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 On Tue, Nov 20, 2018 at 9:22 AM Srilok Srinivasan wrote:

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

Thanks

On Mon, Nov 19, 2018 at 5:38 PM Srilok Srinivasan wrote:

...

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) 907 def make_proper_site_spec(spec, fancy_indexing=False): 908 if callable(spec): --> 909 spec = [spec(i[0]) for i in sites if i[1] is None] 910 if (fancy_indexing and _p.isarray(spec) 911 and not isinstance(spec, np.ndarray)):

~/anaconda3/lib/python3.6/site-packages/kwant/plotter.py in <listcomp>(.0) 907 def make_proper_site_spec(spec, fancy_indexing=False): 908 if callable(spec): --> 909 spec = [spec(i[0]) for i in sites if i[1] is None] 910 if (fancy_indexing and _p.isarray(spec) 911 and not isinstance(spec, np.ndarray)):

~/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

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

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) 907 def make_proper_site_spec(spec, fancy_indexing=False): 908 if callable(spec): --> 909spec = [spec(i[0]) for i in sites if i[1] is None] 910 if (fancy_indexing and _p.isarray(spec) 911 and not isinstance(spec, np.ndarray)):

~/anaconda3/lib/python3.6/site-packages/kwant/plotter.py in <listcomp>(.0) 907 def make_proper_site_spec(spec, fancy_indexing=False): 908 if callable(spec): --> 909spec = [spec(i[0]) for i in sites if i[1] is None] 910 if (fancy_indexing and _p.isarray(spec) 911 and not isinstance(spec, np.ndarray)):

~/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): --> 958return 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)

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 minimal example it succeeds:

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