From b108491cd7bc81488cc33d8b5089c6b8f6ef7fda Mon Sep 17 00:00:00 2001
From: Christoph Groth <christoph.groth@cea.fr>
Date: Mon, 27 May 2013 23:29:58 +0200
Subject: [PATCH] make lattice.shape return a nested function
---
doc/source/reference/kwant.lattice.rst | 1 -
kwant/lattice.py | 181 +++++++++++++------------
2 files changed, 91 insertions(+), 91 deletions(-)
diff --git a/doc/source/reference/kwant.lattice.rst b/doc/source/reference/kwant.lattice.rst
index e3e975fc..6da3fc23 100644
--- a/doc/source/reference/kwant.lattice.rst
+++ b/doc/source/reference/kwant.lattice.rst
@@ -12,7 +12,6 @@ General
general
Monatomic
Polyatomic
- Shape
Library of lattices
-------------------
diff --git a/kwant/lattice.py b/kwant/lattice.py
index 432d24a8..89871662 100644
--- a/kwant/lattice.py
+++ b/kwant/lattice.py
@@ -99,11 +99,99 @@ class Polyatomic(object):
self._voronoi = ta.dot(lll.voronoi(self._reduced_vecs), self._transf)
def shape(self, function, start):
- """Yield sites belonging to a certain shape.
+ """Return a key for all the lattice sites inside a given shape.
- See `~kwant.lattice.Shape` for more information.
+ The object returned by this method is primarily meant to be used as a
+ key for indexing `kwant.Builder` instances. See example below.
+
+ Parameters
+ ----------
+ function : callable
+ A function of real space coordinates that returns a truth value:
+ true for coordinates inside the shape, and false otherwise.
+ start : float vector
+ The origin for the flood-fill algorithm.
+
+ Returns
+ -------
+ shape_sites : function
+
+ Notes
+ -----
+ When the function returned by this method is called, a flood-fill
+ algorithm finds and yields all the lattice sites inside the specified
+ shape starting from the specified position.
+
+ A `~kwant.builder.Symmetry` or `~kwant.builder.Builder` may be passed as
+ sole argument when calling the function returned by this method. This
+ will restrict the flood-fill to the fundamental domain of the symmetry
+ (or the builder's symmetry). Note that unless the shape function has
+ that symmetry itself, the result may be unexpected.
+
+ Examples
+ --------
+ >>> def circle(pos):
+ ... x, y = pos
+ ... return x**2 + y**2 < 100
+ ...
+ >>> lat = kwant.lattice.honeycomb()
+ >>> sys = kwant.Builder()
+ >>> sys[lat.shape(circle, (0, 0))] = 0
+ >>> sys[lat.neighbors()] = 1
"""
- return Shape(self, function, start)
+ def shape_sites(symmetry=None):
+ Site = builder.Site
+
+ if symmetry is None:
+ symmetry = builder.NoSymmetry()
+ elif not isinstance(symmetry, builder.Symmetry):
+ symmetry = symmetry.symmetry
+
+ def fd_site(lat, tag):
+ return symmetry.to_fd(Site(lat, tag, True))
+
+ dim = len(start)
+ if dim != self.prim_vecs.shape[1]:
+ raise ValueError('Dimensionality of start position does not '
+ 'match the space dimensionality.')
+ lats = self.sublattices
+ deltas = list(self._voronoi)
+
+ #### Flood-fill ####
+ sites = []
+ for tag in set(lat.closest(start) for lat in lats):
+ for lat in lats:
+ site = fd_site(lat, tag)
+ if function(site.pos):
+ sites.append(site)
+ if not sites:
+ msg = 'No sites close to {0} are inside the desired shape.'
+ raise ValueError(msg.format(start))
+ tags = set(s.tag for s in sites)
+
+ while sites:
+ old_tags = tags
+ tags = set()
+ for site in sites:
+ yield site
+ tags.add(site.tag)
+ old_tags |= tags
+
+ new_tags = set()
+ for tag in tags:
+ for delta in deltas:
+ new_tag = tag + delta
+ if new_tag not in old_tags:
+ new_tags.add(new_tag)
+
+ sites = set()
+ for tag in new_tags:
+ for lat in lats:
+ site = fd_site(lat, tag)
+ if site.tag not in old_tags and function(site.pos):
+ sites.add(site)
+
+ return shape_sites
def neighbors(self, n=1, eps=1e-8):
"""
@@ -476,93 +564,6 @@ class TranslationalSymmetry(builder.Symmetry):
return result
-class Shape(object):
- def __init__(self, lattice, function, start):
- """A class for finding all the lattice sites inside a shape.
-
- When an instance of this class is called, a flood-fill algorithm finds
- and yields all the sites inside the specified shape starting from the
- specified position.
-
- Parameters
- ----------
- lattice : Polyatomic or Monoatomic lattice
- Lattice, to which the resulting sites should belong.
- function : callable
- A function of real space coordinates that returns a truth value:
- true for coordinates inside the shape, and false otherwise.
- start : float vector
- The origin for the flood-fill algorithm.
-
- Notes
- -----
- A `~kwant.builder.Symmetry` or `~kwant.builder.Builder` may be passed as
- sole argument when calling an instance of this class. This will
- restrict the flood-fill to the fundamental domain of the symmetry (or
- the builder's symmetry). Note that unless the shape function has that
- symmetry itself, the result may be unexpected.
-
- 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
-
- def __call__(self, symmetry=None):
- Site = builder.Site
- lat, func, start = self.lat, self.func, self.start
-
- if symmetry is None:
- symmetry = builder.NoSymmetry()
- elif not isinstance(symmetry, builder.Symmetry):
- symmetry = symmetry.symmetry
-
- def fd_site(lat, tag):
- return symmetry.to_fd(Site(lat, tag, True))
-
- dim = len(start)
- if dim != lat.prim_vecs.shape[1]:
- raise ValueError('Dimensionality of start position does not match'
- ' the space dimensionality.')
- sls = lat.sublattices
- deltas = list(lat._voronoi)
-
- #### Flood-fill ####
- sites = []
- for tag in set(sl.closest(start) for sl in sls):
- for sl in sls:
- site = fd_site(sl, tag)
- if func(site.pos):
- sites.append(site)
- if not sites:
- msg = 'No sites close to {0} are inside the desired shape.'
- raise ValueError(msg.format(start))
- tags = set(s.tag for s in sites)
-
- while sites:
- old_tags = tags
- tags = set()
- for site in sites:
- yield site
- tags.add(site.tag)
- old_tags |= tags
-
- new_tags = set()
- for tag in tags:
- for delta in deltas:
- new_tag = tag + delta
- if new_tag not in old_tags:
- new_tags.add(new_tag)
-
- sites = set()
- for tag in new_tags:
- for sl in sls:
- site = fd_site(sl, tag)
- if site.tag not in old_tags and func(site.pos):
- sites.add(site)
-
-
################ Library of lattices (to be extended)
def chain(a=1, name=''):
--
GitLab