From b0b5327b6fdb20efcc7c530671e73a807201f996 Mon Sep 17 00:00:00 2001
From: Joseph Weston <joseph@weston.cloud>
Date: Tue, 30 Apr 2019 11:46:06 +0200
Subject: [PATCH] convert discretizer example to jupyter-sphinx
---
doc/source/tutorial/discretize.rst | 252 +++++++++++++++++++++++------
1 file changed, 200 insertions(+), 52 deletions(-)
diff --git a/doc/source/tutorial/discretize.rst b/doc/source/tutorial/discretize.rst
index b737b00c..27bab68f 100644
--- a/doc/source/tutorial/discretize.rst
+++ b/doc/source/tutorial/discretize.rst
@@ -18,8 +18,29 @@ continuum models and for discretizing them into tight-binding models.
.. seealso::
The complete source code of this tutorial can be found in
- :download:`discretize.py </code/download/discretize.py>`
+ :jupyter-download:script:`discretize`
+.. jupyter-kernel::
+ :id: discretize
+
+.. jupyter-execute::
+ :hide-code:
+
+ # Tutorial 2.9. Processing continuum Hamiltonians with discretize
+ # ===============================================================
+ #
+ # Physics background
+ # ------------------
+ # - tight-binding approximation of continuous Hamiltonians
+ #
+ # Kwant features highlighted
+ # --------------------------
+ # - kwant.continuum.discretize
+
+ import matplotlib as mpl
+ from matplotlib import pyplot
+
+ import kwant
.. _tutorial_discretizer_introduction:
@@ -55,9 +76,16 @@ Using `~kwant.continuum.discretize` to obtain a template
........................................................
First we must explicitly import the `kwant.continuum` package:
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_import
- :end-before: #HIDDEN_END_import
+.. jupyter-execute::
+
+ import kwant.continuum
+
+.. jupyter-execute::
+ :hide-code:
+
+ import scipy.sparse.linalg
+ import scipy.linalg
+ import numpy as np
The function `kwant.continuum.discretize` takes a symbolic Hamiltonian and
turns it into a `~kwant.builder.Builder` instance with appropriate spatial
@@ -65,17 +93,16 @@ symmetry that serves as a template.
(We will see how to use the template to build systems with a particular
shape later).
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_symbolic_discretization
- :end-before: #HIDDEN_END_symbolic_discretization
+.. jupyter-execute::
+
+ template = kwant.continuum.discretize('k_x * A(x) * k_x')
+ print(template)
It is worth noting that ``discretize`` treats ``k_x`` and ``x`` as
non-commuting operators, and so their order is preserved during the
discretization process.
-The builder produced by ``discretize`` may be printed to show the source code of its onsite and hopping functions (this is a special feature of builders returned by ``discretize``):
-
-.. literalinclude:: /code/figure/discretizer_intro_verbose.txt
+Printing the Builder produced by ``discretize`` shows the source code of its onsite and hopping functions (this is a special feature of builders returned by ``discretize``).
.. specialnote:: Technical details
@@ -139,26 +166,45 @@ where :math:`V(x, y)` is some arbitrary potential.
First, use ``discretize`` to obtain a
builder that we will use as a template:
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_template
- :end-before: #HIDDEN_END_template
+.. jupyter-execute::
+
+ hamiltonian = "k_x**2 + k_y**2 + V(x, y)"
+ template = kwant.continuum.discretize(hamiltonian)
+ print(template)
We now use this system with the `~kwant.builder.Builder.fill`
method of `~kwant.builder.Builder` to construct the system we
want to investigate:
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_fill
- :end-before: #HIDDEN_END_fill
+.. jupyter-execute::
+
+ def stadium(site):
+ (x, y) = site.pos
+ x = max(abs(x) - 20, 0)
+ return x**2 + y**2 < 30**2
+
+ syst = kwant.Builder()
+ syst.fill(template, stadium, (0, 0));
+ syst = syst.finalized()
After finalizing this system, we can plot one of the system's
energy eigenstates:
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_plot_eigenstate
- :end-before: #HIDDEN_END_plot_eigenstate
+.. jupyter-execute::
-.. image:: /code/figure/discretizer_gs.*
+ def plot_eigenstate(syst, n=2, Vx=.0003, Vy=.0005):
+
+ def potential(x, y):
+ return Vx * x + Vy * y
+
+ ham = syst.hamiltonian_submatrix(params=dict(V=potential), sparse=True)
+ evecs = scipy.sparse.linalg.eigsh(ham, k=10, which='SM')[1]
+ kwant.plotter.map(syst, abs(evecs[:, n])**2, show=False)
+
+.. jupyter-execute::
+ :hide-code:
+
+ plot_eigenstate(syst)
Note in the above that we pass the spatially varying potential *function*
to our system via a parameter called ``V``, because the symbol :math:`V`
@@ -176,32 +222,95 @@ model [1]_ [2]_, one can provide matrix input to `~kwant.continuum.discretize`
using ``identity`` and ``kron``. For example, the definition of the BHZ model can be
written succinctly as:
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_define_qsh
- :end-before: #HIDDEN_END_define_qsh
+.. jupyter-execute::
+
+ hamiltonian = """
+ + C * identity(4) + M * kron(sigma_0, sigma_z)
+ - B * (k_x**2 + k_y**2) * kron(sigma_0, sigma_z)
+ - D * (k_x**2 + k_y**2) * kron(sigma_0, sigma_0)
+ + A * k_x * kron(sigma_z, sigma_x)
+ - A * k_y * kron(sigma_0, sigma_y)
+ """
+
+ a = 20
+
+ template = kwant.continuum.discretize(hamiltonian, grid=a)
We can then make a ribbon out of this template system:
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_define_qsh_build
- :end-before: #HIDDEN_END_define_qsh_build
+.. jupyter-execute::
+
+ L, W = 2000, 1000
+
+ def shape(site):
+ (x, y) = site.pos
+ return (0 <= y < W and 0 <= x < L)
+
+ def lead_shape(site):
+ (x, y) = site.pos
+ return (0 <= y < W)
+
+ syst = kwant.Builder()
+ syst.fill(template, shape, (0, 0))
+
+ lead = kwant.Builder(kwant.TranslationalSymmetry([-a, 0]))
+ lead.fill(template, lead_shape, (0, 0))
+
+ syst.attach_lead(lead)
+ syst.attach_lead(lead.reversed())
+
+ syst = syst.finalized()
and plot its dispersion using `kwant.plotter.bands`:
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_plot_qsh_band
- :end-before: #HIDDEN_END_plot_qsh_band
+.. jupyter-execute::
-.. image:: /code/figure/discretizer_qsh_band.*
+ params = dict(A=3.65, B=-68.6, D=-51.1, M=-0.01, C=0)
+
+ kwant.plotter.bands(syst.leads[0], params=params,
+ momenta=np.linspace(-0.3, 0.3, 201), show=False)
+
+ pyplot.grid()
+ pyplot.xlim(-.3, 0.3)
+ pyplot.ylim(-0.05, 0.05)
+ pyplot.xlabel('momentum [1/A]')
+ pyplot.ylabel('energy [eV]')
+ pyplot.show()
In the above we see the edge states of the quantum spin Hall effect, which
we can visualize using `kwant.plotter.map`:
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_plot_qsh_wf
- :end-before: #HIDDEN_END_plot_qsh_wf
+.. jupyter-execute::
+
+ # get scattering wave functions at E=0
+ wf = kwant.wave_function(syst, energy=0, params=params)
-.. image:: /code/figure/discretizer_qsh_wf.*
+ # prepare density operators
+ sigma_z = np.array([[1, 0], [0, -1]])
+ prob_density = kwant.operator.Density(syst, np.eye(4))
+ spin_density = kwant.operator.Density(syst, np.kron(sigma_z, np.eye(2)))
+
+ # calculate expectation values and plot them
+ wf_sqr = sum(prob_density(psi) for psi in wf(0)) # states from left lead
+ rho_sz = sum(spin_density(psi) for psi in wf(0)) # states from left lead
+
+ fig, (ax1, ax2) = pyplot.subplots(1, 2, sharey=True, figsize=(16, 4))
+ kwant.plotter.map(syst, wf_sqr, ax=ax1)
+ kwant.plotter.map(syst, rho_sz, ax=ax2)
+
+ ax = ax1
+ im = [obj for obj in ax.get_children()
+ if isinstance(obj, mpl.image.AxesImage)][0]
+ fig.colorbar(im, ax=ax)
+
+ ax = ax2
+ im = [obj for obj in ax.get_children()
+ if isinstance(obj, mpl.image.AxesImage)][0]
+ fig.colorbar(im, ax=ax)
+
+ ax1.set_title('Probability density')
+ ax2.set_title('Spin density')
+ pyplot.show()
Limitations of discretization
@@ -238,29 +347,62 @@ example. Let us start from the continuum Hamiltonian
We start by defining this model as a string and setting the value of the
:math:`α` parameter:
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_ls_def
- :end-before: #HIDDEN_END_ls_def
+.. jupyter-execute::
+
+ hamiltonian = "k_x**2 * identity(2) + alpha * k_x * sigma_y"
+ params = dict(alpha=.5)
Now we can use `kwant.continuum.lambdify` to obtain a function that computes
:math:`H(k)`:
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_ls_hk_cont
- :end-before: #HIDDEN_END_ls_hk_cont
+.. jupyter-execute::
+
+ h_k = kwant.continuum.lambdify(hamiltonian, locals=params)
+ k_cont = np.linspace(-4, 4, 201)
+ e_cont = [scipy.linalg.eigvalsh(h_k(k_x=ki)) for ki in k_cont]
We can also construct a discretized approximation using
`kwant.continuum.discretize`, in a similar manner to previous examples:
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_ls_hk_tb
- :end-before: #HIDDEN_END_ls_hk_tb
+.. jupyter-execute::
+
+ def plot(ax, a=1):
+ template = kwant.continuum.discretize(hamiltonian, grid=a)
+ syst = kwant.wraparound.wraparound(template).finalized()
+
+ def h_k(k_x):
+ p = dict(k_x=k_x, **params)
+ return syst.hamiltonian_submatrix(params=p)
+
+ k_tb = np.linspace(-np.pi/a, np.pi/a, 201)
+ e_tb = [scipy.linalg.eigvalsh(h_k(k_x=a*ki)) for ki in k_tb]
+
+ ax.plot(k_cont, e_cont, 'r-')
+ ax.plot(k_tb, e_tb, 'k-')
+
+ ax.plot([], [], 'r-', label='continuum')
+ ax.plot([], [], 'k-', label='tight-binding')
+
+ ax.set_xlim(-4, 4)
+ ax.set_ylim(-1, 14)
+ ax.set_title('a={}'.format(a))
+
+ ax.set_xlabel('momentum [a.u.]')
+ ax.set_ylabel('energy [a.u.]')
+ ax.grid()
+ ax.legend()
Below we can see the continuum and tight-binding dispersions for two
different values of the discretization grid spacing :math:`a`:
-.. image:: /code/figure/discretizer_lattice_spacing.*
+.. jupyter-execute::
+ :hide-code:
+
+ _, (ax1, ax2) = pyplot.subplots(1, 2, sharey=True, figsize=(12, 4))
+ plot(ax1, a=1)
+ plot(ax2, a=.25)
+ pyplot.show()
We clearly see that the smaller grid spacing is, the better we approximate
the original continuous dispersion. It is also worth remembering that the
@@ -284,20 +426,26 @@ It is possible to use ``identity`` (for identity matrix), ``kron`` (for Kronecke
expressions involving matrices. Matrices can also be provided explicitly using
square ``[]`` brackets. For example, all following expressions are equivalent:
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_subs_1
- :end-before: #HIDDEN_END_subs_1
+.. jupyter-execute::
+
+ sympify = kwant.continuum.sympify
+ subs = {'sx': [[0, 1], [1, 0]], 'sz': [[1, 0], [0, -1]]}
+
+ e = (
+ sympify('[[k_x**2, alpha * k_x], [k_x * alpha, -k_x**2]]'),
+ sympify('k_x**2 * sigma_z + alpha * k_x * sigma_x'),
+ sympify('k_x**2 * sz + alpha * k_x * sx', locals=subs),
+ )
-.. literalinclude:: /code/figure/discretizer_subs_1.txt
+ print(e[0] == e[1] == e[2])
We can use the ``locals`` keyword parameter to substitute expressions
and numerical values:
-.. literalinclude:: /code/include/discretize.py
- :start-after: #HIDDEN_BEGIN_subs_2
- :end-before: #HIDDEN_END_subs_2
+.. jupyter-execute::
-.. literalinclude:: /code/figure/discretizer_subs_2.txt
+ subs = {'A': 'A(x) + B', 'V': 'V(x) + V_0', 'C': 5}
+ print(sympify('k_x * A * k_x + V + C', locals=subs))
Symbolic expressions obtained in this way can be directly passed to all
``discretizer`` functions.
--
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