QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: dcarogancia on July 26, 2015, 09:58

Title: Translate 2D silicon atoms to fit trigonal or hexagonal shape
Post by: dcarogancia on July 26, 2015, 09:58

Dear all,

  I have a rather simple question. I have constructed 2D silicon structure. I want to translate the atom coordinates such
it will some align or fit with a hexagonal surface. Is there way to do this in the VNL? Pls refer to the attached figure.

Thanks,

dca
 

Title: Re: Translate 2D silicon atoms to fit trigonal or hexagonal shape
Post by: asanchez on July 26, 2015, 14:49

You can always copy the graphene hexagonal lattice available in VNL's structure database. By importing graphene into the builder you get something like:

Code

# Set up lattice
lattice = Hexagonal(2.4612*Angstrom, 6.709*Angstrom)

# Define elements
elements = [Carbon, Carbon]

# Define coordinates
fractional_coordinates = [[ 0.            ,  0.            ,  0.            ],
                          [ 0.333333333333,  0.666666666667,  0.            ]]

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )

If I understand your question correctly you could get what you're looking for by changing that 2.4612 to match the bond length of Si, change the C parameter (6.709) to however much vaccum you think is appropriate for your calculation, and change elements to Silicon instead of Carbon :). Hope this helps.

Title: Re: Translate 2D silicon atoms to fit trigonal or hexagonal shape
Post by: dcarogancia on July 26, 2015, 16:41

Thank you  for your kind response.

It really helps a lot. Actually, I want to construct silicene and fit it in the same hexagonal structure as the
graphene in the VNL database. Is there a way that the buckling in silicene can be include in the basis atoms?
A simple example is greatly appreciated..

Thanks,

dennis

Title: Re: Translate 2D silicon atoms to fit trigonal or hexagonal shape
Post by: Dipankar Saha on July 26, 2015, 17:07

Generally,  we change the lattice type from "Lattice Parameters"  ..., then "wrap" it with-in the hexagonal lattice.....
But, the kind of super-cell that you have shown....you may or may not be able to directly wrap it into the "Hexagonal" Lattice from the "Unit Cell" .... you may try.....

Title: Re: Translate 2D silicon atoms to fit trigonal or hexagonal shape
Post by: Dipankar Saha on July 26, 2015, 17:10

You can check this *.py attached...... / To make it a larger super cell....you may repeat it in A-B directions.... / Extra spacing in C-diec. has been roughly added... You can further modify that also... :)
__ Perhaps,  you need to check the bond lengths also.... Check if those are correct...!! (Because, the struct. is neither Geometry Optimized nor Relaxed....)

Regards_
Dipankar

Title: Re: Translate 2D silicon atoms to fit trigonal or hexagonal shape
Post by: Anders Blom on July 27, 2015, 11:59

Adding buckling is easy, just change the z coordinate. I suggest you look at http://quantumwise.com/publications/tutorials/item/512-opening-a-band-gap-in-silicene-and-bilayer-graphene-with-an-electric-field which has a lot of details on silicene.