Hi everyone, thank you for your answers and suggestions,
First of all i would like to say that im not experienced using Kwant, i
read the examples provided in the web site and i think i understand a
little more about the syntax used in kwant (Thank you Alexandre an Joseph).
But im still confused about some definitions
1) Alexandre, thank you for you suggestions, but honestly Im not pretty
sure how to define a "superatom" that reproduces the structure im working
on. How should i define the sites for each atom in the lattice?
2) Joseph, thank you for the detailed explanation, i rewrote that part of
the code following your instructions and i think is better now, but i cant
figure a way to describe the interactions that occur "inside" the same
atom, for example, Re has 6 orbitals, how can i express the hoppings that
have place in the same site?
Thank you for your time
P.D. The code so far is giving me an error in the leads apparently
/home/sergio/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:197:
RuntimeWarning: When finalizing lead 0: Infinite system with
disconnected cells.
/home/sergio/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:197:
RuntimeWarning: When finalizing lead 1: Infinite system with
disconnected cells.
---------------------------------------------------------------------------ValueError
Traceback (most recent call
last)<ipython-input-3-882bfab14ea6> in <module>() 200 201 if
__name__ == '__main__':--> 202 main()
<ipython-input-3-882bfab14ea6> in main() 196
site_color=family_colors) 197 syst = syst.finalized()--> 198
plot_conductance(syst, energies=[0.01 * i - 0.3 for i in range(100)])
199 200
<ipython-input-3-882bfab14ea6> in plot_conductance(syst, energies)
174 data = [] 175 for energy in energies:--> 176
smatrix = kwant.smatrix(syst, energy) 177
data.append(smatrix.transmission(1, 0)) 178 pyplot.figure()
~/anaconda3/lib/python3.6/site-packages/kwant/solvers/common.py in
smatrix(self, sys, energy, args, out_leads, in_leads,
check_hermiticity, params) 373 374 kept_vars =
np.concatenate([coords for i, coords in--> 375
enumerate(linsys.indices) if i in 376
out_leads]) 377
ValueError: need at least one array to concatenate
Here is the code so far:
import kwant
import tinyarray
import numpy
from matplotlib import pyplot
VecPrim = [(3.176, 0, 0), (1.588, 2.7504, 0), (0, 0, 17.49)]
base = [(0, 0, 0), (1.588, 0.9168, 0.8745), (0, 0, 1.749)]
lat = kwant.lattice.general(prim_vecs = VecPrim, basis = base, name = ['C',
'Re', 'N'], norbs = [3, 6, 3])
C, Re, N = lat.sublattices
C_C_ons = numpy.array ([[-1.888842, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, -1.784936, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0.710443, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
C_C_hop = numpy.array ([[0, -0.014064-0.000409j, 0.026908+0.003422j, 0, 0,
0, 0, 0, 0, 0, 0, 0],
[-0.014064+0.000409j, 0, -0.031384+0.021565j, 0, 0,
0, 0, 0, 0, 0, 0, 0],
[0.026908-0.003422j, -0.031384-0.021565j, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
Re_Re_ons = numpy.array ([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 7.168134, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0.245358, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 1.338059, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 1.325337, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0.362102, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, -0.650839, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
Re_Re_hop = numpy.array ([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, -0.005189-0.047376j,
0.001352+0.000103j, -0.001189-0.00095j, -0.048166-0.007663j,
0.429882+0.00052j, 0, 0, 0],
[0, 0, 0, -0.005189+0.047376j, 0,
0.113162-0.072937j, 0.660849-0.06348j, -0.017571+0.035587j,
0.020961-0.017679j, 0, 0, 0],
[0, 0, 0, 0.001352-0.000103j, 0.113162+0.072937j,
0, -0.003126-0.016285j, -0.624702-0.065652j, 0.002353+0.001639j, 0, 0, 0],
[0, 0, 0, -0.001189+0.00095j, 0.660849+0.06348j,
-0.003126+0.016285j, 0, 0.110694+0.01548j, 0.009041+0.004483j, 0, 0, 0],
[0, 0, 0, -0.048166+0.007663j,
-0.017571-0.035587j, -0.624702+0.065652j, 0.110694-0.01548j, 0,
-0.030934+0.002401j, 0, 0, 0],
[0, 0, 0, 0.429882-0.00052j, 0.020961+0.017679j,
0.002353-0.001639j, 0.009041-0.004483j, -0.030934-0.002401j, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
N_N_ons = numpy.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, -3.398186, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3.401815, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -0.637207]])
N_N_hop = numpy.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.001839+0.001631j,
-0.117366+0.00498j],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0.001839-0.001631j, 0,
0.023339+0.009067j],
[0, 0, 0, 0, 0, 0, 0, 0, 0, -0.117366-0.00498j,
0.023339-0.009067j, 0]])
C_Re_hop = numpy.array([[0, 0, 0, 0.003644+0.00088j, -0.305706-0.050514j,
0.638425-0.083597j, -1.105645+0.086829j, 1.463462-0.012994j,
-0.01338-0.00264j, 0, 0, 0],
[0, 0, 0, -0.046131+0.04229j, -1.963829-0.280977j,
-1.171301-0.088146j, -1.112788-0.056971j, 0.174769+0.106872j,
-0.058159-0.007987j, 0, 0, 0],
[0, 0, 0, 0.23188+0.001924j, -0.597505-0.078772j,
-0.146976-0.012943j, -0.210584+0.002248j, 0.177022+0.031485j,
0.953363-0.001855j, 0, 0, 0],
[0.003644-0.00088j, -0.046131-0.04229j,
0.23188-0.001924j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[-0.305706+0.050514j, -1.963829+0.280977j,
-0.597505+0.078772j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0.638425+0.083597j, -1.171301+0.088146j,
-0.146976+0.012943j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[-1.105645-0.086829j, -1.112788+0.056971j,
-0.210584-0.002248j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[1.463462+0.012994j, 0.174769-0.106872j,
0.177022-0.031485j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[-0.01338+0.00264j, -0.058159+0.007987j,
0.953363+0.001855j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
C_N_hop = numpy.array ([[0, 0, 0, 0, 0, 0, 0, 0, 0, -1.852931+0.147524j,
0.274586-0.034451j, -0.015051-0.001677j],
[0, 0, 0, 0, 0, 0, 0, 0, 0, -0.274338-0.015064j,
-1.796449-0.055331j, -0.034396+0.019407j],
[0, 0, 0, 0, 0, 0, 0, 0, 0, -0.103127+0.001438j,
0.004816-0.00237j, 3.410475+0.001248j],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[-1.852931-0.147524j, -0.274338+0.015064j,
-0.103127-0.001438j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0.274586+0.034451j, -1.796449+0.055331j,
0.004816+0.00237j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[-0.015051+0.001677j, -0.034396-0.019407j,
3.410475-0.001248j, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
Re_N_hop = numpy.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0.184152+0.002778j,
0.321743-0.010571j, 0.183538-0.00067j],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0.275145+0.007691j,
-0.54144+0.012815j, 0.045847+0.015379j],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0.47922+0.015775j,
1.256012+0.007326j, -0.523174+0.00585j],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 1.255561-0.002255j,
1.903063+0.010647j, -0.876392+0.010246j],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 1.282837-0.091022j,
-0.54898+0.001161j, 0.057341-0.004095j],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0.02765-0.001793j,
-0.002902-0.001866j, -0.746426-0.000748j],
[0, 0, 0, 0.184152-0.002778j, 0.275145-0.007691j,
0.47922-0.015775j, 1.255561+0.002255j, 1.282837+0.091022j,
0.02765+0.001793j, 0, 0, 0],
[0, 0, 0, 0.321743+0.010571j, -0.54144-0.012815j,
1.256012-0.007326j, 1.903063-0.010647j,
-0.54898-0.001161j,-0.002902+0.001866j, 0, 0, 0],
[0, 0, 0, 0.183538+0.00067j, 0.045847-0.015379j,
-0.523174-0.00585j, -0.876392-0.010246j,
0.057341+0.004095j,-0.746426+0.000748j, 0, 0, 0]])
def make_cuboid(t=1.0, a=15, b=10, c=5):
def cuboid_shape(pos):
x, y, z = pos
return 0 <= x < a and 0 <= y < b and 0 <= z < c
syst = kwant.Builder()
syst[lat.shape(cuboid_shape, (0, 0, 0))] = 4 * t
syst[C(0, 0, 0)]= C_C_ons
syst[Re(0, 0, 0)]= Re_Re_ons
syst[N(0, 0, 0)]= N_N_ons
syst[C(0, 0, 0), Re(0, 0, 0)] = C_Re_hop
syst[C(0, 0, 0), N(0, 0, 0)] = C_N_hop
syst[Re(0, 0, 0), N(0, 0, 0)] = Re_N_hop
##### syst[C(0, 0, 0), C(0, 0, 0)] = C_C_hop
##### syst[Re(0, 0, 0), Re(0, 0, 0)] = Re_Re_hop
##### syst[N(0, 0, 0), N(0, 0, 0)] = N_N_hop
##### syst[[kwant.builder.HoppingKind(*hopping) for hopping in
hoppings]] = -6
lead = kwant.Builder(kwant.TranslationalSymmetry((-3.176, 0, 0)))
def lead_shape(pos):
return 0 <= pos[1] < b and 0 <= pos[2] < c
lead[lat.shape(lead_shape, (0, 0, 0))] = 4 * t
syst[C(0, 0, 0)]= C_C_ons
syst[Re(0, 0, 0)]= Re_Re_ons
syst[N(0, 0, 0)]= N_N_ons
syst[C(0, 0, 0), Re(0, 0, 0)] = C_Re_hop
syst[C(0, 0, 0), N(0, 0, 0)] = C_N_hop
syst[Re(0, 0, 0), N(0, 0, 0)] = Re_N_hop
#### lead[[kwant.builder.HoppingKind(*hopping) for hopping in hoppings]]
= -6
syst.attach_lead(lead)
syst.attach_lead(lead.reversed())
return syst
def plot_conductance(syst, energies):
data = []
for energy in energies:
smatrix = kwant.smatrix(syst, energy)
data.append(smatrix.transmission(1, 0))
pyplot.figure()
pyplot.plot(energies, data)
pyplot.xlabel("energy [t]")
pyplot.ylabel("conductance [e^2/h]")
pyplot.show()
def main():
syst = make_cuboid()
kwant.plot(syst)
syst = make_cuboid(a=100, b=28, c=4)
def family_colors(site):
if site.family == C:
return 'yellow'
elif site.family == Re:
return 'gray'
else:
return 'blue'
kwant.plot(syst, site_size=0.25, site_lw=0.025, hop_lw=0.05,
site_color=family_colors)
syst = syst.finalized()
plot_conductance(syst, energies=[0.01 * i - 0.3 for i in range(100)])
if __name__ == '__main__':
main()
2018-06-08 1:21 GMT-07:00 Joseph Weston <joseph.westo...@gmail.com>:
> Hi all,
>
>
> Sergio, if you want to create a Polyatomic lattice you have to pass all
> the basis vectors and orbital numbers in a single call to
> 'kwant.lattice.general', otherwise there's no way Kwant can know that you
> want the 3 sublattices to be considered as a single Polyatomic lattice!
>
> prim_vecs = [...] # Bravais lattice vectors
>
> basis [ [...], [...], [...]] # position vectors of the 3 basis atoms
>
> norbs = [3, 6, 3]
>
> lat = general(prim_vecs, basis=basis, norbs=norbs)
>
> a, b, c = lat.sublattices
>
> ...
>
> syst[a(0, 0, 0), b(0, 0, 0)] = [...] # a-b hopping in same unit cell
> syst[a(0, 0, 0), c(1, 0, 0)] = [...] # a-c hopping in between unit
> cells
>
> This is covered briefly in the tutorial [1]; do you think we can improved
> that section of the tutorial in some way?
>
> Happy Kwanting,
>
> Joe
>
>
> [1]: https://kwant-project.org/doc/1/tutorial/graphene
>
>
>
> On 06/07/2018 12:05 PM, alexandre.berna...@u-psud.fr wrote:
>
> Hello,
>
> First of all, I am new to kwant, so I hope I will give you relevant
> insights.
>
> It seems to me that:
>
> 1) There are some mistakes in the syntax you are using, so you should
> check again the examples available in the doc :
> https://kwant-project.org/doc/1/
>
> 2) Since you consider different numbers of orbitals for your atoms, I
> think you should use only one "superatom" with 12 orbitals per unit cell.
> Then Kwant allows to define 12x12 matrices both for the on-site terms
> (your matrix elements within the superatom) and for the hopping terms (your
> matrix elements between superatoms).
>
> I hope this is a bit helpfull.
>
> Best regards,
>
> Alexandre BERNARD
>
> ------------------------------
> *De: *"Sergio Castillo Robles" <sergio.casti...@uabc.edu.mx>
> <sergio.casti...@uabc.edu.mx>
> *À: *kwant-discuss@kwant-project.org
> *Envoyé: *Mercredi 6 Juin 2018 03:54:21
> *Objet: *[Kwant] Defining orbitals in a 3D structure with 3 basis atoms.
>
> Hello everyone, i would appreciate any suggestion you could give me to
> solve this.
>
> Well, im trying to create a structure with 3 basis atoms in the unit cell,
> each atom has a different number of orbitals a=3, b=6 and c=3. I have tried
> with polyatomic module and creating one lattice for each atom with no
> success
>
> The thing is that i cant figure it out how to create a lattice with
> different orbitals in each site. I have the on-site and hopping energies
> matrix so i need to be able to introduce this values.
>
> Im pretty new using kwant so any advice is appreciated.
>
> Here is the code i've working on (ignore the matrix elements for the
> moment):
>
> import kwant
> import tinyarray
> import numpy
> from matplotlib import pyplot
>
> VecPrim = [(3.176, 0, 0), (1.588, 2.7504, 0), (0, 0, 17.49)]
> base = [(0, 0, 0), (1.588, 0.9168, 0.8745), (0, 0, 1.749)]
>
> ### This is the part that i cant get it right, i have tried
> kwant.lattice.polyatomic
> ### and defining 3 lattices one for each atom, but no success
>
> a = kwant.lattice.general(prim_vecs = VecPrim, basis = (0, 0, 0))
> Cpx, Cpy, Cpz, = a.sublattices
> b = kwant.lattice.general(prim_vecs = VecPrim, basis = (1.588, 0.9168,
> 0.8745))
> xy, xz, yz, x2y2, z2, s = b.sublattices
> c = kwant.lattice.general(prim_vecs = VecPrim, basis = (0, 0, 1.749))
> Npx, Npy, Npz = c.sublattices
>
> ### Ignore from here ###
>
> def make_cuboid(t=1.0, a=15, b=10, c=5):
> def cuboid_shape(pos):
> x, y, z = pos
> return 0 <= x < a and 0 <= y < b and 0 <= z < c
> syst = kwant.Builder()
> syst[lat.shape(cuboid_shape, (0, 0, 0))] = 4 * t
>
> syst[lat(0, 0, 0)] = numpy.array([[-1.888842, -0.014064-0.000409j,
> 0.026908+0.003422j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [-0.014064+0.000409j, -1.784936,
> -0.031384+0.021565j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0.026908-0.003422j,
> -0.031384-0.021565j, 0.710443, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0]])
>
> syst[lat(0, 1, 0)] = numpy.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 7.168134,
> -0.005189-0.047376j, 0.001352+0.000103j, -0.001189-0.00095j,
> -0.048166-0.007663j, 0.429882+0.00052j, 0, 0, 0],
> [0, 0, 0, -0.005189+0.047376j,
> 0.245358, 0.113162-0.072937j, 0.660849-0.06348j, -0.017571+0.035587j,
> 0.020961-0.017679j, 0, 0, 0],
> [0, 0, 0, 0.001352-0.000103j,
> 0.113162+0.072937j, 1.338059, -0.003126-0.016285j, -0.624702-0.065652j,
> 0.002353+0.001639j, 0, 0, 0],
> [0, 0, 0, -0.001189+0.00095j,
> 0.660849+0.06348j, -0.003126+0.016285j, 1.325337, 0.110694+0.01548j,
> 0.009041+0.004483j, 0, 0, 0],
> [0, 0, 0, -0.048166+0.007663j,
> -0.017571-0.035587j, -0.624702+0.065652j, 0.110694-0.01548j, 0.362102,
> -0.030934+0.002401j, 0, 0, 0],
> [0, 0, 0, 0.429882-0.00052j,
> 0.020961+0.017679j, 0.002353-0.001639j, 0.009041-0.004483j,
> -0.030934-0.002401j, -0.650839, 0, 0, 0]
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0]])
>
> syst[lat(0, 0, 1)] = numpy.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0,
> -3.398186, 0.001839+0.001631j, -0.117366+0.00498j],
> [0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0.001839-0.001631j, -3.401815, 0.023339+0.009067j],
> [0, 0, 0, 0, 0, 0, 0, 0, 0,
> -0.117366-0.00498j, 0.023339-0.009067j, -0.637207]])
>
> syst[lat(0, 0, 1), lat (0, 0, 0)] = ([[0, 0, 0, 0, 0, 0, 0, 0, 0,
> -1.852931+0.147524j, 0.274586-0.034451j, -0.015051-0.001677j],
> [0, 0, 0, 0, 0, 0, 0, 0, 0,
> -0.274338-0.015064j, -1.796449-0.055331j, -0.034396+0.019407j],
> [0, 0, 0, 0, 0, 0, 0, 0, 0,
> -0.103127+0.001438j, 0.004816-0.00237j, 3.410475+0.001248j],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [-1.852931-0.147524j,
> -0.274338+0.015064j, -0.103127-0.001438j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0.274586+0.034451j,
> -1.796449+0.055331j, 0.004816+0.00237j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [-0.015051+0.001677j,
> -0.034396-0.019407j, 3.410475-0.001248j, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
>
> syst[lat(0, 1, 0), lat(0, 0, 0)] = ([[0, 0, 0, 0.003644+0.00088j,
> -0.305706-0.050514j, 0.638425-0.083597j, -1.105645+0.086829j,
> 1.463462-0.012994j, -0.01338-0.00264j, 0, 0, 0],
> [0, 0, 0, -0.046131+0.04229j,
> -1.963829-0.280977j, -1.171301-0.088146j, -1.112788-0.056971j,
> 0.174769+0.106872j, -0.058159-0.007987j, 0, 0, 0],
> [0, 0, 0, 0.23188+0.001924j,
> -0.597505-0.078772j, -0.146976-0.012943j, -0.210584+0.002248j,
> 0.177022+0.031485j, 0.953363-0.001855j, 0, 0, 0],
> [0.003644-0.00088j,
> -0.046131-0.04229j, 0.23188-0.001924j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [-0.305706+0.050514j,
> -1.963829+0.280977j, -0.597505+0.078772j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0.638425+0.083597j,
> -1.171301+0.088146j, -0.146976+0.012943j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [-1.105645-0.086829j,
> -1.112788+0.056971j, -0.210584-0.002248j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [1.463462+0.012994j,
> 0.174769-0.106872j, 0.177022-0.031485j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [-0.01338+0.00264j,
> -0.058159+0.007987j, 0.953363+0.001855j, 0, 0, 0, 0, 0, 0, 0, 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0]])
>
> syst[lat(0, 0, 1), lat(0, 1, 0)] = ([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0],
> [0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0.184152+0.002778j, 0.321743-0.010571j, 0.183538-0.00067j],
> [0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0.275145+0.007691j, -0.54144+0.012815j, 0.045847+0.015379j],
> [0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0.47922+0.015775j, 1.256012+0.007326j, -0.523174+0.00585j],
> [0, 0, 0, 0, 0, 0, 0, 0, 0,
> 1.255561-0.002255j, 1.903063+0.010647j, -0.876392+0.010246j],
> [0, 0, 0, 0, 0, 0, 0, 0, 0,
> 1.282837-0.091022j, -0.54898+0.001161j, 0.057341-0.004095j],
> [0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0.02765-0.001793j, -0.002902-0.001866j, -0.746426-0.000748j],
> [0, 0, 0, 0.184152-0.002778j,
> 0.275145-0.007691j, 0.47922-0.015775j, 1.255561+0.002255j,
> 1.282837+0.091022j, 0.02765+0.001793j, 0, 0, 0],
> [0, 0, 0, 0.321743+0.010571j,
> -0.54144-0.012815j, 1.256012-0.007326j, 1.903063-0.010647j,
> -0.54898-0.001161j,-0.002902+0.001866j, 0, 0, 0],
> [0, 0, 0, 0.183538+0.00067j,
> 0.045847-0.015379j, -0.523174-0.00585j, -0.876392-0.010246j,
> 0.057341+0.004095j,-0.746426+0.000748j, 0, 0, 0]])
>
> ### 'Till here #####
>
> syst[[kwant.builder.HoppingKind(*hopping) for hopping in hoppings]] =
> -6
> lead = kwant.Builder(kwant.TranslationalSymmetry((-3.176, 0, 0)))
> def lead_shape(pos):
> return 0 <= pos[1] < b and 0 <= pos[2] < c
> lead[lat.shape(lead_shape, (0, 0, 0))] = 4 * t
> lead[[kwant.builder.HoppingKind(*hopping) for hopping in hoppings]] =
> -6
> syst.attach_lead(lead)
> syst.attach_lead(lead.reversed())
> return syst
>
> def plot_conductance(syst, energies):
> data = []
> for energy in energies:
> smatrix = kwant.smatrix(syst, energy)
> data.append(smatrix.transmission(1, 0))
> pyplot.figure()
> pyplot.plot(energies, data)
> pyplot.xlabel("energy [t]")
> pyplot.ylabel("conductance [e^2/h]")
> pyplot.show()
>
> def main():
> syst = make_cuboid()
> kwant.plot(syst)
> syst = make_cuboid(a=100, b=28, c=4)
> def family_colors(site):
> if site.family == d:
> return 'yellow'
> elif site.family == e:
> return 'gray'
> else:
> return 'blue'
> kwant.plot(syst, site_size=0.25, site_lw=0.025, hop_lw=0.05,
> site_color=family_colors)
> syst = syst.finalized()
> plot_conductance(syst, energies=[0.01 * i - 0.3 for i in range(100)])
>
>
> if __name__ == '__main__':
> main()
>
>
>
>
