From ccb722a9b77c61c2051d1c036e95b7743836197c Mon Sep 17 00:00:00 2001
From: Anton Akhmerov <anton.akhmerov@gmail.com>
Date: Tue, 30 Jul 2013 10:56:43 +0200
Subject: [PATCH] make tolerance in neighbor search relative to the shortest
lattice vector
---
kwant/lattice.py | 10 +++++++---
kwant/tests/test_lattice.py | 6 +++---
2 files changed, 10 insertions(+), 6 deletions(-)
diff --git a/kwant/lattice.py b/kwant/lattice.py
index 85d6bca..d50bcfa 100644
--- a/kwant/lattice.py
+++ b/kwant/lattice.py
@@ -251,15 +251,15 @@ class Polyatomic(object):
return wire_sites
def neighbors(self, n=1, eps=1e-8):
- """
- Return n-th nearest neighbor hoppings.
+ """Return n-th nearest neighbor hoppings.
Parameters
----------
n : integer
Order of the hoppings to return.
eps : float
- A cutoff for when to consider lengths to be approximately equal.
+ Tolerance relative to the length of the shortest lattice vector for
+ when to consider lengths to be approximately equal.
Returns
-------
@@ -276,6 +276,9 @@ class Polyatomic(object):
# This algorithm is not designed to be fast and can be improved,
# however there is no real need.
sls = self.sublattices
+ shortest_hopping = sls[0].n_closest(sls[0](*([0] * sls[0].dim)).pos,
+ 2)[-1]
+ eps *= np.linalg.norm(self.vec(shortest_hopping))
nvec = len(self.prim_vecs)
sublat_pairs = [(i, j) for (i, j) in product(sls, sls)
if sls.index(j) >= sls.index(i)]
@@ -289,6 +292,7 @@ class Polyatomic(object):
continue
return True
+
# Find the correct number of neighbors to calculate on each lattice.
cutoff = n + 2
while True:
diff --git a/kwant/tests/test_lattice.py b/kwant/tests/test_lattice.py
index 8dc2140..6331520 100644
--- a/kwant/tests/test_lattice.py
+++ b/kwant/tests/test_lattice.py
@@ -44,13 +44,13 @@ def test_general():
def test_neighbors():
- lat = lattice.honeycomb()
+ lat = lattice.honeycomb(1e-10)
num_nth_nearest = [len(lat.neighbors(n)) for n in range(5)]
assert num_nth_nearest == [2, 3, 6, 3, 6]
- lat = lattice.square()
+ lat = lattice.square(1e8)
num_nth_nearest = [len(lat.neighbors(n)) for n in range(5)]
assert num_nth_nearest == [1, 2, 2, 2, 4]
- lat = lattice.chain()
+ lat = lattice.chain(1e-10)
num_nth_nearest = [len(lat.neighbors(n)) for n in range(5)]
assert num_nth_nearest == 5 * [1]
--
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