[Kwant] Error visualizing the zigzag graphene lattice using kwant.plot() in tutorial

[Srilok Srinivasan]

Sorry I forgot to mention that I am using the Kwant version 1.4.01a1

Thanks

Hello Kwant users,
I am very new to kwant and I am still learning to use the code. So my
apologizes for any trivial questions.
I working on the tutorial notebooks I found in the here (
https://kwant-project.org/mm16). In the tutorial 3.4.graphene_qshe.ipynb
I am trying to visualize the zigzag graphene lattice created using the
kwant.Builder and .shape() module using kwant.plot(*sys*). I am getting
the following error
zigzag_ribbon = kwant.Builder(kwant.TranslationalSymmetry([1, 0]))
#zigzag_ribbon[graphene.shape((lambda pos: abs(pos[1]) < 9 and pos[1]%2
==1), (0, 0))] = 0.2
#zigzag_ribbon[graphene.shape((lambda pos: abs(pos[1]) < 9 and pos[1]%2
==0), (0, 0))] = -0.2
zigzag_ribbon[graphene.shape((lambda pos: abs(pos[1]) < 9), (0, 0))] = 0
zigzag_ribbon[graphene.neighbors(1)] = 1
zigzag_ribbon.finalized()
kwant.plotter.plot(zigzag_ribbon)
#kwant.plotter.bands(zigzag_ribbon.finalized());
---------------------------------------------------------------------------KeyError Traceback (most recent call last)<ipython-input-84-0b886d56dec5> in <module> 5 zigzag_ribbon[graphene.neighbors(1)] = 1 6 zigzag_ribbon.finalized()----> 7 kwant.plotter.plot(zigzag_ribbon) 8 #kwant.plotter.bands(zigzag_ribbon.finalized());
~/anaconda3/lib/python3.6/site-packages/kwant/plotter.py in plot(sys, num_lead_cells, unit, site_symbol, site_size, site_color, site_edgecolor, site_lw, hop_color, hop_lw, lead_site_symbol, lead_site_size, lead_color, lead_site_edgecolor, lead_site_lw, lead_hop_lw, pos_transform, cmap, colorbar, file, show, dpi, fig_size, ax) 962 963 site_size = make_proper_site_spec(site_size, fancy_indexing)--> 964 site_color = make_proper_site_spec(site_color, fancy_indexing) 965 site_edgecolor = make_proper_site_spec(site_edgecolor, fancy_indexing) 966 site_lw = make_proper_site_spec(site_lw, fancy_indexing)
~/anaconda3/lib/python3.6/site-packages/kwant/plotter.py in site_color(site) 956 color_mapping = dict(zip(families, cycle)) 957 def site_color(site):--> 958 return color_mapping[site.family] 959 else: 960 # Unknown finalized system, no sites access.
KeyError: kwant.lattice.Monatomic([[1.0, 0.0], [0.5, 0.8660254037844386]], [0.0, 0.5773502691896258], '1', None)
However, I am able to plot the dispersion and all that. Also, I am able to
visualize the square lattice presented in other tutorials. Do we have to do
something different to visualize non-square lattice ?
Thanks for your help
--
Srilok Srinivasan
Graduate Student
Mechanical Engineering
Iowa State University, Ames, IA

[Anton Akhmerov]

Hi Srilok,

Right now plotting of detached finalized leads isn't supported and is
tracked in the issue
https://gitlab.kwant-project.org/kwant/kwant/issues/18

Cheers,
Anton

Post by Srilok Srinivasan
Sorry I forgot to mention that I am using the Kwant version 1.4.01a1
Thanks

Hello Kwant users,
I am very new to kwant and I am still learning to use the code. So my apologizes for any trivial questions.
I working on the tutorial notebooks I found in the here (https://kwant-project.org/mm16). In the tutorial 3.4.graphene_qshe.ipynb I am trying to visualize the zigzag graphene lattice created using the kwant.Builder and .shape() module using kwant.plot(sys). I am getting the following error
zigzag_ribbon = kwant.Builder(kwant.TranslationalSymmetry([1, 0]))
#zigzag_ribbon[graphene.shape((lambda pos: abs(pos[1]) < 9 and pos[1]%2 ==1), (0, 0))] = 0.2
#zigzag_ribbon[graphene.shape((lambda pos: abs(pos[1]) < 9 and pos[1]%2 ==0), (0, 0))] = -0.2
zigzag_ribbon[graphene.shape((lambda pos: abs(pos[1]) < 9), (0, 0))] = 0
zigzag_ribbon[graphene.neighbors(1)] = 1
zigzag_ribbon.finalized()
kwant.plotter.plot(zigzag_ribbon)
#kwant.plotter.bands(zigzag_ribbon.finalized());
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
<ipython-input-84-0b886d56dec5> in <module>
5 zigzag_ribbon[graphene.neighbors(1)] = 1
6 zigzag_ribbon.finalized()
----> 7 kwant.plotter.plot(zigzag_ribbon)
8 #kwant.plotter.bands(zigzag_ribbon.finalized());
~/anaconda3/lib/python3.6/site-packages/kwant/plotter.py in plot(sys, num_lead_cells, unit, site_symbol, site_size, site_color, site_edgecolor, site_lw, hop_color, hop_lw, lead_site_symbol, lead_site_size, lead_color, lead_site_edgecolor, lead_site_lw, lead_hop_lw, pos_transform, cmap, colorbar, file, show, dpi, fig_size, ax)
962
963 site_size = make_proper_site_spec(site_size, fancy_indexing)
--> 964 site_color = make_proper_site_spec(site_color, fancy_indexing)
965 site_edgecolor = make_proper_site_spec(site_edgecolor, fancy_indexing)
966 site_lw = make_proper_site_spec(site_lw, fancy_indexing)
~/anaconda3/lib/python3.6/site-packages/kwant/plotter.py in make_proper_site_spec(spec, fancy_indexing)
--> 909 spec = [spec(i[0]) for i in sites if i[1] is None]
910 if (fancy_indexing and _p.isarray(spec)
~/anaconda3/lib/python3.6/site-packages/kwant/plotter.py in <listcomp>(.0)
--> 909 spec = [spec(i[0]) for i in sites if i[1] is None]
910 if (fancy_indexing and _p.isarray(spec)
~/anaconda3/lib/python3.6/site-packages/kwant/plotter.py in site_color(site)
956 color_mapping = dict(zip(families, cycle))
--> 958 return color_mapping[site.family]
960 # Unknown finalized system, no sites access.
KeyError: kwant.lattice.Monatomic([[1.0, 0.0], [0.5, 0.8660254037844386]], [0.0, 0.5773502691896258], '1', None)
However, I am able to plot the dispersion and all that. Also, I am able to visualize the square lattice presented in other tutorials. Do we have to do something different to visualize non-square lattice ?
Thanks for your help
--
Srilok Srinivasan
Graduate Student
Mechanical Engineering
Iowa State University, Ames, IA

--
Srilok Srinivasan
Graduate Student
Mechanical Engineering
Iowa State University, Ames, IA

[Joseph Weston]

Post by Anton Akhmerov
Right now plotting of detached finalized leads isn't supported and is
tracked in the issue
https://gitlab.kwant-project.org/kwant/kwant/issues/18

zigzag_ribbon = kwant.Builder(kwant.TranslationalSymmetry([1, 0]))
#zigzag_ribbon[graphene.shape((lambda pos: abs(pos[1]) < 9 and pos[1]%2 ==1), (0, 0))] = 0.2
#zigzag_ribbon[graphene.shape((lambda pos: abs(pos[1]) < 9 and pos[1]%2 ==0), (0, 0))] = -0.2
zigzag_ribbon[graphene.shape((lambda pos: abs(pos[1]) < 9), (0, 0))] = 0
zigzag_ribbon[graphene.neighbors(1)] = 1
zigzag_ribbon.finalized()
kwant.plotter.plot(zigzag_ribbon)
#kwant.plotter.bands(zigzag_ribbon.finalized());

so this should totally still work (and indeed it does on Kwant 1.3.3, or
when taking a minimal example as I illustrated in my email.


Joe

[Joseph Weston]

Hi Srilok,

I am very new to kwant and I am still learning to use the code. So
my apologizes for any trivial questions.
I working on the tutorial notebooks I found in the here
(https://kwant-project.org/mm16). In the tutorial
3.4.graphene_qshe.ipynb I am trying to visualize the zigzag
graphene lattice created using the kwant.Builder and .shape()
module using kwant.plot(/sys/). I am getting the following error
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
<ipython-input-84-0b886d56dec5> in <module>
5 zigzag_ribbon[graphene.neighbors(1)] = 1
6 zigzag_ribbon.finalized()
----> 7kwant.plotter.plot(zigzag_ribbon)
8 #kwant.plotter.bands(zigzag_ribbon.finalized());
~/anaconda3/lib/python3.6/site-packages/kwant/plotter.py in plot(sys, num_lead_cells, unit, site_symbol, site_size,
site_color, site_edgecolor, site_lw, hop_color, hop_lw,
lead_site_symbol, lead_site_size, lead_color, lead_site_edgecolor,
lead_site_lw, lead_hop_lw, pos_transform, cmap, colorbar, file,
show, dpi, fig_size, ax)
962
963 site_size = make_proper_site_spec(site_size, fancy_indexing)
--> 964site_color = make_proper_site_spec(site_color, fancy_indexing)
965 site_edgecolor = make_proper_site_spec(site_edgecolor, fancy_indexing)
966 site_lw = make_proper_site_spec(site_lw, fancy_indexing)
~/anaconda3/lib/python3.6/site-packages/kwant/plotter.py in make_proper_site_spec(spec, fancy_indexing)
--> 909spec = [spec(i[0]) for i in sites if i[1] is None]
910 if (fancy_indexing and _p.isarray(spec)
~/anaconda3/lib/python3.6/site-packages/kwant/plotter.py in <listcomp>(.0)
--> 909spec = [spec(i[0]) for i in sites if i[1] is None]
910 if (fancy_indexing and _p.isarray(spec)
~/anaconda3/lib/python3.6/site-packages/kwant/plotter.py in site_color(site)
956 color_mapping = dict(zip(families, cycle))
--> 958return color_mapping[site.family]
960 # Unknown finalized system, no sites access.
KeyError: kwant.lattice.Monatomic([[1.0, 0.0], [0.5, 0.8660254037844386]], [0.0, 0.5773502691896258], '1', None)

Thanks for the bug report!

This is very strange; when I download the notebook and run it I indeed
see the error that you reported, however when I try to run the following

import numpy as np
import matplotlib.pyplot
import kwant
graphene = kwant.lattice.general([[1, 0], [1/2, np.sqrt(3)/2]],  #
lattice vectors
                                 [[0, 0], [0, 1/np.sqrt(3)]])  #
Coordinates of the sites
zigzag_ribbon = kwant.Builder(kwant.TranslationalSymmetry([1, 0]))
zigzag_ribbon[graphene.shape((lambda pos: abs(pos[1]) < 9), (0, 0))] = 0
zigzag_ribbon[graphene.neighbors(1)] = 1
print(kwant.__version__)
kwant.plot(zigzag_ribbon);

I'll investigate a bit more and report my results.


Happy Kwanting,


Joe

[Joseph Weston]

Hi everyone,

Post by Joseph Weston
This is very strange; when I download the notebook and run it I indeed
see the error that you reported, however when I try to run the

import numpy as np
import matplotlib.pyplot
import kwant
graphene = kwant.lattice.general([[1, 0], [1/2, np.sqrt(3)/2]],  #
lattice vectors
                                 [[0, 0], [0, 1/np.sqrt(3)]])  #
Coordinates of the sites
zigzag_ribbon = kwant.Builder(kwant.TranslationalSymmetry([1, 0]))
zigzag_ribbon[graphene.shape((lambda pos: abs(pos[1]) < 9), (0, 0))] = 0
zigzag_ribbon[graphene.neighbors(1)] = 1
print(kwant.__version__)
kwant.plot(zigzag_ribbon);

I'll investigate a bit more and report my results.

Found it! In Kwant 1.4.0a1 we tweaked Kwant's plotting so that sites
from different families (sublattices) would use the colors from
Matplotlib's color cycle by default. In the March Meeting tutorial

Post by Joseph Weston
%run matplotlib_setup.ipy

that loads some custom matplotlib setup to make the plots look a bit
better in the notebooks. Looking into 'matplotlib_setup.ipy' we see the

Post by Joseph Weston
mpl.rc('axes', prop_cycle=mpl.cycler('color', ['black']))

which was included to stop all the bandstructure plots being
multicolored (because it's distracting), however because there are fewer
colors than there are site families (2 site families in graphene) the
color cycling in Kwant's plotter broke.


This is a bug in Kwant, and I've opened an issue [1] on our bugtracker.
I'll fix this today and it'll go into the v1.4.0 release (that we will
make sometime between now and christmas).


In the short term you can fix this in a couple of ways:

+ either downgrade to Kwant 1.3.3

+ or change the offending line in 'matplotlib_setup.ipy' to:

    mpl.rc('axes', prop_cycle=mpl.cycler('color', ['black', 'black']))

+ or wait until I push a change to the tutorial notebooks later today
and then re-download them


Thanks for the report, and happy kwanting!


Joe


[1]: https://gitlab.kwant-project.org/kwant/kwant/issues/257