provide downloads for tutorial 6

doc/source/tutorial/tutorial6.rst

@@ -4,16 +4,15 @@ Plotting Kwant systems and data in various styles
 The plotting functionality of Kwant has been used extensively (through
 `~kwant.plotter.plot` and `~kwant.plotter.map`) in the previous tutorials. In
 addition to this basic use, `~kwant.plotter.plot` offers many options to change
-the plotting style extensively. It is the goal of this tutorial to show
-how these options can be used to achieve various very different objectives.
+the plotting style extensively. It is the goal of this tutorial to show how
+these options can be used to achieve various very different objectives.
 
 2D example: graphene quantum dot
 ................................
 
-We begin by first considering a circular graphene quantum dot (similar
-to what has been used in parts of the tutorial :ref:`tutorial-graphene`.)
-In contrast to previous examples, we will also use hoppings beyond
-next-nearest neighbors:
+We begin by first considering a circular graphene quantum dot (similar to what
+has been used in parts of the tutorial :ref:`tutorial-graphene`.)  In contrast
+to previous examples, we will also use hoppings beyond next-nearest neighbors:
 
 .. literalinclude:: plot_graphene.py
     :start-after: #HIDDEN_BEGIN_makesys
@@ -22,9 +21,9 @@ next-nearest neighbors:
 Note that adding hoppings hoppings to the `n`-th nearest neighbors can be
 simply done by passing `n` as an argument to
 `~kwant.lattice.Polyatomic.neighbors`. Also note that we use the method
-`~kwant.builder.Builder.eradicate_dangling` to get rid of single atoms sticking out of
-the shape. It is necessary to do so *before* adding the next-nearest-neighbor
-hopping [#]_.
+`~kwant.builder.Builder.eradicate_dangling` to get rid of single atoms sticking
+out of the shape. It is necessary to do so *before* adding the
+next-nearest-neighbor hopping [#]_.
 
 Of course, the system can be plotted simply with default settings:
 
@@ -38,11 +37,11 @@ busy plot:
 .. image:: ../images/plot_graphene_sys1.*
 
 A much clearer plot can be obtained by using different colors for both
-sublattices, and by having different line widths for different hoppings.
-This can be achieved by passing a function to the arguments of
+sublattices, and by having different line widths for different hoppings.  This
+can be achieved by passing a function to the arguments of
 `~kwant.plotter.plot`, instead of a constant. For properties of sites, this
-must be a function taking one site as argument, for hoppings
-a function taking the start end end site of hopping as arguments:
+must be a function taking one site as argument, for hoppings a function taking
+the start end end site of hopping as arguments:
 
 .. literalinclude:: plot_graphene.py
     :start-after: #HIDDEN_BEGIN_plotsys2
@@ -54,47 +53,47 @@ that is more intelligible, still carrying all information:
 
 .. image:: ../images/plot_graphene_sys2.*
 
-Apart from plotting the *system* itself, `~kwant.plotter.plot` can also be
-used to plot *data* living on the system.
+Apart from plotting the *system* itself, `~kwant.plotter.plot` can also be used
+to plot *data* living on the system.
 
-As an example, we now compute the eigenstates of the graphene quantum dot
-and intend to plot the wave function probability in the quantum dot. For
-aesthetic reasons (the wave functions look a bit nicer), we restrict ourselves
-to nearest-neighbor hopping.
-Computing the wave functions is done in the usual way (note that for
-a large-scale system, one would probably want to use sparse linear algebra):
+As an example, we now compute the eigenstates of the graphene quantum dot and
+intend to plot the wave function probability in the quantum dot. For aesthetic
+reasons (the wave functions look a bit nicer), we restrict ourselves to
+nearest-neighbor hopping.  Computing the wave functions is done in the usual
+way (note that for a large-scale system, one would probably want to use sparse
+linear algebra):
 
 .. literalinclude:: plot_graphene.py
     :start-after: #HIDDEN_BEGIN_plotdata1
     :end-before: #HIDDEN_END_plotdata1
 
 In most cases, to plot the wave function probability, one wouldn't use
-`~kwant.plotter.plot`, but rather `~kwant.plotter.map`. Here, we plot
-the `n`-th wave function using it:
+`~kwant.plotter.plot`, but rather `~kwant.plotter.map`. Here, we plot the
+`n`-th wave function using it:
 
 .. literalinclude:: plot_graphene.py
     :start-after: #HIDDEN_BEGIN_plotdata2
     :end-before: #HIDDEN_END_plotdata2
 
-This results in a standard pseudocolor plot, showing in this case (``n=225``)
-a graphene edge state, i.e. a wave function mostly localized at the zigzag
-edges of the quantum dot.
+This results in a standard pseudocolor plot, showing in this case (``n=225``) a
+graphene edge state, i.e. a wave function mostly localized at the zigzag edges
+of the quantum dot.
 
 .. image:: ../images/plot_graphene_data1.*
 
-However although in general preferable, `~kwant.plotter.map`
-has a few deficiencies for this small system: For example, there are
-a few distortions at the edge of the dot. (This cannot be avoided in the type
-of interpolation used in `~kwant.plotter.map`). However, we can also use
-`~kwant.plotter.plot` to achieve a similar, but smoother result.
+However although in general preferable, `~kwant.plotter.map` has a few
+deficiencies for this small system: For example, there are a few distortions at
+the edge of the dot. (This cannot be avoided in the type of interpolation used
+in `~kwant.plotter.map`). However, we can also use `~kwant.plotter.plot` to
+achieve a similar, but smoother result.
 
-For this note that `~kwant.plotter.plot` can also take an array of
-floats (or function returning floats) as value for the
-`site_color` argument (the same holds for the hoppings). Via the
-colormap specified in `cmap` these are mapped to color, just as
-`~kwant.plotter.map` does! In addition, we can also change the symbol shape
-depending on the sublattice. With a triangle pointing up and down on the
-respective sublattice, the symbols used by plot fill the space completely:
+For this note that `~kwant.plotter.plot` can also take an array of floats (or
+function returning floats) as value for the `site_color` argument (the same
+holds for the hoppings). Via the colormap specified in `cmap` these are mapped
+to color, just as `~kwant.plotter.map` does! In addition, we can also change
+the symbol shape depending on the sublattice. With a triangle pointing up and
+down on the respective sublattice, the symbols used by plot fill the space
+completely:
 
 .. literalinclude:: plot_graphene.py
     :start-after: #HIDDEN_BEGIN_plotdata3
@@ -107,8 +106,8 @@ takes all sizes in units of the nearest-neighbor spacing. ``site_size=0.5``
 thus means half the distance between neighboring sites (and for the triangles
 this is interpreted as the radius of the inner circle).
 
-Finally, note that since we are dealing with a finalized system now,
-a site `i` is represented by an integer. In order to obtain the original
+Finally, note that since we are dealing with a finalized system now, a site `i`
+is represented by an integer. In order to obtain the original
 `~kwant.builder.Site`, ``sys.site(i)`` can be used.
 
 With this we arrive at
@@ -126,10 +125,9 @@ probability using the symbols itself:
     :start-after: #HIDDEN_BEGIN_plotdata4
     :end-before: #HIDDEN_END_plotdata4
 
-Here, we choose the symbol size proportional to the wave function
-probability, while the site color is transparent to also allow
-for overlapping symbols to be visible. The hoppings are also plotted in order
-to show the underlying lattice.
+Here, we choose the symbol size proportional to the wave function probability,
+while the site color is transparent to also allow for overlapping symbols to be
+visible. The hoppings are also plotted in order to show the underlying lattice.
 
 With this, we arrive at
 
@@ -137,20 +135,23 @@ With this, we arrive at
 
 which shows the edge state nature of the wave function most clearly.
 
+.. seealso::
+    The full source code can be found in
+    :download:`tutorial/plot_graphene.py <../../../tutorial/plot_graphene.py>`
+
 .. rubric:: Footnotes
 
-.. [#] A dangling site is defined as having only one hopping connecting
-       it to the rest. With next-nearest-neighbor hopping also all sites
-       that are dangling with only nearest-neighbor hopping have more than
-       one hopping.
+.. [#] A dangling site is defined as having only one hopping connecting it to
+       the rest. With next-nearest-neighbor hopping also all sites that are
+       dangling with only nearest-neighbor hopping have more than one hopping.
 
 3D example: zincblende structure
 ................................
 
-Zincblende is a very common crystal structure of semiconductors. It is
-a face-centered cubic crystal with two inequivalent atoms in the
-unit cell (i.e. two different types of atoms, unlike diamond which has
-the same crystal structure, but to equivalent atoms per unit cell).
+Zincblende is a very common crystal structure of semiconductors. It is a
+face-centered cubic crystal with two inequivalent atoms in the unit cell
+(i.e. two different types of atoms, unlike diamond which has the same crystal
+structure, but to equivalent atoms per unit cell).
 
 It is very easily generated in Kwant with `kwant.lattice.general`:
 
@@ -160,17 +161,16 @@ It is very easily generated in Kwant with `kwant.lattice.general`:
 
 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:
+A three-dimensional structure is created as easily as in two dimensions, by
+using the `~kwant.lattice.PolyatomicLattice.shape`-functionality:
 
 .. literalinclude:: plot_zincblende.py
     :start-after: #HIDDEN_BEGIN_zincblende2
     :end-before: #HIDDEN_END_zincblende2
 
-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 real calculation, several atomic orbitals would have to be
-considered).
+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
+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:
@@ -184,20 +184,20 @@ resulting in
 .. image:: ../images/plot_zincblende_sys1.*
 
 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 instead represented by little "balls" touching each other (which
-is achieved by a default ``site_size=0.5``). In fact, this style of
-plotting 3D shows quite decently the overall geometry of the system.
+3D than in 2D. For example, by default hoppings are not printed, but sites are
+instead represented by little "balls" touching each other (which is achieved by
+a default ``site_size=0.5``). In fact, this style of plotting 3D shows quite
+decently the overall geometry of the system.
 
 When plotting into a window, the 3D plots can also be rotated and scaled
 arbitrarily, allowing for a good inspection of the geometry from all sides.
 
 .. note::
 
-    Interactive 3D plots usually have not the proper aspect ratio, but are
-    a bit squashed. This is due to bugs in matplotlib's 3D plotting
-    module that does not properly honor the corresponding arguments. By resizing
-    the plot window however one can manually adjust the aspect ratio.
+    Interactive 3D plots usually have not the proper aspect ratio, but are a
+    bit squashed. This is due to bugs in matplotlib's 3D plotting module that
+    does not properly honor the corresponding arguments. By resizing the plot
+    window however one can manually adjust the aspect ratio.
 
 Also for 3D it is possible to customize the plot. For example, we
 can explicitly plot the hoppings as lines, and color sites differently
@@ -222,3 +222,7 @@ crystal lattices out there!
       3d module)
     - Plotting hoppings in 3D is inherently much slower than plotting sites.
       Hence, this is not done by default.
+
+.. seealso::
+    The full source code can be found in :download:`tutorial/plot_zincblende.py
+    <../../../tutorial/plot_zincblende.py>`