Le 12 mai 2022 à 16:23, Blackwell, Raymond <rblackwel@bnl.gov> a écrit :

Hi Xavier, 

 

I appreciate your help! I updated my code to the following but now I receive an error that traces back to the Random_sites line and says that the list index is out of range. If I attempt to print sites2 then the output is an empty list. This is a bit confusing to me, is it because the system is not yet finalized? Once again thank you so much for your help!

 

 

def make_syst(r=30, t=-1, a=1):

    

    syst = kwant.Builder()

    lat = kwant.lattice.honeycomb(a, norbs=1)

    sites2 = list(syst.sites())

    Random_sites = random.choices(sites2, k = 10)

    

    def onsite(site): 

        return 0.5 * kwant.digest.uniform(repr(Random_sites)) + 0.5

 

    def circle(pos):

        x, y = pos

        return x ** 2 + y ** 2 < r ** 2

    

 

    syst[lat.shape(circle, Random_sites)] = onsite

    syst[lat.neighbors()] = t

    syst.eradicate_dangling()

 

    return syst

 

From: Xavier Waintal <xavier.waintal@cea.fr> 
Sent: Thursday, May 12, 2022 2:25 AM
To: Blackwell, Raymond <rblackwel@bnl.gov>
Cc: kwant-discuss@python.org
Subject: Re: [Kwant] Help: Inputting Random Potential on Graphene 

 

Dear Raymond,

 

I think that the problem comes from the last line of your code.

 

syst[lat.shape(circle, (0, 0))] = onsite(bytes(3),bytes(3))

 

calls the function onsite with the 2 arguments you provided and then assign the result to all the sites.

What you want to do is

 

syst[lat.shape(circle, (0, 0))] = onsite

 

In that case, when iterating over the sites, kwant will call the onsite function for each site.

See the documentation for providing the salt parameter, e.g. https://kwant-project.org/doc/1/tutorial/spin_potential_shape in the quantum_well.py example.

 

Best regards,

 

Xavier

 

 

Le 12 mai 2022 à 00:26, Blackwell, Raymond <rblackwel@bnl.gov> a écrit :

 

Hello, 

 

My name is Raymond Blackwell and I am attempting to use Kwant to simulate some experimental data. Our data involves dopant atoms intercalated under graphene, so I would like to simulate the LDOS but with a potential that randomly varies at several points within the system. I am trying to modify the code for the kernel_polynominal_method, but I cannot seem to get a random potential. I have used a similar method to randomly select a few points and modify the hopping parameter, but I am struggling with the seemingly more simple case where the potential varies. 

 

The relevant portion of my code is below. 

 

def make_syst(r=30, t=-1, a=1):

    syst = kwant.Builder()

    lat = kwant.lattice.honeycomb(a, norbs=1)

 

    def circle(pos):

        x, y = pos

        return x ** 2 + y ** 2 < r ** 2

    sites2 = list(syst.sites())

    Random_sites= random.choices(sites2, k=10)

    

    def onsite(site, salt): 

        return 0.5 * kwant.digest.gauss(repr(Random_sites), salt)

 

    syst[lat.shape(circle, (0, 0))] = onsite(bytes(3),bytes(3))

 

Any help is greatly appreciated! 

 

Best, 

-Raymond