Can you be more specific? A lead must by definition have a translational symmetry.

I should have explained more accurate. Of course, there is translational symmetry; I meant that CNT cross section is not round anymore. I have attached a .cif file to show what I mean. I'm pretty sure you know how to visualize this structure, but for the ones who don't, they can use visualization softwares like VESTA

Bests

Hello

Hi,

...

I should have explained more accurate. Of course, there is translational symmetry; I meant that CNT cross section is not round anymore. I have attached a .cif file to show what I mean. I'm pretty sure you know how to visualize this structure, but > for the ones who don't, they can use visualization softwares like VESTA

Kwant just does tight binding models where *you* provide the tight-binding parameters (these may come from discretizing a continuous Hamiltonian, or from a DFT calculation or whatever, Kwant is completely agnostic of this). This means that Kwant doesn't know anything about whether the CNT is "squashed" or not if you don't change the tight-binding model itself. Calculating the way in which such a deformation affects the tight-binding parameters is beyond the scope of Kwant and you would need to use a different tool to do this for you.

Hope that clarifies,

Joe

Dear Joe,

Thanks for explanation; but my question was not about tight binding. I have constructed my tight binding model and I know matrix elements between all pairs of atoms.

My question was about how to enter the geometry of a (1D) CNT in KWANT. Suppose that I want to enter the attached output.cif file, as a lead. How should I enter the atomic positions and ensure that the periodicity of the CNT is preserved?

Many thanks

Roohollah Hafizi wrote:

My question was about how to enter the geometry of a (1D) CNT in KWANT. Suppose that I want to enter the attached output.cif file, as a lead. How should I enter the atomic positions and ensure that the periodicity of the CNT is preserved?

The easiest way is to use 2d graphene with periodic boundary conditions. You create a Kwant builder with _two_ translational symmetry directions: one is the usual longitudinal translational symmetry of the lead, the other the transversal periodicity.

Kwant currently does not allow the finalization of builders with more than a single translational symmetry, but the wraparound module [1] will help you. Let's say symmetry 0 is the longitudinal one and symmetry 1 is the transversal periodicity. Then

syst_wrapped = wraparound.wraparound(syst, keep=0)

will give you a Kwant builder with only a single symmetry that can be finalized. Compared to syst, syst_wrapped has gained an argument: the transversal momentum. When using the finalized syst_wrapped with solvers, you will have to provide a value for that argument. For periodic boundary conditions it should be simply set to zero.

You could also create "real" 3d CNTs in Kwant by creating a new site family. See the documentation of SiteFamily for more information.

Hope this helps, Christoph

[1] https://gitlab.kwant-project.org/cwg/wraparound