On 2021-07-19 02:21, Adel Belayadi wrote:

Dear Djawad,

Great that you have fixed your previous problem. No back to you issues

A)

There was no problem with scattering regions and also for lead-related to the cubic lattice, but the one which related to my new structure had an unexpected shape. You can see both in the attachment. I use the following code to define the shape of leads for both structures. If it is possible for you please check them and let me know what did I not consider?

For this part, I cannot suggest anything since you have not said anything about your new structure. Depicted figure says nothing to me. It is better to explain more.

B)

When we want to connect two different lattices, we have to do it manually. If I connect the two lattices in the following way, I will not lose anything?

###################

for i in range(-a,a):
for j in range(-a,a):
for k in range(-a,a):

Same answer, you are talking about two different lattices but I don't see any lattice in your script. However, I can highlight one remark in your script. If you are connecting the two lattices in the z directions you don't  use for k in range(-a,a). you have to provide only the z position where the two lattices will be connected. This is fully explained in Kwant FAQ.

From my side, what you have given is not clear enough to help.

Best, Adel

Le dim. 18 juil. 2021 à 13:46, tavakkolidjawad <tavakkolidjawad@ut.ac.ir> a écrit :

On 2021-06-22 20:26, Adel Belayadi wrote:

Dera Djawad,

I do not see why the angle is different. From my side, I have updated my system recently and I am having a problem with the 3D plot in kwant ''AttributeError: 'Path3DCollection' object has no attribute'_z_markers_idx'''.

 

 

However, I can suggest the following propositions.

1. Since you are not using a magnetic field in your system, the angle does not affect your results. In fact the physical quantities would only depend on the hopping, scattering direction and number of sites. So you can step forward with this structure.

2. In the def main():you have written syst.attach_lead(lead) I don't see why since you have already attached the lead in your main script.

3. Try to see the following link which provides an example on how to add a lead in a 3d space (scroll down and you will see).

 

ps

https://kwant-project.org/doc/dev/tutorial/faq

 

Cheers, Adel

Le dim. 20 juin 2021 à 10:45, tavakkolidjawad <tavakkolidjawad@ut.ac.ir> a écrit :

On 2021-06-19 01:30, Adel Belayadi wrote:

Dear Javad tavakoli,

 

I think you need to see the kwant documentation carefully. From the first look at your script I can notice the following statements.

 

 

So let us start with the symmetry and the shape of your lead.

 

First you have used  kwant.TranslationalSymmetry((0,0,1)) which means you are going along the z direction where -2pi/z<Kz<+2pi/z.

 

Second you have defined the lead shape as a finite shape since you have included 10 <= z < 25

 

def lead_shape(pos):
   x,y,z = pos
   return 0 <= x < a and 0 <= y < b and 10 <= z < 25

 

I guess if you omit  10 <= z < 25 from def lead_shape(pos) you would get something meaningful.

 

Try to fix this problem and let me know if working or not

Best wishes

Adel

Le ven. 18 juin 2021 à 22:33, tavakkolidjawad <tavakkolidjawad@ut.ac.ir> a écrit :

Dear all

In the following code I have defined a three-dimensional structure.
The geometry of the lead and the scattering region are the same, but the lead is not ploted as I expected.
I expected the lead to have a cubic structure.
What is the problem with my code?

Thanks

Javad tavakoli

############################################################################

############################################################################

import kwant

lat = kwant.lattice.general([(0, 0.5, 0.5), (0.5, 0, 0.5), (0.5, 0.5, 0)],
[(0, 0, 10), (0.25, 0.25, 10.25)], name=['a1', 'a2'])
a1, a2 = lat.sublattices

def make_system(a=10, b=10, c=30):

syst = kwant.Builder()

def cuboid_shape(pos):
x, y, z = pos
return 0 <= x < a and 0 <= y < b and 0 <= z < 10

syst[a1.shape(cuboid_shape, (0, 0, 0))] = 1
syst[a2.shape(cuboid_shape, (0, 0, 0))] = 1
syst[lat.neighbors()] = 1


def lead_shape(pos):
x,y,z = pos
return 0 <= x < a and 0 <= y < b and 10 <= z < 25

lead = kwant.Builder(kwant.TranslationalSymmetry((0,0,1)))
lead[a1.shape(lead_shape, (0, 0, 10))] = 1
lead[a2.shape(lead_shape, (0, 0, 10))] = 1
lead[lat.neighbors()] = 1


syst.attach_lead(lead)
syst.attach_lead(lead.reversed())


return syst , lead

def main():

syst,lead= make_system()

kwant.plot(syst)

syst,lead = make_system(a=1.1, b=1.1, c=1.1)

syst.attach_lead(lead)

if __name__ == '__main__':
main()

###########################################################################

Dear Adel

I greatly appreciate your consideration.

I fix the problem. Now I have the same shape in the scattering region and lead.

A new problem that arises is that the angles of the structure are different. 

dear Adel

Thank you for your response.
This email has two parts. The first part is related to the previous email and in the second part, I asked about hopping between sites of two different lattices.

A)

As you suggested, I read the documentation again.
I can straightforwardly work with cubic lattice and build the scattering region and leads properly.
As I mentioned in my previous email, the structure had different angles. I try to plot the scattering region and lead separately for both cubic lattice and my new structure. There was no problem with scattering regions and also for lead-related to the cubic lattice, but the one which related to my new structure had an unexpected shape. you can see both in the attachment. I use the following code to define the shape of leads for both structures. If it is possible for you please check them and let me know what did I not consider?

######################################

def lead_shape(pos):
x,y,z= pos
return 0 <= x < 15 and 0 <= y < 15

lead = kwant.Builder(kwant.TranslationalSymmetry((0,0,1)))
lead[a1.shape(lead_shape, (0, 0, 25))] = 4
lead[a2.shape(lead_shape, (0, 0, 25))] = 4
lead[lat.neighbors()] = 1

======================================

def lead_shape(pos):
x,y,z = pos
return 0 <= x < 15 and 0 <= y < 15

lead = kwant.Builder(kwant.TranslationalSymmetry((0,0,1)))
lead[lat.shape(lead_shape, (0, 0, 25))] = 4
lead[lat.neighbors()] = 1

######################################

B)

When we want to connect two different lattices, we have to do it manually. If I connect the two lattices in the following way, I will not lose anything?

###################

for i in range(-a,a):
for j in range(-a,a):
for k in range(-a,a):
try:
syst[(a1(i,j,k), subA(i,j))] = 1j
syst[(a2(i,j,k), subB(i,j))] = 1j
syst[(a1(i,j,k), subB(i,j))] = 1j
syst[(a2(i,j,k), subA(i,j))] = 1j
except:
pass

###################

 

Regards

Javad 

dear Adel

for more explanation of part one, I defined a lead in the polyatomic lattice:

###############################################################

import kwant

lat = kwant.lattice.general([(0, 0.5, 0.5), (0.5, 0, 0.5), (0.5, 0.5, 0)],
[(0, 0, 0), (0.25, 0.25, 0.25)], name=['a1', 'a2'])
a1, a2 = lat.sublattices

def make_system(a=10, b=10, c=30):

syst = kwant.Builder()

def cuboid_shape(pos):
x, y, z = pos
return 0 <= x < a and 0 <= y < b and 0 <= z < 10

syst[a1.shape(cuboid_shape, (0, 0, 0))] = 1
syst[a2.shape(cuboid_shape, (0, 0, 0))] = 1
syst[lat.neighbors()] = 1


def lead_shape(pos):
x,y,z = pos
return 0 <= x < a and 0 <= y < b 

lead = kwant.Builder(kwant.TranslationalSymmetry((0,0,-1)))
lead[a1.shape(lead_shape, (0, 0, 0))] = 1
lead[a2.shape(lead_shape, (0, 0, 0))] = 1
lead[lat.neighbors()] = 1


syst.attach_lead(lead)
syst.attach_lead(lead.reversed())


return syst , lead

def main():

syst,lead= make_system()

kwant.plot(syst)

kwant.plot(lead)

if __name__ == '__main__':
main()

###############################################################

I want to know in spite of that I don't consider Z direction in the shape function (15,15,0), why the resulting lead has value in the Z direction?

I was expecting to get a square lead in the X and Y direction just like the one I get with the same idea from the cubic lattice.

You can also see the cube structure code below which worked well as I expected. If you run the following code you will see a square lead in the direction of x, y, and z = 0.

###############################################################

import kwant
lat = kwant.lattice.cubic(1)

def make_system(l=15 , b=15, c=25):

syst = kwant.Builder()

def cuboid_shape(pos):
x, y, z = pos
return 0 <= x < l and 0 <= y < b and 0 <= z < c

syst[lat.shape(cuboid_shape, (0, 0, 0))] = 4
syst[lat.neighbors()] = 1


def lead_shape(pos):
x,y,z = pos
return 0 <= x < 15 and 0 <= y < 15

lead = kwant.Builder(kwant.TranslationalSymmetry((0,0,1)))
lead[lat.shape(lead_shape, (0, 0, 25))] = 4
lead[lat.neighbors()] = 1

return syst , lead

def main():

syst,lead= make_system()

kwant.plot(syst,fig_size=(10,9))
kwant.plot(lead)

if __name__ == '__main__':
main()

###############################################################

 

Finally, thank you very much for your unwavering support.

 

Regards

Javad