Hi everyone,
I am trying to implement a carbon nanotube lattice inside of Kwant and I am not
sure if my approach is correct. The CNT is slightly different, I think, than
the other examples of lattices I have seen implemented in Kwant.
My approach, which I have used in the past in my own NEGF code, is to generate
the atoms of a single unit cell (just a ring for a (10, 0) tube) and then
translate them using the translation vector for the ring. For a (10, 0) tube
oriented along the z-direction the vector would be approximately (0, 0, 4.26)
Angstrom.
So, we have a 3D structure, but really only one lattice translation vector.
The problem I am observing in my implementation of this in Kwant is that the
Polyatomic lattice code seems to expect three primitive vectors for a 3D
structure. In the case of the CNT, this does not really apply. When I run my
code (an example for the (10, 0) tube is pasted below) I get the following
error when I try to get the 1st nearest neighbors of the lattice:
File "C:\Python27\lib\site-packages\kwant\lattice.py", line 282, in neighbors
shortest_hopping = sls[0].n_closest(sls[0](*([0] * sls[0].dim)).pos,
File " C:\Python27\lib\site-packages\kwant\builder.py", line 155, in
__call__
return Site(self, tag)
File "C:\Python27\lib\site-packages\kwant\builder.py", line 71, in __new__
raise t(msg.format(repr(tag), repr(family), v))
ValueError: Tag (0, 0, 0) is not allowed for site family
kwant.lattice.Monatomic([[0.0, 0.0, 4.26]], [3.86624196507323,
0.6123525697973589, -0.355], '0'): Dimensionality mismatch.
Does anyone have any advice for how I might get around this? With shape
functions I am able to successfully translate the CNT to create/plot a system
inside of Kwant- the only issue I have is with defining hoppings right now. I'm
thinking that it might be possible to manually define the hoppings inside of
the unit cell, but I am not exactly sure how to go about it for a problem of
this size.
Hopefully the way I've described my problem makes some sense! I am really
hoping to get this working in Kwant- my NEGF code served my purposes for a
while, but it is really quite terrible compared to Kwant, haha.
##Code snip:
import kwant
t_vec = [(0,0,4.26)] #(10,0) translation vector
#unit cell coordinates for (10, 0)
coords = [(3.86624196507323, 0.6123525697973589, -0.355), (3.86624196507323,
-0.6123525697973589, 0.355), (3.48778726384012, 1.7771163733490807, 1.775),
(3.86624196507323, 0.6123525697973589, 2.485), (2.7679236443795503,
2.76792364437955, -0.355), (3.48778726384012, 1.7771163733490807, 0.355),
(1.7771163733490811, 3.4877872638401195, 1.775), (2.7679236443795503,
2.76792364437955, 2.485), (0.6123525697973591, 3.86624196507323, -0.355),
(1.7771163733490811, 3.4877872638401195, 0.355), (-0.6123525697973586,
3.86624196507323, 1.775), (0.6123525697973591, 3.86624196507323, 2.485),
(-1.7771163733490805, 3.48778726384012, -0.355), (-0.6123525697973586,
3.86624196507323, 0.355), (-2.76792364437955, 2.7679236443795503, 1.775),
(-1.7771163733490805, 3.48778726384012, 2.485), (-3.4877872638401195,
1.7771163733490811, -0.355), (-2.76792364437955, 2.7679236443795503, 0.355),
(-3.8662419650732294, 0.6123525697973593, 1.775), (-3.4877872638401195,
1.7771163733490811, 2.485), (-3.86624196507323, -0.6123525697973583, -0.355),
(-3.8662419650732294, 0.6123525697973593, 0.355), (-3.48778726384012,
-1.7771163733490802, 1.775), (-3.86624196507323, -0.6123525697973583, 2.485),
(-2.7679236443795507, -2.76792364437955, -0.355), (-3.48778726384012,
-1.7771163733490802, 0.355), (-1.7771163733490813, -3.4877872638401195, 1.775),
(-2.7679236443795507, -2.76792364437955, 2.485), (-0.6123525697973595,
-3.8662419650732294, -0.355), (-1.7771163733490813, -3.4877872638401195,
0.355), (0.6123525697973581, -3.86624196507323, 1.775), (-0.6123525697973595,
-3.8662419650732294, 2.485), (1.7771163733490802, -3.4877872638401204, -0.355),
(0.6123525697973581, -3.86624196507323, 0.355), (2.7679236443795494,
-2.7679236443795507, 1.775), (1.7771163733490802, -3.4877872638401204, 2.485),
(3.4877872638401195, -1.7771163733490816, -0.355), (2.7679236443795494,
-2.7679236443795507, 0.355), (3.8662419650732294, -0.6123525697973597, 1.775),
(3.4877872638401195, -1.7771163733490816, 2.485)]
nanotube = kwant.lattice.Polyatomic(t_vec,coords)
print nanotube.neighbors(1) #this is the line which gives an error
##End code snip
Any assistance that anyone could offer would be hugely appreciated!
Thanks very much,
Sam LaGasse
