Re: [Kwant] Error visualizing the zigzag graphene lattice using kwant.plot() in tutorial
Hi everyone,
> 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.
>
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
notebooks there is a line:
> %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
following suspicious line:
> 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
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Re: [Kwant] Error visualizing the zigzag graphene lattice using kwant.plot() in tutorial
Just to respond to Anton: > 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 They're not plotting a finalized system: >>> 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 signature.asc Description: OpenPGP digital signature
Re: [Kwant] Error visualizing the zigzag graphene lattice using kwant.plot() in tutorial
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) > in > 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 (.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
Re: [Kwant] Error visualizing the zigzag graphene lattice using kwant.plot() in tutorial
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) >> in >> 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 (.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 >
[Kwant] Error visualizing the zigzag graphene lattice using kwant.plot() in tutorial
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) in 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 (.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
Re: [Kwant] Error visualizing the zigzag graphene lattice using kwant.plot() in tutorial
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) in 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 (.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
