From 18a08c37b1bb794d5b9ee98882ea68fc5df0fd5f Mon Sep 17 00:00:00 2001
From: Joseph Weston <joseph@weston.cloud>
Date: Wed, 21 Aug 2019 10:53:40 +0200
Subject: [PATCH] specify 'norbs' on lattice creation in all tutorials
---
doc/source/tutorial/faq.rst | 32 ++++++++++----------
doc/source/tutorial/first_steps.rst | 11 ++++---
doc/source/tutorial/graphene.rst | 3 +-
doc/source/tutorial/magnetic_field.rst | 2 +-
doc/source/tutorial/plotting.rst | 5 +--
doc/source/tutorial/spectrum.rst | 2 +-
doc/source/tutorial/spin_potential_shape.rst | 13 +++++---
doc/source/tutorial/superconductors.rst | 2 +-
8 files changed, 39 insertions(+), 31 deletions(-)
diff --git a/doc/source/tutorial/faq.rst b/doc/source/tutorial/faq.rst
index 22f0ad71..e82d0f18 100644
--- a/doc/source/tutorial/faq.rst
+++ b/doc/source/tutorial/faq.rst
@@ -68,7 +68,7 @@ For example let us create an empty tight binding system and add two sites:
.. jupyter-execute::
a = 1
- lat = kwant.lattice.square(a)
+ lat = kwant.lattice.square(a, norbs=1)
syst = kwant.Builder()
syst[lat(1, 0)] = 4
@@ -165,9 +165,9 @@ the origins of the two lattices:
# Two monatomic lattices
primitive_vectors = [(1, 0), (0, 1)]
- lat_a = kwant.lattice.Monatomic(primitive_vectors, offset=(0, 0))
- lat_b = kwant.lattice.Monatomic(primitive_vectors, offset=(0.5, 0.5))
- # lat1 is equivalent to kwant.lattice.square()
+ lat_a = kwant.lattice.Monatomic(primitive_vectors, offset=(0, 0), norbs=1)
+ lat_b = kwant.lattice.Monatomic(primitive_vectors, offset=(0.5, 0.5), norbs=1)
+ # lat1 is equivalent to kwant.lattice.square(norbs=1)
syst = kwant.Builder()
@@ -182,7 +182,7 @@ two sites in the basis:
.. jupyter-execute::
# One polyatomic lattice containing two sublattices
- lat = kwant.lattice.Polyatomic([(1, 0), (0, 1)], [(0, 0), (0.5, 0.5)])
+ lat = kwant.lattice.Polyatomic([(1, 0), (0, 1)], [(0, 0), (0.5, 0.5)], norbs=1)
sub_a, sub_b = lat.sublattices
The two sublattices ``sub_a`` and ``sub_b`` are nothing else than ``Monatomic``
@@ -204,7 +204,7 @@ In the following example we shall use a kagome lattice, which has three sublatti
.. jupyter-execute::
- lat = kwant.lattice.kagome()
+ lat = kwant.lattice.kagome(norbs=1)
syst = kwant.Builder()
a, b, c = lat.sublattices # The kagome lattice has 3 sublattices
@@ -258,7 +258,7 @@ The following example shows how this can be used:
# Create hopping between neighbors with HoppingKind
a = 1
syst = kwant.Builder()
- lat = kwant.lattice.square(a)
+ lat = kwant.lattice.square(a, norbs=1)
syst[ (lat(i, j) for i in range(5) for j in range(5)) ] = 4
syst[kwant.builder.HoppingKind((1, 0), lat)] = -1
@@ -271,7 +271,7 @@ the sublattices when creating a ``HoppingKind``:
.. jupyter-execute::
:hide-code:
- lat = kwant.lattice.kagome()
+ lat = kwant.lattice.kagome(norbs=1)
syst = kwant.Builder()
a, b, c = lat.sublattices # The kagome lattice has 3 sublattices
@@ -323,7 +323,7 @@ that returns a list of ``HoppingKind`` instances that connect sites with their
# Create hoppings with lat.neighbors()
syst = kwant.Builder()
- lat = kwant.lattice.square()
+ lat = kwant.lattice.square(norbs=1)
syst[(lat(i, j) for i in range(3) for j in range(3))] = 4
syst[lat.neighbors()] = -1 # Equivalent to lat.neighbors(1)
@@ -344,7 +344,7 @@ sublattices:
.. jupyter-execute::
# Create the system
- lat = kwant.lattice.kagome()
+ lat = kwant.lattice.kagome(norbs=1)
syst = kwant.Builder()
a, b, c = lat.sublattices # The kagome lattice has 3 sublattices
@@ -382,7 +382,7 @@ region:
# Define the lattice and the (empty) system
a = 2
- lat = kwant.lattice.cubic(a)
+ lat = kwant.lattice.cubic(a, norbs=1)
syst = kwant.Builder()
L = 10
@@ -424,7 +424,7 @@ We can access the sites of a ``Builder`` by using its `~kwant.builder.Builder.si
:hide-code:
builder = kwant.Builder()
- lat = kwant.lattice.square()
+ lat = kwant.lattice.square(norbs=1)
builder[(lat(i, j) for i in range(3) for j in range(3))] = 4
.. jupyter-execute::
@@ -472,7 +472,7 @@ First we construct the central system:
L = 5
W = 5
- lat = kwant.lattice.honeycomb()
+ lat = kwant.lattice.honeycomb(norbs=1)
subA, subB = lat.sublattices
syst = kwant.Builder()
@@ -487,7 +487,7 @@ and the lead:
.. jupyter-execute::
# Create a lead
- lat_lead = kwant.lattice.square()
+ lat_lead = kwant.lattice.square(norbs=1)
sym_lead1 = kwant.TranslationalSymmetry((0, 1))
lead1 = kwant.Builder(sym_lead1)
@@ -535,7 +535,7 @@ For example, say we want to create a simple model on a cubic lattice:
.. jupyter-execute::
# Create 3d model.
- cubic = kwant.lattice.cubic()
+ cubic = kwant.lattice.cubic(norbs=1)
sym_3d = kwant.TranslationalSymmetry([1, 0, 0], [0, 1, 0], [0, 0, 1])
model = kwant.Builder(sym_3d)
model[cubic(0, 0, 0)] = 4
@@ -587,7 +587,7 @@ system in a `~kwant.physics.PropagatingModes` object:
.. jupyter-execute::
- lat = kwant.lattice.square()
+ lat = kwant.lattice.square(norbs=1)
lead = kwant.Builder(kwant.TranslationalSymmetry((-1, 0)))
lead[(lat(0, i) for i in range(3))] = 4
diff --git a/doc/source/tutorial/first_steps.rst b/doc/source/tutorial/first_steps.rst
index 801bb3e5..41ed21bb 100644
--- a/doc/source/tutorial/first_steps.rst
+++ b/doc/source/tutorial/first_steps.rst
@@ -128,14 +128,16 @@ a square lattice. For simplicity, we set the lattice constant to unity:
.. jupyter-execute::
a = 1
- lat = kwant.lattice.square(a)
+ lat = kwant.lattice.square(a, norbs=1)
Since we work with a square lattice, we label the points with two
integer coordinates `(i, j)`. `~kwant.builder.Builder` then
allows us to add matrix elements corresponding to lattice points:
``syst[lat(i, j)] = ...`` sets the on-site energy for the point `(i, j)`,
and ``syst[lat(i1, j1), lat(i2, j2)] = ...`` the hopping matrix element
-**from** point `(i2, j2)` **to** point `(i1, j1)`.
+**from** point `(i2, j2)` **to** point `(i1, j1)`. In specifying ``norbs=1``
+in the definition of the lattice we tell Kwant that there is 1 degree
+of freedom per lattice site.
Note that we need to specify sites for `~kwant.builder.Builder`
in the form ``lat(i, j)``. The lattice object `lat` does the
@@ -472,7 +474,8 @@ file and defining the a square lattice and empty scattering region.
# Start with an empty tight-binding system and a single square lattice.
# `a` is the lattice constant (by default set to 1 for simplicity).
- lat = kwant.lattice.square(a)
+ # Each lattice site has 1 degree of freedom, hence norbs=1.
+ lat = kwant.lattice.square(a, norbs=1)
syst = kwant.Builder()
@@ -681,7 +684,7 @@ return a Kwant ``Builder``:
.. jupyter-execute::
def make_system(L, W, a=1, t=1.0):
- lat = kwant.lattice.square(a)
+ lat = kwant.lattice.square(a, norbs=1)
syst = kwant.Builder()
syst[(lat(i, j) for i in range(L) for j in range(W))] = 4 * t
diff --git a/doc/source/tutorial/graphene.rst b/doc/source/tutorial/graphene.rst
index 4243b7ff..792d4521 100644
--- a/doc/source/tutorial/graphene.rst
+++ b/doc/source/tutorial/graphene.rst
@@ -59,7 +59,8 @@ explicitly here to show how to define a new lattice:
.. jupyter-execute::
graphene = kwant.lattice.general([(1, 0), (sin_30, cos_30)],
- [(0, 0), (0, 1 / sqrt(3))])
+ [(0, 0), (0, 1 / sqrt(3))],
+ norbs=1)
a, b = graphene.sublattices
The first argument to the `~kwant.lattice.general` function is the list of
diff --git a/doc/source/tutorial/magnetic_field.rst b/doc/source/tutorial/magnetic_field.rst
index add388bf..a3c98b95 100644
--- a/doc/source/tutorial/magnetic_field.rst
+++ b/doc/source/tutorial/magnetic_field.rst
@@ -137,7 +137,7 @@ a discretization in realspace.
.. jupyter-execute::
- lat = kwant.lattice.square()
+ lat = kwant.lattice.square(norbs=1)
syst = kwant.Builder(kwant.TranslationalSymmetry((-1, 0)))
def peierls(to_site, from_site, B):
diff --git a/doc/source/tutorial/plotting.rst b/doc/source/tutorial/plotting.rst
index fc4b65c8..bf6b51ae 100644
--- a/doc/source/tutorial/plotting.rst
+++ b/doc/source/tutorial/plotting.rst
@@ -53,7 +53,7 @@ to previous examples, we will also use hoppings beyond next-nearest neighbors:
.. jupyter-execute::
- lat = kwant.lattice.honeycomb()
+ lat = kwant.lattice.honeycomb(norbs=1)
a, b = lat.sublattices
def make_system(r=8, t=-1, tp=-0.1):
@@ -241,7 +241,8 @@ It is very easily generated in Kwant with `kwant.lattice.general`:
.. 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)])
+ [(0, 0, 0), (0.25, 0.25, 0.25)],
+ norbs=1)
a, b = lat.sublattices
Note how we keep references to the two different sublattices for later use.
diff --git a/doc/source/tutorial/spectrum.rst b/doc/source/tutorial/spectrum.rst
index 5e70ba9b..2b6d86a0 100644
--- a/doc/source/tutorial/spectrum.rst
+++ b/doc/source/tutorial/spectrum.rst
@@ -54,7 +54,7 @@ usual way:
def make_lead(a=1, t=1.0, W=10):
# Start with an empty lead with a single square lattice
- lat = kwant.lattice.square(a)
+ lat = kwant.lattice.square(a, norbs=1)
sym_lead = kwant.TranslationalSymmetry((-a, 0))
lead = kwant.Builder(sym_lead)
diff --git a/doc/source/tutorial/spin_potential_shape.rst b/doc/source/tutorial/spin_potential_shape.rst
index 05aad2e6..b87eaa7f 100644
--- a/doc/source/tutorial/spin_potential_shape.rst
+++ b/doc/source/tutorial/spin_potential_shape.rst
@@ -109,7 +109,7 @@ we can simply write:
.. jupyter-execute::
:hide-code:
- lat = kwant.lattice.square()
+ lat = kwant.lattice.square(norbs=2)
syst = kwant.Builder()
.. jupyter-execute::
@@ -124,6 +124,9 @@ we can simply write:
syst[kwant.builder.HoppingKind((0, 1), lat, lat)] = \
-t * sigma_0 - 1j * alpha * sigma_x / 2
+Note that we specify ``norbs=2`` when creating the lattice, as each site
+has 2 degrees of freedom associated with it, giving us 2x2 matrices as
+onsite/hopping terms.
Note that the Zeeman energy adds to the onsite term, whereas the Rashba
spin-orbit term adds to the hoppings (due to the derivative operator).
Furthermore, the hoppings in x and y-direction have a different matrix
@@ -298,7 +301,7 @@ Kwant now allows us to pass a function as a value to
def onsite(site, pot):
return 4 * t + potential(site, pot)
- lat = kwant.lattice.square(a)
+ lat = kwant.lattice.square(a, norbs=1)
syst = kwant.Builder()
syst[(lat(x, y) for x in range(L) for y in range(W))] = onsite
@@ -457,7 +460,7 @@ provided by the lattice:
a = 1
t = 1.0
- lat = kwant.lattice.square(a)
+ lat = kwant.lattice.square(a, norbs=1)
syst = kwant.Builder()
syst[lat.shape(ring, (0, r1 + 1))] = 4 * t
@@ -620,7 +623,7 @@ period of one flux quantum.
W = 10
r1, r2 = 10, 20
- lat = kwant.lattice.square()
+ lat = kwant.lattice.square(norbs=1)
syst = kwant.Builder()
def ring(pos):
(x, y) = pos
@@ -675,7 +678,7 @@ period of one flux quantum.
W = 10
r1, r2 = 10, 20
- lat = kwant.lattice.square(a)
+ lat = kwant.lattice.square(a, norbs=1)
syst = kwant.Builder()
def ring(pos):
(x, y) = pos
diff --git a/doc/source/tutorial/superconductors.rst b/doc/source/tutorial/superconductors.rst
index 9e0b1d7a..f2e3b323 100644
--- a/doc/source/tutorial/superconductors.rst
+++ b/doc/source/tutorial/superconductors.rst
@@ -133,7 +133,7 @@ and we declare the square lattice and construct the scattering region with the f
# Hoppings
syst[lat.neighbors()] = -t * tau_z
-Note the new argument ``norbs`` to `~kwant.lattice.square`. This is
+Note the argument ``norbs`` to `~kwant.lattice.square`. This is
the number of orbitals per site in the discretized BdG Hamiltonian - of course,
``norbs = 2``, since each site has one electron orbital and one hole orbital.
It is necessary to specify ``norbs`` here, such that we may later separate the
--
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