Sergio Castillo Robles
2018-09-07 07:55:18 UTC
Hello everyone, i would appreciate any suggestion you could give me to
solve this
Im trying to plot the conductance for a two dimensional array of 3 basis
atoms, i have defined the atoms positions, the onsite energies and hoppings
matrices and the leads but it is showing me this error:
(i search in the mailing list but theres no info about it)
ValueError Traceback (most recent call
last)<ipython-input-1-ee484ce5ea50> in <module>() 111 112 if
__name__ == '__main__':--> 113 main()
<ipython-input-1-ee484ce5ea50> in main() 107
site_color=family_colors) 108 syst = syst.finalized()--> 109
plot_conductance(syst, energies=[0.01 * i - 0.3 for i in range(100)])
110 111
<ipython-input-1-ee484ce5ea50> in plot_conductance(syst, energies)
85 data = [] 86 for energy in energies:---> 87
smatrix = kwant.smatrix(syst, energy) 88
data.append(smatrix.transmission(1, 0)) 89 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) 370 linsys, lead_info =
self._make_linear_sys(syst, in_leads, energy, args, 371
check_hermiticity, False,--> 372
params=params)
373 374 kept_vars = np.concatenate([coords for i, coords
in
~/anaconda3/lib/python3.6/site-packages/kwant/solvers/common.py in
_make_linear_sys(self, sys, in_leads, energy, args, check_hermiticity,
realspace, params) 162 lhs, norb =
syst.hamiltonian_submatrix(args, sparse=True, 163
return_norb=True,--> 164
params=params)[:2] 165 lhs =
getattr(lhs, 'to' + self.lhsformat)() 166 lhs = lhs -
energy * sp.identity(lhs.shape[0], format=self.lhsformat)
kwant/_system.pyx in kwant._system.hamiltonian_submatrix()
kwant/_system.pyx in kwant._system.make_sparse_full()
ValueError: Hopping from site 407 to site 814 does not match the
dimensions of onsite Hamiltonians of these sites.
Here is the code so far:
import kwant
import tinyarray
import numpy
from matplotlib import pyplot
%matplotlib notebook
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)
c1, c2, c3 = lat.sublattices
c1_ons = numpy.array([[-1.888842, -0.014064-0.000409j, 0.026908+0.003422j],
[-0.014064+0.000409j, -1.784936, -0.031384+0.021565j],
[0.026908-0.003422j, -0.031384-0.021565j, 0.710443]])
c2_ons = numpy.array([[7.168134, -0.005189-0.047376j, 0.001352+0.000103j,
-0.001189-0.00095j, -0.048166-0.007663j, 0.429882+0.00052j],
[-0.005189+0.047376j, 0.245358, 0.113162-0.072937j,
0.660849-0.06348j, -0.017571+0.035587j, 0.020961-0.017679j],
[0.001352-0.000103j, 0.113162+0.072937j, 1.338059,
-0.003126-0.016285j, -0.624702-0.065652j, 0.002353+0.001639j],
[-0.001189+0.00095j, 0.660849+0.06348j,
-0.003126+0.016285j, 1.325337, 0.110694+0.01548j, 0.009041+0.004483j],
[-0.048166+0.007663j, -0.017571-0.035587j,
-0.624702+0.065652j, 0.110694-0.01548j, 0.362102, -0.030934+0.002401j],
[0.429882-0.00052j, 0.020961+0.017679j,
0.002353-0.001639j, 0.009041-0.004483j, -0.030934-0.002401j, -0.650839]])
c3_ons = numpy.array([[-3.398186, 0.001839+0.001631j, -0.117366+0.00498j],
[0.001839-0.001631j, -3.401815, 0.023339+0.009067j],
[-0.117366-0.00498j, 0.023339-0.009067j, -0.637207]])
c1_c3_hop = numpy.array([[-1.852931-0.147524j, -0.274338+0.015064j,
-0.103127-0.001438j],
[0.274586+0.034451j, -1.796449+0.055331j,
0.004816+0.00237j],
[-0.015051+0.001677j, -0.034396-0.019407j,
3.410475-0.001248j]])
c1_c2_hop = numpy.array([[0.003644-0.00088j, -0.046131-0.04229j,
0.23188-0.001924j],
[-0.305706+0.050514j, -1.963829+0.280977j,
-0.597505+0.078772j],
[0.638425+0.083597j, -1.171301+0.088146j,
-0.146976+0.012943j],
[-1.105645-0.086829j, -1.112788+0.056971j,
-0.210584-0.002248j],
[1.463462+0.012994j, 0.174769-0.106872j,
0.177022-0.031485j],
[-0.01338+0.00264j, -0.058159+0.007987j,
0.953363+0.001855j]])
c2_c3_hop = numpy.array([[0.184152+0.002778j, 0.321743-0.010571j,
0.183538-0.00067j],
[0.275145+0.007691j, -0.54144+0.012815j,
0.045847+0.015379j],
[0.47922+0.015775j, 1.256012+0.007326j,
-0.523174+0.00585j],
[1.255561-0.002255j, 1.903063+0.010647j,
-0.876392+0.010246j],
[1.282837-0.091022j, -0.54898+0.001161j,
0.057341-0.004095j],
[0.02765-0.001793j, -0.002902-0.001866j,
-0.746426-0.000748j]])
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[c1.shape(cuboid_shape, (0, 0, 0))] = c1_ons
syst[c2.shape(cuboid_shape, (0, 1, 0))] = c2_ons
syst[c3.shape(cuboid_shape, (0, 0, 1))] = c3_ons
syst[kwant.builder.HoppingKind((0, 0, 0), c2, c1)] = c1_c2_hop
syst[kwant.builder.HoppingKind((-1, 0, 0), c2, c1)] = c1_c2_hop
syst[kwant.builder.HoppingKind((0, -1, 0), c2, c1)] = c1_c2_hop
syst[kwant.builder.HoppingKind((0, 0, 0), c3, c2)] = c2_c3_hop
syst[kwant.builder.HoppingKind((1, 0, 0), c3, c2)] = c2_c3_hop
syst[kwant.builder.HoppingKind((0, 1, 0), c3, c2)] = c2_c3_hop
lead = kwant.Builder(kwant.TranslationalSymmetry((-3.176, 0, 0)))
lead[c1.shape(cuboid_shape, (0, 0, 0))] = c1_ons
lead[c2.shape(cuboid_shape, (0, 1, 0))] = c2_ons
lead[c3.shape(cuboid_shape, (0, 0, 1))] = c3_ons
lead[kwant.builder.HoppingKind((0, 0, 0), c2, c1)] = c1_c2_hop
lead[kwant.builder.HoppingKind((-1, 0, 0), c2, c1)] = c1_c2_hop
lead[kwant.builder.HoppingKind((0, -1, 0), c2, c1)] = c1_c2_hop
lead[kwant.builder.HoppingKind((0, 0, 0), c3, c2)] = c2_c3_hop
lead[kwant.builder.HoppingKind((1, 0, 0), c3, c2)] = c2_c3_hop
lead[kwant.builder.HoppingKind((0, 1, 0), c3, c2)] = c2_c3_hop
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 == c1:
return 'yellow'
elif site.family == c2:
return 'gray'
else:
return 'blue'
kwant.plot(syst, site_size=0.05, site_lw=0.01, hop_lw=0.01,
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()
solve this
Im trying to plot the conductance for a two dimensional array of 3 basis
atoms, i have defined the atoms positions, the onsite energies and hoppings
matrices and the leads but it is showing me this error:
(i search in the mailing list but theres no info about it)
ValueError Traceback (most recent call
last)<ipython-input-1-ee484ce5ea50> in <module>() 111 112 if
__name__ == '__main__':--> 113 main()
<ipython-input-1-ee484ce5ea50> in main() 107
site_color=family_colors) 108 syst = syst.finalized()--> 109
plot_conductance(syst, energies=[0.01 * i - 0.3 for i in range(100)])
110 111
<ipython-input-1-ee484ce5ea50> in plot_conductance(syst, energies)
85 data = [] 86 for energy in energies:---> 87
smatrix = kwant.smatrix(syst, energy) 88
data.append(smatrix.transmission(1, 0)) 89 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) 370 linsys, lead_info =
self._make_linear_sys(syst, in_leads, energy, args, 371
check_hermiticity, False,--> 372
params=params)
373 374 kept_vars = np.concatenate([coords for i, coords
in
~/anaconda3/lib/python3.6/site-packages/kwant/solvers/common.py in
_make_linear_sys(self, sys, in_leads, energy, args, check_hermiticity,
realspace, params) 162 lhs, norb =
syst.hamiltonian_submatrix(args, sparse=True, 163
return_norb=True,--> 164
params=params)[:2] 165 lhs =
getattr(lhs, 'to' + self.lhsformat)() 166 lhs = lhs -
energy * sp.identity(lhs.shape[0], format=self.lhsformat)
kwant/_system.pyx in kwant._system.hamiltonian_submatrix()
kwant/_system.pyx in kwant._system.make_sparse_full()
ValueError: Hopping from site 407 to site 814 does not match the
dimensions of onsite Hamiltonians of these sites.
Here is the code so far:
import kwant
import tinyarray
import numpy
from matplotlib import pyplot
%matplotlib notebook
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)
c1, c2, c3 = lat.sublattices
c1_ons = numpy.array([[-1.888842, -0.014064-0.000409j, 0.026908+0.003422j],
[-0.014064+0.000409j, -1.784936, -0.031384+0.021565j],
[0.026908-0.003422j, -0.031384-0.021565j, 0.710443]])
c2_ons = numpy.array([[7.168134, -0.005189-0.047376j, 0.001352+0.000103j,
-0.001189-0.00095j, -0.048166-0.007663j, 0.429882+0.00052j],
[-0.005189+0.047376j, 0.245358, 0.113162-0.072937j,
0.660849-0.06348j, -0.017571+0.035587j, 0.020961-0.017679j],
[0.001352-0.000103j, 0.113162+0.072937j, 1.338059,
-0.003126-0.016285j, -0.624702-0.065652j, 0.002353+0.001639j],
[-0.001189+0.00095j, 0.660849+0.06348j,
-0.003126+0.016285j, 1.325337, 0.110694+0.01548j, 0.009041+0.004483j],
[-0.048166+0.007663j, -0.017571-0.035587j,
-0.624702+0.065652j, 0.110694-0.01548j, 0.362102, -0.030934+0.002401j],
[0.429882-0.00052j, 0.020961+0.017679j,
0.002353-0.001639j, 0.009041-0.004483j, -0.030934-0.002401j, -0.650839]])
c3_ons = numpy.array([[-3.398186, 0.001839+0.001631j, -0.117366+0.00498j],
[0.001839-0.001631j, -3.401815, 0.023339+0.009067j],
[-0.117366-0.00498j, 0.023339-0.009067j, -0.637207]])
c1_c3_hop = numpy.array([[-1.852931-0.147524j, -0.274338+0.015064j,
-0.103127-0.001438j],
[0.274586+0.034451j, -1.796449+0.055331j,
0.004816+0.00237j],
[-0.015051+0.001677j, -0.034396-0.019407j,
3.410475-0.001248j]])
c1_c2_hop = numpy.array([[0.003644-0.00088j, -0.046131-0.04229j,
0.23188-0.001924j],
[-0.305706+0.050514j, -1.963829+0.280977j,
-0.597505+0.078772j],
[0.638425+0.083597j, -1.171301+0.088146j,
-0.146976+0.012943j],
[-1.105645-0.086829j, -1.112788+0.056971j,
-0.210584-0.002248j],
[1.463462+0.012994j, 0.174769-0.106872j,
0.177022-0.031485j],
[-0.01338+0.00264j, -0.058159+0.007987j,
0.953363+0.001855j]])
c2_c3_hop = numpy.array([[0.184152+0.002778j, 0.321743-0.010571j,
0.183538-0.00067j],
[0.275145+0.007691j, -0.54144+0.012815j,
0.045847+0.015379j],
[0.47922+0.015775j, 1.256012+0.007326j,
-0.523174+0.00585j],
[1.255561-0.002255j, 1.903063+0.010647j,
-0.876392+0.010246j],
[1.282837-0.091022j, -0.54898+0.001161j,
0.057341-0.004095j],
[0.02765-0.001793j, -0.002902-0.001866j,
-0.746426-0.000748j]])
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[c1.shape(cuboid_shape, (0, 0, 0))] = c1_ons
syst[c2.shape(cuboid_shape, (0, 1, 0))] = c2_ons
syst[c3.shape(cuboid_shape, (0, 0, 1))] = c3_ons
syst[kwant.builder.HoppingKind((0, 0, 0), c2, c1)] = c1_c2_hop
syst[kwant.builder.HoppingKind((-1, 0, 0), c2, c1)] = c1_c2_hop
syst[kwant.builder.HoppingKind((0, -1, 0), c2, c1)] = c1_c2_hop
syst[kwant.builder.HoppingKind((0, 0, 0), c3, c2)] = c2_c3_hop
syst[kwant.builder.HoppingKind((1, 0, 0), c3, c2)] = c2_c3_hop
syst[kwant.builder.HoppingKind((0, 1, 0), c3, c2)] = c2_c3_hop
lead = kwant.Builder(kwant.TranslationalSymmetry((-3.176, 0, 0)))
lead[c1.shape(cuboid_shape, (0, 0, 0))] = c1_ons
lead[c2.shape(cuboid_shape, (0, 1, 0))] = c2_ons
lead[c3.shape(cuboid_shape, (0, 0, 1))] = c3_ons
lead[kwant.builder.HoppingKind((0, 0, 0), c2, c1)] = c1_c2_hop
lead[kwant.builder.HoppingKind((-1, 0, 0), c2, c1)] = c1_c2_hop
lead[kwant.builder.HoppingKind((0, -1, 0), c2, c1)] = c1_c2_hop
lead[kwant.builder.HoppingKind((0, 0, 0), c3, c2)] = c2_c3_hop
lead[kwant.builder.HoppingKind((1, 0, 0), c3, c2)] = c2_c3_hop
lead[kwant.builder.HoppingKind((0, 1, 0), c3, c2)] = c2_c3_hop
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 == c1:
return 'yellow'
elif site.family == c2:
return 'gray'
else:
return 'blue'
kwant.plot(syst, site_size=0.05, site_lw=0.01, hop_lw=0.01,
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()