_interface.html?highlight=interface

Regrads,
Daniele

Title: Re: Change bond lengths and atoms in half of the system
Post by: James on May 27, 2016, 21:44

Hello Dan,

Thanks for the advice!

By the way, once I got the interface, I wanna make a ripple on the surface of the material, say a sin(x) function shape, i . e. , different atoms along the interface will be lifted by some amount based on their coordinates. Do you think that's possible?

Best,
James

Title: Re: Change bond lengths and atoms in half of the system
Post by: Jess Wellendorff on May 30, 2016, 08:53

You may need to do such an operational manually in the python script after building the interface in the Builder. See attached script, where the x coordinates in the central region are changed to sin(x). Not that you should not touch the coordinates of the left and right electrode extensions (otherwise NEGF will not work).

Title: Re: Change bond lengths and atoms in half of the system
Post by: Anders Blom on May 30, 2016, 09:38

You can also use the plugin "Transform by expression" or the plugins for buckling graphene which are part of the "Fun with graphene" tutorial:
http://docs.quantumwise.com/tutorials/exploring_graphene.html

Title: Re: Change bond lengths and atoms in half of the system
Post by: Anders Blom on May 30, 2016, 09:39

Sorry, that tutorial is only half-done...  :-\
But if you install the plugin "Fun with graphene" via the AddOn Manager, and restart VNL, you will see a "Buckler" tool in the Builder that you can use for this.

Title: Re: Change bond lengths and atoms in half of the system
Post by: James on May 31, 2016, 04:40

WoW!! This looks awesome!! ;D ;D ;D
Thanks a lot!