Commit 72a96c4a authored by Joseph Weston's avatar Joseph Weston
Browse files

merge change of Builder.fill() behavior

parents dc02e80e 20b86bd2
Pipeline #3895 failed with stages
in 69 minutes and 50 seconds
......@@ -16,7 +16,7 @@ import inspect
import tinyarray as ta
import numpy as np
from scipy import sparse
from . import system, graph, UserCodeError
from . import system, graph, KwantDeprecationWarning, UserCodeError
from .linalg import lll
from .operator import Density
from .physics import DiscreteSymmetry
......@@ -333,22 +333,16 @@ class Symmetry(metaclass=abc.ABCMeta):
def isstrictsupergroup(self, other):
"""Test whether `self` is a strict supergroup of `other`...
def has_subgroup(self, other):
"""Test whether `self` has the subgroup `other`...
or, in other words, whether `other` is a subgroup of `self`. The
reason why this is the abstract method (and not `issubgroup`) is that
reason why this is the abstract method (and not `is_subgroup`) is that
in general it's not possible for a subgroup to know its supergroups.
def issubgroup(self, other):
"""Test whether `self` is a subgroup of `other`."""
return other.isstrictsupergroup(self)
__le__ = issubgroup
class NoSymmetry(Symmetry):
"""A symmetry with a trivial symmetry group."""
......@@ -389,8 +383,8 @@ class NoSymmetry(Symmetry):
raise ValueError('Generators must be empty for NoSymmetry.')
return NoSymmetry(generators)
def isstrictsupergroup(self, other):
return False
def has_subgroup(self, other):
return isinstance(other, NoSymmetry)
......@@ -778,11 +772,6 @@ class Builder:
Attaching a lead manually (without the use of `~Builder.attach_lead`)
amounts to creating a `Lead` object and appending it to this list.
``builder0 += builder1`` adds all the sites, hoppings, and leads of
``builder1`` to ``builder0``. Sites and hoppings present in both systems
are overwritten by those in ``builder1``. The leads of ``builder1`` are
appended to the leads of the system being extended.
.. warning::
If functions are used to set values in a builder with a symmetry, then
......@@ -1244,17 +1233,48 @@ class Builder:
result = site
return result
def __iadd__(self, other):
def update(self, other):
"""Update builder from `other`.
All sites and hoppings of `other`, together with their values, are
written to `self`, overwriting already existing sites and hoppings.
The leads of `other` are appended to the leads of the system being
This method requires that both builders share the same symmetry.
if (not self.symmetry.has_subgroup(other.symmetry)
or not other.symmetry.has_subgroup(self.symmetry)):
raise ValueError("Both builders involved in update() must have "
"equal symmetries.")
for site, value in other.site_value_pairs():
self[site] = value
for hop, value in other.hopping_value_pairs():
self[hop] = value
def __iadd__(self, other):
warnings.warn("The += operator of builders is deprecated. Use "
"'Builder.update()' instead.", KwantDeprecationWarning,
return self
def fill(self, template, shape, start, *, overwrite=False, max_sites=10**7):
def fill(self, template, shape, start, *, max_sites=10**7):
"""Populate builder using another one as a template.
Starting from one or multiple sites, traverse the graph of the template
builder and copy sites and hoppings to the target builder. The
traversal stops at sites that are already present in the target and on
sites that are not inside the provided shape.
This function takes into account translational symmetry. As such,
typically the template will have a higher symmetry than the target.
Newly added sites are connected by hoppings to sites that were already
present. This facilitates construction of a system by a series of
calls to 'fill'.
template : `Builder` instance
......@@ -1268,10 +1288,6 @@ class Builder:
The site(s) at which the the flood-fill starts. If start is an
iterable of numbers, the starting site will be
overwrite : boolean
Whether existing sites or hoppings in the target builder should be
overwritten. When overwriting is disabled (the default), existing
sites act as boundaries for the flood-fill.
max_sites : positive number
The maximal number of sites that may be added before
``RuntimeError`` is raised. Used to prevent using up all memory.
......@@ -1303,7 +1319,7 @@ class Builder:
templ_sym = template.symmetry
# Check that symmetries are commensurate.
if not self.symmetry <= templ_sym:
if not templ_sym.has_subgroup(self.symmetry):
raise ValueError("Builder symmetry is not a subgroup of the "
"template symmetry")
......@@ -1322,7 +1338,7 @@ class Builder:
congested = True
for s in start:
s = to_fd(s)
if overwrite or s not in H:
if s not in H:
congested = False
if shape(s):
......@@ -1373,21 +1389,21 @@ class Builder:
if (head_fd not in old_active
and head_fd not in new_active):
# The 'head' site has not been filled yet.
if not shape(head_fd):
if overwrite or head_fd not in H:
# Fill 'head' site.
H.setdefault(head_fd, [head_fd, None])
# The 'head' site exists and won't be visited:
# fill the incoming edge as well to balance the
# hopping.
if head_fd in H:
# The 'head' site exists. (It doesn't matter
# whether it's in the shape or not.) Fill the
# incoming edge as well to balance the hopping.
other_value = template._get_edge(
*templ_sym.to_fd(head, tail))
self._set_edge(*to_fd(head, tail)
+ (other_value,))
if not shape(head_fd):
# There is no site at 'head' and it's
# outside the shape.
H.setdefault(head_fd, [head_fd, None])
# Fill the outgoing edge.
if head in old_heads:
......@@ -555,7 +555,7 @@ class TranslationalSymmetry(builder.Symmetry):
raise ValueError('Generators must be sequences of integers.')
return TranslationalSymmetry(*, self.periods))
def isstrictsupergroup(self, other):
def has_subgroup(self, other):
if isinstance(other, builder.NoSymmetry):
return True
elif not isinstance(other, TranslationalSymmetry):
......@@ -129,7 +129,7 @@ class VerySimpleSymmetry(builder.Symmetry):
def num_directions(self):
return 1
def isstrictsupergroup(self, other):
def has_subgroup(self, other):
if isinstance(other, builder.NoSymmetry):
return True
elif isinstance(other, VerySimpleSymmetry):
......@@ -556,7 +556,8 @@ def test_hamiltonian_evaluation():
# test with infinite system
inf_syst = kwant.Builder(VerySimpleSymmetry(2))
inf_syst += syst
for k, v in it.chain(syst.site_value_pairs(), syst.hopping_value_pairs()):
inf_syst[k] = v
inf_fsyst = inf_syst.finalized()
hop = tuple(map(inf_fsyst.sites.index, new_hop))
test_raising(inf_fsyst, hop)
......@@ -652,12 +653,15 @@ def test_fill():
return -100 <= site.pos[0] < 100
## Test that copying a builder by "fill" preserves everything.
for sym, func in [(kwant.TranslationalSymmetry(*np.diag([3, 4, 5])),
lambda pos: True),
lambda pos:, pos) < 17)]:
cubic = kwant.lattice.general(ta.identity(3))
sym = kwant.TranslationalSymmetry((3, 0, 0), (0, 4, 0), (0, 0, 5))
# Make a weird system.
orig = kwant.Builder(sym)
sites = cubic.shape(lambda pos: True, (0, 0, 0))
sites = cubic.shape(func, (0, 0, 0))
for i, site in enumerate(orig.expand(sites)):
if i % 7 == 0:
......@@ -677,7 +681,8 @@ def test_fill():
# Verify that both are identical.
assert set(clone.site_value_pairs()) == set(orig.site_value_pairs())
assert set(clone.hopping_value_pairs()) == set(orig.hopping_value_pairs())
assert (set(clone.hopping_value_pairs())
== set(orig.hopping_value_pairs()))
## Test for warning when "start" is out.
target = builder.Builder()
......@@ -688,11 +693,10 @@ def test_fill():
## Test filling of infinite builder.
for n in [1, 2, 4]:
sym_n = kwant.TranslationalSymmetry((n, 0))
for ow in [False, True]:
for start in [g(0, 0), g(20, 0)]:
target = builder.Builder(sym_n)
sites = target.fill(template_1d, lambda s: True, start,
overwrite=ow, max_sites=10)
assert len(sites) == n
assert len(list(target.hoppings())) == n
assert set(sym_n.to_fd(s) for s in sites) == set(target.sites())
......@@ -711,14 +715,8 @@ def test_fill():
target = builder.Builder()
added_sites = target.fill(template_1d, line_200, g(0, 0))
assert len(added_sites) == 200
## test overwrite=False
with warns(RuntimeWarning):
target.fill(template_1d, line_200, g(0, 0))
## test overwrite=True
added_sites = target.fill(template_1d, line_200, g(0, 0),
assert len(added_sites) == 200
## test multiplying unit cell size in 1D
n_cells = 10
......@@ -779,19 +777,55 @@ def test_fill():
target = builder.Builder(kwant.TranslationalSymmetry((-2,)))
target[lat(0)] = None
to_target_fd = target.symmetry.to_fd
# refuses to fill the target because target already contains the starting
# site and 'overwrite == False'.
# Refuses to fill the target because target already contains the starting
# site.
with warns(RuntimeWarning):
target.fill(template, lambda x: True, lat(0))
# should only add a single site (and hopping)
new_sites = target.fill(template, lambda x: True, lat(1), overwrite=False)
new_sites = target.fill(template, lambda x: True, lat(1))
assert target[lat(0)] is None # should not be overwritten by template
assert target[lat(-1)] == template[lat(0)]
assert len(new_sites) == 1
assert to_target_fd(new_sites[0]) == to_target_fd(lat(-1))
def test_fill_sticky():
"""Test that adjacent regions are properly interconnected when filled
# Generate model template.
lat = kwant.lattice.kagome()
template = kwant.Builder(kwant.TranslationalSymmetry(
lat.vec((1, 0)), lat.vec((0, 1))))
for i, sl in enumerate(lat.sublattices):
template[sl(0, 0)] = i
for i in range(1, 3):
for j, hop in enumerate(template.expand(lat.neighbors(i))):
template[hop] = j * 1j
def disk(site):
pos = site.pos
return, pos) < 13
def halfplane(site):
return - (-1, 1), (-0.9, 0.63)) > 0
# Fill in one go.
syst0 = kwant.Builder()
syst0.fill(template, disk, (0, 0))
# Fill in two stages.
syst1 = kwant.Builder()
syst1.fill(template, lambda s: disk(s) and halfplane(s), (-2, 1))
syst1.fill(template, lambda s: disk(s) and not halfplane(s), (0, 0))
# Verify that both results are identical.
assert set(syst0.site_value_pairs()) == set(syst1.site_value_pairs())
assert (set(syst0.hopping_value_pairs())
== set(syst1.hopping_value_pairs()))
def test_attach_lead():
fam = builder.SimpleSiteFamily()
fam_noncommensurate = builder.SimpleSiteFamily(name='other')
......@@ -907,7 +941,7 @@ def test_closest():
assert dd >= 0.999999 * dist
def test_iadd():
def test_update():
lat = builder.SimpleSiteFamily()
syst = builder.Builder()
......@@ -930,7 +964,7 @@ def test_iadd():
lead1 = builder.BuilderLead(lead1, [lat(2,)])
syst += other_syst
assert syst.leads == [lead0, lead1]
expected = sorted([((0,), 1), ((1,), 2), ((2,), 2)])
assert sorted(((s.tag, v) for s, v in syst.site_value_pairs())) == expected
......@@ -251,21 +251,23 @@ def test_symmetry_act():
sym.act(ta.array(el), site)
def test_symmetry_subgroup():
def test_symmetry_has_subgroup():
rng = np.random.RandomState(0)
## test whether actual subgroups are detected as such
vecs = rng.randn(3, 3)
sym1 = lattice.TranslationalSymmetry(*vecs)
assert sym1 >= sym1
assert sym1 >= builder.NoSymmetry()
assert sym1 >= lattice.TranslationalSymmetry(2 * vecs[0],
3 * vecs[1] + 4 * vecs[2])
assert not sym1 <= lattice.TranslationalSymmetry(*(0.8 * vecs))
ns = builder.NoSymmetry()
assert ns.has_subgroup(ns)
assert sym1.has_subgroup(sym1)
assert sym1.has_subgroup(ns)
assert sym1.has_subgroup(lattice.TranslationalSymmetry(
2 * vecs[0], 3 * vecs[1] + 4 * vecs[2]))
assert not lattice.TranslationalSymmetry(*(0.8 * vecs)).has_subgroup(sym1)
## test subgroup creation
for dim in range(1, 4):
generators = rng.randint(10, size=(dim, 3))
assert sym1.subgroup(*generators) <= sym1
assert sym1.has_subgroup(sym1.subgroup(*generators))
# generators are not linearly independent
with raises(ValueError):
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