Mailman 3 January 2021 - Kwant-discuss

plot circle/line in kwant plot
by Nafise Nouri 22 Jan '21

22 Jan '21

Dear all, I need to highlight some parts of my kwant.plot(syst) with some lines and circles. Is there anyone to help me? Best, Nafise

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Defining shape of leads to avoid generation of extra lattice sites
by Henry Axt 22 Jan '21

22 Jan '21

Hello, I am modeling a graphene lattice that is rectangular in shape. graphene = kwant.lattice.general([(1, 0), (sin_30, os_30)], [(0, 0), (0, 1 / sqrt(3))]) When you attach the leads (with symmetry parallel to the rectangle edges), extra lattice sites get added. I want to avoid this and my thinking is that you define a seperate lattice for the leads, such that it is a unit cell translatable like a square lattice, which in this case would be something like: lattice_lead = kwant.lattice.general([(1, 0), (0, 2*cos_30)], [(0, 0), (0, l(1 / sqrt(3))),(0.5,((1/sqrt(3))+(tan_30*0.5))),(0.5,((2/sqrt(3))+(tan_30*0.5)))]) My question is firstly, is this the way to go about it? And secondly, how does this interplay with the sublattices and thier hoppings?

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Is there a way to create polymorphic lattices in Kwant?
by Ran Mutc 15 Jan '21

15 Jan '21

Hello, I am trying to create a modified graphene lattice which consists of not hexagons but pentagons and heptagons, like the one in the following link: https://www.researchgate.net/figure/Geometrically-optimized-structure-of-5-… Can anyone help how can I do that? Thanks, Ran

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Defining hoppings between two lattices, each with a set of sublattices - Outputting list of hoppings
by henry.axt＠physik.rwth-aachen.de 14 Jan '21

14 Jan '21

Hello, I have set up a system in which I want to define hoppings in a lead between sites that originate from two sublattices: LatticeA has sublatices a and b, LatticeB has sublattices c and d. Currently, I believe I am achieving this via: for site in lead2.sites(): (x,y) = site.pos if str(site.family) == "<Monatomic lattice e0>": lead2[c(x,y),a(x,y)] = Delta if str(site.family) == "<Monatomic lattice e1>": lead2[d(x,y),b(x,y)] = Delta and thereby connecting sublattices c and a, and d and b. Is this accurate? Can this be done with HoppingKind? And is there a way for me to list all the hoppings created to check if this was successful?

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About spin density calculations
by Yizhou Liu 09 Jan '21

09 Jan '21

Hello, I'm confused by some problem when doing time-dependent spin related transport calculations by tkwant. Let me briefly introduce what the main problem is. I'm now considering a 1D chain model with some magnetic spin moment on some of the sites. By applying a voltage to one lead, I want to know how the spin accumulate near the other lead. My problem is that in my code the calculated spin density and charge density near the second lead are always same which I believe should not be true because this means that only one spin channel is always occupied and the other is always empty! My code is as follows: import tkwant import kwant from matplotlib import pyplot as plt from math import pi, sqrt, cos, sin from cmath import atan import numpy as np ############ spin matrix ############# s0=np.array([[1,0],[0,1]]) sx=np.array([[0,1],[1,0]]) sy=np.array([[0,-1j],[1j,0]]) sz=np.array([[1,0],[0,-1]]) length=10 l_M=1 M=0.2 t=1 times=range(200) lat = kwant.lattice.general([(5,0,0),(0,5,0),(0,0,1)], [(2.5,2.5,0)],norbs=2) def scattering_region(pos): x,y,z=pos return abs(x-2.5)<=1 and abs(y-2.5)<=1 and z>=0 and z<=length-1 def mag_region0(pos): x,y,z=pos return abs(x-2.5)<=1 and abs(y-2.5)<=1 and z<=-1 and z>=-l_M def mag_region1(pos): x,y,z=pos return abs(x-2.5)<=1 and abs(y-2.5)<=1 and z>=length and z<=length+l_M-1 syst=kwant.Builder() syst[lat.shape(scattering_region, (2.5, 2.5, 0))]=0*s0 syst[lat.shape(mag_region0, (2.5, 2.5, -1))]=M*sz syst[lat.shape(mag_region1, (2.5, 2.5, length))]=M*sz for i in range (length+2*l_M-1): syst[lat.sublattices[0](0,0,i-l_M),lat.sublattices[0](0,0,i-l_M+1)]=t*s0 def lead_region(pos): x,y,z=pos return abs(x-2.5)<=1 and abs(y-2.5)<=1 lead=kwant.Builder(kwant.TranslationalSymmetry(lat.vec((0,0,-1))),conservation_law=-sz) lead[lat.shape(lead_region, (2.5,2.5,0))]=0*s0 lead[lat.neighbors()]=t*s0 def phi(time): Vb, tau= 0.6, 20 if time > tau: return Vb*time - Vb*tau/2 return Vb*time*time/2/tau syst.attach_lead(lead) syst.attach_lead(lead.reversed()) kwant.plot(syst,site_size=0.2,site_lw=0.01,hop_lw=0.05) tkwant.leads.add_voltage(syst,0,phi) syst=syst.finalized() def current_cut(site_to, site_from): return site_from.pos[2]<=length-1 and site_to.pos[2]>length-1 def density_cut(site): return site.pos[2]>=length and site.pos[2]<=length+l_M-1 current_operator=kwant.operator.Current(syst,where=current_cut) charge_density_operator=kwant.operator.Density(syst,s0,where=density_cut) spin_density_operator=kwant.operator.Density(syst,sz,where=density_cut) occupy=tkwant.manybody.lead_occupation(chemical_potential=-0.5) print('make up of state ...') state=tkwant.manybody.State(syst,tmax=max(times),occupations=occupy,refine=False,combine=True) Currents=[] Charge=[] Spin=[] for time in times: print('%.4f percent ...' % (100*times.index(time)/len(times))) state.evolve(time) current=state.evaluate(current_operator) charge=state.evaluate(charge_density_operator) spin=state.evaluate(spin_density_operator) Currents.append(current) Charge.append(charge) Spin.append(spin) np.savetxt('Times_linear_chain.txt',times) np.savetxt('Current_linear_chain.txt',Currents) np.savetxt('Charge_density_linear_chain.txt',Charge) np.savetxt('Spin_density_linear_chain.txt',Spin) plt.figure() plt.plot(times,Currents) plt.xlabel('time $t$') plt.ylabel('Current $I$') plt.show() plt.figure() plt.subplot(211) plt.plot(times,Charge) plt.xlabel('time $t$') plt.ylabel('Charge density') plt.subplot(212) plt.plot(times,Spin) plt.xlabel('time $t$') plt.ylabel('Spin density') plt.show() Does anyone know where the problem is? -Yizhou LIU

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How to build a non-hermitian system?
by Liu Feng 07 Jan '21

07 Jan '21

Dear colleagues, I would like to study a non-hermitian system using kwant. It seems that the Builder class forcibly ensures hermitian hoppings, is there any method to turn it off? Many thanks! Best regards Feng Liu

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