Re: [Kwant] Issue in display wave function in 3D lattice

[Anton Akhmerov]

Hi Liming,

As far as I know, upgrading won't help: the bug is due to some changes
in recent versions of matplotlib.

As far as workarounds go, you could use the argument `pos_transform`
of the plotter to map the 3D system into 2D instead of defining a
different one. Or you can take a look at the bug and help fix it :)

Best,
Anton

On Tue, Jul 26, 2016 at 9:31 PM, L.M J  wrote:
> Hi Anton
>
> My matplotlib version is 1.5.1. Can I solve this problem by updating the
> matplotlib package?
>
> I came out another way to get around with this bug. I built a system that
> has same sites except it is 2-d. Then I plot the wavefunction calculated by
> 3-d on the 2-d system. It seems works, but I'm not sure whether this is a
> right way to do. Is this accurate?
>
> Thanks
>
> Sincerely,
> Liming
>
> On 27 July 2016 at 00:27, Anton Akhmerov 
> wrote:
>>
>> Hi Liming,
>>
>> I believe this is related to a known outstanding bug:
>> https://gitlab.kwant-project.org/kwant/kwant/issues/39
>>
>> What version of matplotlib you are using?
>>
>> Best,
>> Anton
>>
>> On Wed, Jul 20, 2016 at 2:58 AM, L.M J  wrote:
>> > Dear all
>> >
>> > I was trying to plot the wavefunction on each site of a 3-D lattice and
>> > each
>> > site is described by a 4x4 matrix. However, it turned out the that
>> > plotted
>> > wave function is overlapped with the surrounding site and I could not
>> > identify the magnitude of wave function on each site. The code I had
>> > implemented for plotting was the same as the codes in
>> > "http://kwant-project.org/doc/1.0/tutorial/tutorial6; with a copy of
>> > specific plot command as below.
>> >
>> > I have varied the value "3" before wf[i] to tune the size however it
>> > turned
>> > out this value cannot tune the plot size of the wavefunction. I think
>> > I'm
>> > not doing it correctly.
>> >
>> > def site_size(i):
>> > return 3 * wf[i] / wf.max()
>> >
>> > kwant.plot(sys, site_size=site_size, site_color=(0, 0, 1, 0.3),
>> >hop_lw=0.1)
>> >
>> > This method works perfectly for 2-D lattice plot. However, it cannot
>> > display
>> > the wavefunction properly in 3-d lattice. My question is, how can I plot
>> > the
>> > wavefunction in 3-d lattice clearly? (Or maybe I can force the kwant to
>> > plot
>> > it in 2-d by configuring the kwant.plot?)
>> >
>> > Thank you for advance.
>> >
>> > Sincerely,
>> >
>> > Liming
>
>

Re: [Kwant] Issue in display wave function in 3D lattice

[L.M J]

Hi Anton

My matplotlib version is 1.5.1. Can I solve this problem by updating the
matplotlib package?

I came out another way to get around with this bug. I built a system that
has same sites except it is 2-d. Then I plot the wavefunction calculated by
3-d on the 2-d system. It seems works, but I'm not sure whether this is a
right way to do. Is this accurate?

Thanks

Sincerely,
Liming

On 27 July 2016 at 00:27, Anton Akhmerov 
wrote:

> Hi Liming,
>
> I believe this is related to a known outstanding bug:
> https://gitlab.kwant-project.org/kwant/kwant/issues/39
>
> What version of matplotlib you are using?
>
> Best,
> Anton
>
> On Wed, Jul 20, 2016 at 2:58 AM, L.M J  wrote:
> > Dear all
> >
> > I was trying to plot the wavefunction on each site of a 3-D lattice and
> each
> > site is described by a 4x4 matrix. However, it turned out the that
> plotted
> > wave function is overlapped with the surrounding site and I could not
> > identify the magnitude of wave function on each site. The code I had
> > implemented for plotting was the same as the codes in
> > "http://kwant-project.org/doc/1.0/tutorial/tutorial6; with a copy of
> > specific plot command as below.
> >
> > I have varied the value "3" before wf[i] to tune the size however it
> turned
> > out this value cannot tune the plot size of the wavefunction. I think I'm
> > not doing it correctly.
> >
> > def site_size(i):
> > return 3 * wf[i] / wf.max()
> >
> > kwant.plot(sys, site_size=site_size, site_color=(0, 0, 1, 0.3),
> >hop_lw=0.1)
> >
> > This method works perfectly for 2-D lattice plot. However, it cannot
> display
> > the wavefunction properly in 3-d lattice. My question is, how can I plot
> the
> > wavefunction in 3-d lattice clearly? (Or maybe I can force the kwant to
> plot
> > it in 2-d by configuring the kwant.plot?)
> >
> > Thank you for advance.
> >
> > Sincerely,
> >
> > Liming
>

Re: [Kwant] Issue in display wave function in 3D lattice

[Anton Akhmerov]

Hi Liming,

I believe this is related to a known outstanding bug:
https://gitlab.kwant-project.org/kwant/kwant/issues/39

What version of matplotlib you are using?

Best,
Anton

On Wed, Jul 20, 2016 at 2:58 AM, L.M J  wrote:
> Dear all
>
> I was trying to plot the wavefunction on each site of a 3-D lattice and each
> site is described by a 4x4 matrix. However, it turned out the that plotted
> wave function is overlapped with the surrounding site and I could not
> identify the magnitude of wave function on each site. The code I had
> implemented for plotting was the same as the codes in
> "http://kwant-project.org/doc/1.0/tutorial/tutorial6; with a copy of
> specific plot command as below.
>
> I have varied the value "3" before wf[i] to tune the size however it turned
> out this value cannot tune the plot size of the wavefunction. I think I'm
> not doing it correctly.
>
> def site_size(i):
> return 3 * wf[i] / wf.max()
>
> kwant.plot(sys, site_size=site_size, site_color=(0, 0, 1, 0.3),
>hop_lw=0.1)
>
> This method works perfectly for 2-D lattice plot. However, it cannot display
> the wavefunction properly in 3-d lattice. My question is, how can I plot the
> wavefunction in 3-d lattice clearly? (Or maybe I can force the kwant to plot
> it in 2-d by configuring the kwant.plot?)
>
> Thank you for advance.
>
> Sincerely,
>
> Liming