From b707296be781bf0e1e1731a5f6a122b3e10bb658 Mon Sep 17 00:00:00 2001
From: Joseph Weston <joseph@weston.cloud>
Date: Mon, 29 Apr 2019 13:33:43 +0200
Subject: [PATCH] convert zincblende plotting example to jupyter-sphinx
---
doc/source/tutorial/plotting.rst | 70 ++++++++++++++++++++++++--------
1 file changed, 52 insertions(+), 18 deletions(-)
diff --git a/doc/source/tutorial/plotting.rst b/doc/source/tutorial/plotting.rst
index ef1ec556..0b84f555 100644
--- a/doc/source/tutorial/plotting.rst
+++ b/doc/source/tutorial/plotting.rst
@@ -193,7 +193,28 @@ visible. The hoppings are also plotted in order to show the underlying lattice.
.. seealso::
The complete source code of this example can be found in
- :download:`plot_zincblende.py </code/download/plot_zincblende.py>`
+ :jupyter-download:script:`plot_zincblende`
+
+.. jupyter-kernel::
+ :id: plot_zincblende
+
+.. jupyter-execute::
+ :hide-code:
+
+ # Tutorial 2.8.2. 3D example: zincblende structure
+ # ================================================
+ #
+ # Physical background
+ # -------------------
+ # - 3D Bravais lattices
+ #
+ # Kwant features highlighted
+ # --------------------------
+ # - demonstrate different ways of plotting in 3D
+
+ from matplotlib import pyplot
+
+ import kwant
Zincblende is a very common crystal structure of semiconductors. It is a
face-centered cubic crystal with two inequivalent atoms in the unit cell
@@ -202,18 +223,29 @@ structure, but two equivalent atoms per unit cell).
It is very easily generated in Kwant with `kwant.lattice.general`:
-.. literalinclude:: /code/include/plot_zincblende.py
- :start-after: #HIDDEN_BEGIN_zincblende1
- :end-before: #HIDDEN_END_zincblende1
+.. jupyter-execute::
+
+ lat = kwant.lattice.general([(0, 0.5, 0.5), (0.5, 0, 0.5), (0.5, 0.5, 0)],
+ [(0, 0, 0), (0.25, 0.25, 0.25)])
+ a, b = lat.sublattices
Note how we keep references to the two different sublattices for later use.
A three-dimensional structure is created as easily as in two dimensions, by
using the `~kwant.lattice.PolyatomicLattice.shape`-functionality:
-.. literalinclude:: /code/include/plot_zincblende.py
- :start-after: #HIDDEN_BEGIN_zincblende2
- :end-before: #HIDDEN_END_zincblende2
+.. jupyter-execute::
+
+ def make_cuboid(a=15, b=10, c=5):
+ def cuboid_shape(pos):
+ x, y, z = pos
+ return 0 <= x < a and 0 <= y < b and 0 <= z < c
+
+ syst = kwant.Builder()
+ syst[lat.shape(cuboid_shape, (0, 0, 0))] = None
+ syst[lat.neighbors()] = None
+
+ return syst
We restrict ourselves here to a simple cuboid, and do not bother to add real
values for onsite and hopping energies, but only the placeholder ``None`` (in a
@@ -222,13 +254,11 @@ real calculation, several atomic orbitals would have to be considered).
`~kwant.plotter.plot` can plot 3D systems just as easily as its two-dimensional
counterparts:
-.. literalinclude:: /code/include/plot_zincblende.py
- :start-after: #HIDDEN_BEGIN_plot1
- :end-before: #HIDDEN_END_plot1
+.. jupyter-execute::
-resulting in
+ syst = make_cuboid()
-.. image:: /code/figure/plot_zincblende_syst1.*
+ kwant.plot(syst);
You might notice that the standard options for plotting are quite different in
3D than in 2D. For example, by default hoppings are not printed, but sites are
@@ -250,14 +280,18 @@ Also for 3D it is possible to customize the plot. For example, we
can explicitly plot the hoppings as lines, and color sites differently
depending on the sublattice:
-.. literalinclude:: /code/include/plot_zincblende.py
- :start-after: #HIDDEN_BEGIN_plot2
- :end-before: #HIDDEN_END_plot2
+.. jupyter-execute::
-which results in a 3D plot that allows to interactively (when plotted
-in a window) explore the crystal structure:
+ syst = make_cuboid(a=1.5, b=1.5, c=1.5)
-.. image:: /code/figure/plot_zincblende_syst2.*
+ def family_colors(site):
+ return 'r' if site.family == a else 'g'
+
+ kwant.plot(syst, site_size=0.18, site_lw=0.01, hop_lw=0.05,
+ site_color=family_colors);
+
+which results in a 3D plot that allows to interactively (when plotted
+in a window) explore the crystal structure.
Hence, a few lines of code using Kwant allow to explore all the different
crystal lattices out there!
--
GitLab