diff --git a/kwant/builder.py b/kwant/builder.py
index 42ddc3f843f20165eedb52f8b51201dade04549a..059242d5b067b2b14a2cf516add37d941525972e 100644
--- a/kwant/builder.py
+++ b/kwant/builder.py
@@ -505,6 +505,13 @@ class BuilderLead(Lead):
Sequence of sites in the scattering region to which the lead is
attached.
+ Attributes
+ ----------
+ builder : `Builder`
+ The tight-binding system of a lead.
+ interface : list of `Site` instances
+ A sorted list of interface sites.
+
Notes
-----
The hopping from the scattering region to the lead is assumed to be equal to
@@ -512,15 +519,13 @@ class BuilderLead(Lead):
symmetry vector (i.e. the lead is 'leaving' the system and starts with a
hopping).
- The given order of interface sites is preserved throughout finalization.
-
Every system has an attribute `leads`, which stores a list of
`BuilderLead` objects with all the information about the leads that are
attached.
"""
def __init__(self, builder, interface):
self.builder = builder
- self.interface = tuple(interface)
+ self.interface = tuple(sorted(interface))
def finalized(self):
"""Return a `kwant.system.InfiniteSystem` corresponding to the
@@ -1244,7 +1249,7 @@ class Builder:
assert self.symmetry.num_directions == 0
#### Make translation tables.
- sites = tuple(self.H)
+ sites = tuple(sorted(self.H))
id_by_site = {}
for site_id, site in enumerate(sites):
id_by_site[site] = site_id
@@ -1316,6 +1321,7 @@ class Builder:
sym = self.symmetry
assert sym.num_directions == 1
+
#### For each site of the fundamental domain, determine whether it has
#### neighbors in the previous domain or not.
lsites_with = [] # Fund. domain sites with neighbors in prev. dom
@@ -1340,7 +1346,9 @@ class Builder:
minus_one = ta.array((-1,))
plus_one = ta.array((1,))
if interface_order is None:
+ # interface must be sorted
interface = [sym.act(minus_one, s) for s in lsites_with]
+ interface.sort()
else:
lsites_with_set = set(lsites_with)
lsites_with = []
@@ -1370,9 +1378,13 @@ class Builder:
if lsites_with_set:
raise ValueError(
'interface_order did not contain all interface sites.')
+ # `interface_order` *must* be sorted, hence `interface` should also
+ if interface != sorted(interface):
+ raise ValueError('Interface sites must be sorted.')
del lsites_with_set
- sites = lsites_with + lsites_without + interface
+ # we previously sorted the interface, so don't sort it again
+ sites = sorted(lsites_with) + sorted(lsites_without) + interface
del lsites_with
del lsites_without
del interface
@@ -1447,7 +1459,8 @@ class FiniteSystem(system.FiniteSystem):
----------
sites : sequence
``sites[i]`` is the `~kwant.builder.Site` instance that corresponds
- to the integer-labeled site ``i`` of the low-level system.
+ to the integer-labeled site ``i`` of the low-level system. The sites
+ are ordered first by their family and then by their tag.
id_by_site : dict
The inverse of ``sites``; maps from ``i`` to ``sites[i]``.
"""
@@ -1494,10 +1507,17 @@ class InfiniteSystem(system.InfiniteSystem):
Attributes
----------
sites : sequence
- Mapping from site IDs (integers) to the associated
- `~kwant.builder.Site` objects.
+ ``sites[i]`` is the `~kwant.builder.Site` instance that corresponds
+ to the integer-labeled site ``i`` of the low-level system.
id_by_site : dict
- The inverse of the ``sites`` mapping.
+ The inverse of ``sites``; maps from ``i`` to ``sites[i]``.
+
+ Notes
+ -----
+ In infinite systems ``sites`` consists of 3 parts: sites in the fundamental
+ domain (FD) with hoppings to neighboring cells, sites in the FD with no
+ hoppings to neighboring cells, and sites in FD+1 attached to the FD by
+ hoppings. Each of these three subsequences is individually sorted.
"""
def hamiltonian(self, i, j, *args):
diff --git a/kwant/tests/test_builder.py b/kwant/tests/test_builder.py
index 27e7546708888641931fa63850f3c8635977048f..ba19b2a1f003882848519fa2278eb0deca660d4d 100644
--- a/kwant/tests/test_builder.py
+++ b/kwant/tests/test_builder.py
@@ -9,7 +9,7 @@
import warnings
from random import Random
import itertools as it
-from nose.tools import assert_raises, assert_true, assert_not_equal
+from nose.tools import assert_raises, assert_true, assert_not_equal, assert_less
from numpy.testing import assert_equal, assert_almost_equal
import tinyarray as ta
import numpy as np
@@ -367,6 +367,8 @@ def test_finalization():
check_id_by_site(fsyst)
check_onsite(fsyst, sr_sites)
check_hoppings(fsyst, sr_hops)
+ # check that sites are sorted
+ assert_equal(fsyst.sites, sorted(fam(*site) for site in sr_sites))
# Build lead from blueprint and test it.
lead = builder.Builder(kwant.TranslationalSymmetry((size, 0)))
@@ -403,6 +405,22 @@ def test_finalization():
assert_raises(ValueError, syst.finalized)
# Attach lead properly.
+ syst.leads[-1] = builder.BuilderLead(
+ lead, (builder.Site(fam, n) for n in neighbors))
+ fsyst = syst.finalized()
+ assert_equal(len(fsyst.lead_interfaces), 1)
+ assert_equal([fsyst.sites[i].tag for i in fsyst.lead_interfaces[0]],
+ neighbors)
+
+ # test that we cannot finalize a system with a badly sorted interface order
+ assert_raises(ValueError, lead._finalized_infinite,
+ [builder.Site(fam, n) for n in reversed(neighbors)])
+ # site ordering independent of whether interface was specified
+ flead_order = lead._finalized_infinite([builder.Site(fam, n)
+ for n in neighbors])
+ assert_equal(flead.sites, flead_order.sites)
+
+
syst.leads[-1] = builder.BuilderLead(
lead, (builder.Site(fam, n) for n in neighbors))
fsyst = syst.finalized()