From 01a617a984600d4c4f61601633ba82d970236724 Mon Sep 17 00:00:00 2001
From: Anton Akhmerov <anton.akhmerov@gmail.com>
Date: Sun, 28 Apr 2013 01:37:39 -0400
Subject: [PATCH] update docs, and use the new functionality in tutorial
---
doc/source/reference/kwant.lattice.rst | 1 +
doc/source/reference/kwant.linalg.rst | 5 +++--
doc/source/tutorial/ab_ring.py | 2 +-
doc/source/tutorial/graphene.py | 8 +++-----
doc/source/whatsnew/0.3.rst | 11 +++++++++++
kwant/lattice.py | 15 +++++++++++----
6 files changed, 30 insertions(+), 12 deletions(-)
diff --git a/doc/source/reference/kwant.lattice.rst b/doc/source/reference/kwant.lattice.rst
index 6da3fc23..e3e975fc 100644
--- a/doc/source/reference/kwant.lattice.rst
+++ b/doc/source/reference/kwant.lattice.rst
@@ -12,6 +12,7 @@ General
general
Monatomic
Polyatomic
+ Shape
Library of lattices
-------------------
diff --git a/doc/source/reference/kwant.linalg.rst b/doc/source/reference/kwant.linalg.rst
index d535789b..8ce1346b 100644
--- a/doc/source/reference/kwant.linalg.rst
+++ b/doc/source/reference/kwant.linalg.rst
@@ -4,8 +4,9 @@
.. module:: kwant.linalg
This package wraps some selected LAPACK functionality not available via NumPy
-and also contains a Python-wrapper for MUMPS. It is meant for internal use by
-kwant itself, but of course nothing prevents you from using it directly.
+and also contains a Python-wrapper for MUMPS. It also has several algorithms
+for finding approximately orthonormal lattice bases. It is meant for internal
+use by kwant itself, but of course nothing prevents you from using it directly.
The documentation of this package is not included here on purpose in order not
to add too many things to this reference. Please consult the source code
diff --git a/doc/source/tutorial/ab_ring.py b/doc/source/tutorial/ab_ring.py
index 1877973c..9ca3130a 100644
--- a/doc/source/tutorial/ab_ring.py
+++ b/doc/source/tutorial/ab_ring.py
@@ -73,7 +73,7 @@ def make_system(a=1, t=1.0, W=10, r1=10, r2=20):
def lead_shape(pos):
(x, y) = pos
- return (-1 < x < 1) and (-W / 2 < y < W / 2)
+ return (-W / 2 < y < W / 2)
lead[lat.shape(lead_shape, (0, 0))] = 4 * t
lead[lat.nearest] = -t
diff --git a/doc/source/tutorial/graphene.py b/doc/source/tutorial/graphene.py
index 5da94114..32a57dc4 100644
--- a/doc/source/tutorial/graphene.py
+++ b/doc/source/tutorial/graphene.py
@@ -70,7 +70,7 @@ def make_system(r=10, w=2.0, pot=0.1):
def lead0_shape(pos):
x, y = pos
- return (-1 < x < 1) and (-0.4 * r < y < 0.4 * r)
+ return (-0.4 * r < y < 0.4 * r)
lead0 = kwant.Builder(sym0)
lead0[graphene.shape(lead0_shape, (0, 0))] = -pot
@@ -80,10 +80,8 @@ def make_system(r=10, w=2.0, pot=0.1):
sym1 = kwant.TranslationalSymmetry(graphene.vec((0, 1)))
def lead1_shape(pos):
- x, y = pos
- u = x * sin_30 + y * cos_30
- v = y * sin_30 - x * cos_30
- return (-1 < u < 1) and (-0.4 * r < v < 0.4 * r)
+ v = pos[1] * sin_30 - pos[0] * cos_30
+ return (-0.4 * r < v < 0.4 * r)
lead1 = kwant.Builder(sym1)
lead1[graphene.shape(lead1_shape, (0, 0))] = pot
diff --git a/doc/source/whatsnew/0.3.rst b/doc/source/whatsnew/0.3.rst
index a99b3fca..ab56c599 100644
--- a/doc/source/whatsnew/0.3.rst
+++ b/doc/source/whatsnew/0.3.rst
@@ -120,3 +120,14 @@ containing all the parameters as attributes::
Arguments can be passed in an equivalent way in calls to
`~kwant.solvers.default.wave_function` and `~kwant.solvers.default.ldos`.
+
+Lattice and shape improvements
+------------------------------
+`~kwant.lattice.Monoatomic.closest` now returns an exact, and not approximately
+closest point. A new method `~kwant.lattice.Monoatomic.n_closest` was added,
+which returns n closest lattice points. Likewise
+`~kwant.lattice.Polyatomic.shape` has acquired an improved flood-fill
+algorithm, making it work better on narrow ribbon (which were sometimes buggy
+before with non-square lattices). Additionally, it was made symmetry-aware, so
+if a shape is used for a lead, no conditions with regard to coordnate parallel
+to the lead period are required.
diff --git a/kwant/lattice.py b/kwant/lattice.py
index d117e04a..ca085e94 100644
--- a/kwant/lattice.py
+++ b/kwant/lattice.py
@@ -74,10 +74,6 @@ class Polyatomic(object):
------
ValueError
If dimensionalities do not match.
-
- Notes
- -----
-
"""
def __init__(self, prim_vecs, basis, name=''):
prim_vecs = ta.array(prim_vecs, float)
@@ -408,6 +404,17 @@ class Shape(object):
and False otherwise.
start : float vector
The origin for the flood-fill algorithm.
+
+ Notes
+ -----
+ A ``Shape`` is a callable object: When called with a
+ `~kwant.builder.Builder` as sole argument, an instance of this class will
+ return an iterator over all the sites from the shape that are in the fundamental domain of the builder's symmetry.
+
+ Because a `~kwant.builder.Builder` can be indexed with functions or
+ iterables of functions, ``Shape`` instances (or any non-tuple
+ iterables of them, e.g. a list) can be used directly as "wildcards" when
+ setting or deleting sites.
"""
self.lat, self.func, self.start = lattice, function, start
--
GitLab