Hi Mitchell,
Looks good, thanks for sharing. Are you satisfied with the usefulness of
such a plot?
By the way you could get a better looking result by using any plotting
library that supports true 3D graphics (matplotlib does not do actual 3D
rendering). Within Python world, possible options are plotly, mayavi, or
ipyvolume.
Cheers,
Anton
On Wed, Oct 4, 2017 at 10:23 AM, Mitchell Greenberg <
mitchell.greenb...@my.jcu.edu.au> wrote:
> Hi Anton,
>
>
> Had a go with getting the quiver plot working and from what I get it seems
> I've produced a graph that makes sense. My only thing I'm not 100% sure
> I've done right is the handling of the negative values; I assume that if I
> have site a and site b with a negative current value it means current is
> flowing from b to a, whereas if the current value is positive current is
> flowing from a to b.
>
>
> In order to account for this in the graph I plot each quiver point
> separately, see if the current is negative and if it is change the arrow to
> point into the site. I account for the magnitude of the current by setting
> the line width to each point to be proportional to the absolute value of
> the current. The attached code is below:
>
>
> #Plot current over hoppings
> wf = kwant.wave_function(syst, E,args=[gate])
> print('Calculated Wavefunctions')
> J_0 = kwant.operator.Current(syst)
> psi = wf(0)[0]
>
> current = J_0(psi)
>
> orderedcurrent = [(syst.pos(i), syst.pos(j), k) for (i, j), k in
> zip(syst.graph, current)]
>
> #From ordered current we know that the first array contains the
> start location of the hopping
> #and the second array contains the end location thus we can get
> XYZ,UVW from this.
>
> X = [orderedcurrent[i][0][0] for i in range(len(orderedcurrent))]
> Y = [orderedcurrent[i][0][1] for i in range(len(orderedcurrent))]
> Z = [orderedcurrent[i][0][2] for i in range(len(orderedcurrent))]
> U = [orderedcurrent[i][1][0] for i in range(len(orderedcurrent))]
> V = [orderedcurrent[i][1][1] for i in range(len(orderedcurrent))]
> W = [orderedcurrent[i][1][2] for i in range(len(orderedcurrent))]
>
>
> #Get the current magnitude at each hopping
> Mag = [orderedcurrent[i][2] for i in range(len(orderedcurrent))]
>
>
> fig = pyplot.figure(figsize=(12,10),dpi=100)
> ax = fig.gca(projection='3d')
> #Plot each point individually, if the current magnitude is
> negative, plot the arrow head going into the site rather than out
> for i in range(len(orderedcurrent)):
> if Mag[i] < 0:
> ax.quiver(X[i], Y[i], Z[i], U[i], V[i], W[i], length =
> (abs(Mag[i])), pivot="tip")
> else:
> ax.quiver(X[i], Y[i], Z[i], U[i], V[i], W[i], length =
> (abs(Mag[i])), pivot="tail")
> pyplot.show()
>
>
> Thank You,
>
> Mitchell Greenberg
>
> ------------------------------
> *From:* anton.akhme...@gmail.com <anton.akhme...@gmail.com> on behalf of
> Anton Akhmerov <anton.akhmerov...@gmail.com>
> *Sent:* Tuesday, October 3, 2017 11:22:26 PM
> *To:* Mitchell Greenberg
>
> *Cc:* kwant-discuss@kwant-project.org
> *Subject:* Re: [Kwant] 2D Current Density Streamplot of 3D System
>
> Hi Mitchell,
>
> There's nothing readily available, but it should certainly be doable.
> Firstly you need to calculate the coordinates of all sites, combine this
> with the graph information, and feed all this data to e.g. the matplotlib's
> quiver plot ( https://matplotlib.org/mpl_toolkits/mplot3d/tutorial.html#
> mpl_toolkits.mplot3d.Axes3D.quiver ). See the recent reply of Joe (
> https://www.mail-archive.com/kwant-discuss@kwant-project.org/msg01425.html
> ) for assemblying the coordinates of all hoppings.
>
> Please share your code and your experience with this kind of plot if you
> succeed—do you think it would be universally useful?
>
> Best,
> Anton
>
> On Tue, Oct 3, 2017 at 3:15 PM, mitchell.greenberg <
> mitchell.greenb...@my.jcu.edu.au> wrote:
>
>> Hi Joseph and Anton,
>>
>> Today I had a talk with my supervisor and he wondered if it was possible
>> to plot the raw current data before interpolation, just to see how current
>> travels through each of the hoppings.
>>
>> From previous questions I know that the current array returned from J0
>> (psi) is in the same from as the system graph, however I was wondering if
>> there was a simple way to plot this array to see the current vectors at
>> each site position.
>>
>> Sorry if this question is naive.
>>
>> Thank You,
>> Mitchell Greenberg
>>
>>
>> Sent from Samsung Mobile
>>
>>
>> -------- Original message --------
>> From: "mitchell.greenberg"
>> Date:17/09/2017 7:32 PM (GMT+10:00)
>> To: Anton Akhmerov
>> Cc: kwant-discuss@kwant-project.org
>> Subject: Re: [Kwant] 2D Current Density Streamplot of 3D System
>>
>> This sender failed our fraud detection checks and may not be
>> who they appear to be. Learn about spoofing
>> <http://aka.ms/LearnAboutSpoofing>
>> Feedback <http://aka.ms/SafetyTipsFeedback>
>> Hi Anton,
>>
>> Thanks for that. While my lattice is polyatomic I just switched site.pos
>> to site.tag in the code I posted last message to get the tags for my
>> lattice. Doing that I see the tags for the z axis range from 0 to 9 (makes
>> sense as I have 10 layers), which explains why 5.3 worked when I used it
>> but not 10. My function runs now an accurately deletes the sites without
>> any problems.
>>
>> Thank You,
>> Mitchell Greenberg
>>
>>
>> Sent from Samsung Mobile
>>
>>
>> -------- Original message --------
>> From: Anton Akhmerov
>> Date:17/09/2017 5:11 AM (GMT+10:00)
>> To: Mitchell Greenberg
>> Cc: Joseph Weston ,kwant-discuss@kwant-project.org
>> Subject: Re: [Kwant] 2D Current Density Streamplot of 3D System
>>
>> Hi Mitchel,
>>
>> Deleting and adding sites is done by their lattice coordinates
>> (site.tag), not their real space position (site.pos); if you want to
>> access a site close to a certain position, you can use the method
>> Monatomic.closest (see
>> https://kwant-project.org/doc/1/reference/generated/kwant.la
>> ttice.Monatomic#kwant.lattice.Monatomic.closest).
>>
>> Best,
>> Anton
>>
>> On Sat, Sep 16, 2017 at 2:34 PM, Mitchell Greenberg
>> <mitchell.greenb...@my.jcu.edu.au> wrote:
>> > Hi Joseph and Anton,
>> >
>> >
>> > Thank you for the advice with getting the 2d graph up and running, its
>> now
>> > producing results that look good. Sorry that I haven't replied in over 2
>> > weeks, uni has gotten into full swing.
>> >
>> >
>> > I wasn't sure if I needed to start a new topic for this (if I need to
>> let me
>> > know) but I am now trying to remove lattice points randomly from my
>> sample.
>> > I have created a function that can remove random lattice points (it is
>> > rather messy) however I have noticed that when I try to delete sites for
>> > layers other than at z=0 and z=5.3 I get the following error.:
>> >
>> >
>> > KeyError: Site(kwant.lattice.Monatomic([[4.3763, 0.0, 0.0], [0.0,
>> 3.3136,
>> > 0.0], [0.0, 0.0, 5.3]], [0.0, 0.0, 0.0], '0', 1), array([50, 50, 10]))
>> >
>> >
>> > This error seems to pop up when I try to delete a site that doesn't
>> exist at
>> > the specified coordinates however when I use:
>> >
>> > Positions=[syst.sites[i].pos for i in range(len(syst.sites))]
>> >
>> >
>> > I see that sites definitely exist for z=10 (should be 10.6 but the error
>> > output seems to round). I was therefore wondering if there is something
>> I am
>> > missing when it comes to deleting sites and if there is an easy way to
>> > delete random sites from a 3d sample.
>> >
>> >
>> > Thank You,
>> >
>> > Mitchell Greenberg
>> >
>> >
>> > ________________________________
>> > From: Joseph Weston <joseph.westo...@gmail.com>
>> > Sent: Wednesday, August 30, 2017 8:33:01 PM
>> > To: Mitchell Greenberg; kwant-discuss@kwant-project.org
>> > Subject: Re: [Kwant] 2D Current Density Streamplot of 3D System
>> >
>> > Hi Mitchell,
>> >
>> >> Sorry again for the reply, I've had a look at the documentation and it
>> >> seems that relwidth and abswidth control the size of the arrays. What
>> >> I'm stuck on though is that my system has L = 80, W = 450 and H =52,
>> >> I was expecting field to return something of the form (80,450,52,3), I
>> >> must apologise again, I'm pretty new to all things python so my
>> >> knowledge in the more complex areas is lacking.
>> >
>> > The input to 'interpolate_current' is a current defined on the hoppings
>> > of your system. The output is a current defined over a realspace grid.
>> > First the current defined on the hoppings is convoluted with a bump
>> > function to smooth it out, then the resulting continuous vector field is
>> > sampled on a regular grid. The docstring explains how this is done. The
>> > interpolation grid does not in general coincide with the "grid" of sites
>> > that form your system. Typically there will be several interpolation
>> > points between neighboring sites.
>> >
>> > The 'box' returned by 'interpolate_current' allows you to calculate the
>> > realspace position of the interpolation points.
>> >
>> > Also the modifications to 'interpolate_current' so that it functions
>> > correctly for 3D systems just landed on the most recent development
>> > version of kwant [1].
>> >
>> >
>> > Happy Kwanting,
>> >
>> > Joe
>> >
>> >
>> > [1]:
>> > https://gitlab.kwant-project.org/kwant/kwant/commit/be364e7c
>> 64c316caf86869df397446399bcef1af
>> >
>> >
>>
>
>
