kwant/tests/test_builder.py

@@ -19,7 +19,7 @@ from pytest import raises, warns
 from numpy.testing import assert_almost_equal
 
 import kwant
-from kwant import builder
+from kwant import builder, system
 from kwant._common import ensure_rng
 
 
@@ -28,7 +28,7 @@ def test_bad_keys():
     def setitem(key):
         syst[key] = None
 
-    fam = builder.SimpleSiteFamily()
+    fam = builder.SimpleSiteFamily(norbs=1)
     syst = builder.Builder()
 
     failures = [
@@ -97,9 +97,9 @@ def test_bad_keys():
 
 def test_site_families():
     syst = builder.Builder()
-    fam = builder.SimpleSiteFamily()
-    ofam = builder.SimpleSiteFamily()
-    yafam = builder.SimpleSiteFamily('another_name')
+    fam = builder.SimpleSiteFamily(norbs=1)
+    ofam = builder.SimpleSiteFamily(norbs=1)
+    yafam = builder.SimpleSiteFamily('another_name', norbs=1)
 
     syst[fam(0)] = 7
     assert syst[fam(0)] == 7
@@ -162,7 +162,7 @@ class VerySimpleSymmetry(builder.Symmetry):
 # made.
 def check_construction_and_indexing(sites, sites_fd, hoppings, hoppings_fd,
                                     unknown_hoppings, sym=None):
-    fam = builder.SimpleSiteFamily()
+    fam = builder.SimpleSiteFamily(norbs=1)
     syst = builder.Builder(sym)
     t, V = 1.0j, 0.0
     syst[sites] = V
@@ -212,7 +212,7 @@ def check_construction_and_indexing(sites, sites_fd, hoppings, hoppings_fd,
 
 def test_construction_and_indexing():
     # Without symmetry
-    fam = builder.SimpleSiteFamily()
+    fam = builder.SimpleSiteFamily(norbs=1)
     sites = [fam(0, 0), fam(0, 1), fam(1, 0)]
     hoppings = [(fam(0, 0), fam(0, 1)),
                 (fam(0, 1), fam(1, 0)),
@@ -250,7 +250,7 @@ def test_hermitian_conjugation():
             raise ValueError
 
     syst = builder.Builder()
-    fam = builder.SimpleSiteFamily()
+    fam = builder.SimpleSiteFamily(norbs=1)
     syst[fam(0)] = syst[fam(1)] = ta.identity(2)
 
     syst[fam(0), fam(1)] = f
@@ -266,7 +266,7 @@ def test_hermitian_conjugation():
 def test_value_equality_and_identity():
     m = ta.array([[1, 2], [3j, 4j]])
     syst = builder.Builder()
-    fam = builder.SimpleSiteFamily()
+    fam = builder.SimpleSiteFamily(norbs=1)
 
     syst[fam(0)] = m
     syst[fam(1)] = m
@@ -378,7 +378,7 @@ def test_finalization():
 
     # Build scattering region from blueprint and test it.
     syst = builder.Builder()
-    fam = kwant.lattice.general(ta.identity(2))
+    fam = kwant.lattice.general(ta.identity(2), norbs=1)
     for site, value in sr_sites.items():
         syst[fam(*site)] = value
     for hop, value in sr_hops.items():
@@ -421,12 +421,12 @@ def test_finalization():
 
     # Attach lead with improper interface.
     syst.leads[-1] = builder.BuilderLead(
-        lead, 2 * tuple(builder.Site(fam, n) for n in neighbors))
+        lead, 2 * tuple(system.Site(fam, n) for n in neighbors))
     raises(ValueError, syst.finalized)
 
     # Attach lead properly.
     syst.leads[-1] = builder.BuilderLead(
-        lead, (builder.Site(fam, n) for n in neighbors))
+        lead, (system.Site(fam, n) for n in neighbors))
     fsyst = syst.finalized()
     assert len(fsyst.lead_interfaces) == 1
     assert ([fsyst.sites[i].tag for i in fsyst.lead_interfaces[0]] ==
@@ -434,15 +434,15 @@ def test_finalization():
 
     # test that we cannot finalize a system with a badly sorted interface order
     raises(ValueError, builder.InfiniteSystem, lead,
-           [builder.Site(fam, n) for n in reversed(neighbors)])
+           [system.Site(fam, n) for n in reversed(neighbors)])
     # site ordering independent of whether interface was specified
-    flead_order = builder.InfiniteSystem(lead, [builder.Site(fam, n)
+    flead_order = builder.InfiniteSystem(lead, [system.Site(fam, n)
                                                 for n in neighbors])
     assert flead.sites == flead_order.sites
 
 
     syst.leads[-1] = builder.BuilderLead(
-        lead, (builder.Site(fam, n) for n in neighbors))
+        lead, (system.Site(fam, n) for n in neighbors))
     fsyst = syst.finalized()
     assert len(fsyst.lead_interfaces) == 1
     assert ([fsyst.sites[i].tag for i in fsyst.lead_interfaces[0]] ==
@@ -488,8 +488,11 @@ def test_site_ranges():
         ranges = syst.finalized().site_ranges
         expected = [(0, lat.norbs, 0), (10, 0, 10 * lat.norbs)]
         assert ranges == expected
-        # poison system with a single site with no norbs defined
-        syst[kwant.lattice.chain()(0)] = 1
+        # poison system with a single site with no norbs defined.
+        # Also catch the deprecation warning.
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore")
+            syst[kwant.lattice.chain(norbs=None)(0)] = 1
         ranges = syst.finalized().site_ranges
         assert ranges == None
 
@@ -506,7 +509,7 @@ def test_hamiltonian_evaluation():
     edges = [(0, 1), (0, 2), (0, 3), (1, 2)]
 
     syst = builder.Builder()
-    fam = builder.SimpleSiteFamily()
+    fam = builder.SimpleSiteFamily(norbs=1)
     sites = [fam(*tag) for tag in tags]
     syst[(fam(*tag) for tag in tags)] = f_onsite
     syst[((fam(*tags[i]), fam(*tags[j])) for (i, j) in edges)] = f_hopping
@@ -570,7 +573,7 @@ def test_dangling():
         #       / \
         #    3-0---2-4-5  6-7  8
         syst = builder.Builder()
-        fam = builder.SimpleSiteFamily()
+        fam = builder.SimpleSiteFamily(norbs=1)
         syst[(fam(i) for i in range(9))] = None
         syst[[(fam(0), fam(1)), (fam(1), fam(2)), (fam(2), fam(0))]] = None
         syst[[(fam(0), fam(3)), (fam(2), fam(4)), (fam(4), fam(5))]] = None
@@ -596,7 +599,7 @@ def test_dangling():
 
 
 def test_builder_with_symmetry():
-    g = kwant.lattice.general(ta.identity(3))
+    g = kwant.lattice.general(ta.identity(3), norbs=1)
     sym = kwant.TranslationalSymmetry((0, 0, 3), (0, 2, 0))
     syst = builder.Builder(sym)
 
@@ -642,7 +645,7 @@ def test_builder_with_symmetry():
 
 
 def test_fill():
-    g = kwant.lattice.square()
+    g = kwant.lattice.square(norbs=1)
     sym_x = kwant.TranslationalSymmetry((-1, 0))
     sym_xy = kwant.TranslationalSymmetry((-1, 0), (0, 1))
 
@@ -658,7 +661,7 @@ def test_fill():
                        lambda pos: True),
                       (builder.NoSymmetry(),
                        lambda pos: ta.dot(pos, pos) < 17)]:
-        cubic = kwant.lattice.general(ta.identity(3))
+        cubic = kwant.lattice.general(ta.identity(3), norbs=1)
 
         # Make a weird system.
         orig = kwant.Builder(sym)
@@ -769,7 +772,7 @@ def test_fill():
     assert sorted(target.hoppings()) == sorted(should_be_syst.hoppings())
 
     ## test that 'fill' respects the symmetry of the target builder
-    lat = kwant.lattice.chain(a=1)
+    lat = kwant.lattice.chain(a=1, norbs=1)
     template = builder.Builder(kwant.TranslationalSymmetry((-1,)))
     template[lat(0)] = 2
     template[lat.neighbors()] = -1
@@ -796,7 +799,7 @@ def test_fill():
         target.fill(template, lambda x: True, lat(0))
 
     # Test for warning when one of the starting sites is outside the template
-    lat = kwant.lattice.square()
+    lat = kwant.lattice.square(norbs=1)
     template = builder.Builder(kwant.TranslationalSymmetry((-1, 0)))
     template[lat(0, 0)] = None
     template[lat.neighbors()] = None
@@ -811,7 +814,7 @@ def test_fill_sticky():
     separately.
     """
     # Generate model template.
-    lat = kwant.lattice.kagome()
+    lat = kwant.lattice.kagome(norbs=1)
     template = kwant.Builder(kwant.TranslationalSymmetry(
         lat.vec((1, 0)), lat.vec((0, 1))))
     for i, sl in enumerate(lat.sublattices):
@@ -844,7 +847,7 @@ def test_fill_sticky():
 
 def test_attach_lead():
     fam = builder.SimpleSiteFamily(norbs=1)
-    fam_noncommensurate = builder.SimpleSiteFamily(name='other')
+    fam_noncommensurate = builder.SimpleSiteFamily(name='other', norbs=1)
 
     syst = builder.Builder()
     syst[fam(1)] = 0
@@ -901,7 +904,7 @@ def test_attach_lead():
 
 
 def test_attach_lead_incomplete_unit_cell():
-    lat = kwant.lattice.chain()
+    lat = kwant.lattice.chain(norbs=1)
     syst = kwant.Builder()
     lead = kwant.Builder(kwant.TranslationalSymmetry((2,)))
     syst[lat(1)] = lead[lat(0)] = lead[lat(1)] = 0
@@ -912,7 +915,7 @@ def test_attach_lead_incomplete_unit_cell():
 def test_neighbors_not_in_single_domain():
     sr = builder.Builder()
     lead = builder.Builder(VerySimpleSymmetry(-1))
-    fam = builder.SimpleSiteFamily()
+    fam = builder.SimpleSiteFamily(norbs=1)
     sr[(fam(x, y) for x in range(3) for y in range(3) if x >= y)] = 0
     sr[builder.HoppingKind((1, 0), fam)] = 1
     sr[builder.HoppingKind((0, 1), fam)] = 1
@@ -935,7 +938,7 @@ def test_closest():
     rng = ensure_rng(10)
     for sym_dim in range(1, 4):
         for space_dim in range(sym_dim, 4):
-            lat = kwant.lattice.general(ta.identity(space_dim))
+            lat = kwant.lattice.general(ta.identity(space_dim), norbs=1)
 
             # Choose random periods.
             while True:
@@ -967,7 +970,7 @@ def test_closest():
 
 
 def test_update():
-    lat = builder.SimpleSiteFamily()
+    lat = builder.SimpleSiteFamily(norbs=1)
 
     syst = builder.Builder()
     syst[[lat(0,), lat(1,)]] = 1
@@ -1006,8 +1009,8 @@ def test_update():
 # ghgh    hhgh
 #
 def test_HoppingKind():
-    g = kwant.lattice.general(ta.identity(3), name='some_lattice')
-    h = kwant.lattice.general(ta.identity(3), name='another_lattice')
+    g = kwant.lattice.general(ta.identity(3), name='some_lattice', norbs=1)
+    h = kwant.lattice.general(ta.identity(3), name='another_lattice', norbs=1)
     sym = kwant.TranslationalSymmetry((0, 2, 0))
     syst = builder.Builder(sym)
     syst[((h if max(x, y, z) % 2 else g)(x, y, z)
@@ -1047,8 +1050,8 @@ def test_HoppingKind():
 
 
 def test_invalid_HoppingKind():
-    g = kwant.lattice.general(ta.identity(3))
-    h = kwant.lattice.general(np.identity(3)[:-1])  # 2D lattice in 3D
+    g = kwant.lattice.general(ta.identity(3), norbs=1)
+    h = kwant.lattice.general(np.identity(3)[:-1], norbs=1)  # 2D lattice in 3D
 
     delta = (1, 0, 0)
 
@@ -1062,7 +1065,7 @@ def test_invalid_HoppingKind():
 
 
 def test_ModesLead_and_SelfEnergyLead():
-    lat = builder.SimpleSiteFamily()
+    lat = builder.SimpleSiteFamily(norbs=1)
     hoppings = [builder.HoppingKind((1, 0), lat),
                 builder.HoppingKind((0, 1), lat)]
     rng = Random(123)
@@ -1139,7 +1142,7 @@ def test_ModesLead_and_SelfEnergyLead():
 
 
 def test_site_pickle():
-    site = kwant.lattice.square()(0, 0)
+    site = kwant.lattice.square(norbs=1)(0, 0)
     assert pickle.loads(pickle.dumps(site)) == site
 
 
@@ -1202,7 +1205,7 @@ def test_discrete_symmetries():
 # all the deprecation warnings in the test logs
 @pytest.mark.filterwarnings("ignore:.*'args' parameter")
 def test_argument_passing():
-    chain = kwant.lattice.chain()
+    chain = kwant.lattice.chain(norbs=1)
 
     # Test for passing parameters to hamiltonian matrix elements
     def onsite(site, p1, p2):
@@ -1272,7 +1275,7 @@ def test_argument_passing():
 
     # Some common, some different args for value functions
     def onsite2(site, a, b):
-        return site.pos + a + b
+        return site.pos[0] + a + b
 
     def hopping2(site1, site2, a, c, b):
         return a + b + c
@@ -1336,7 +1339,7 @@ def test_subs():
         salt = str(b) + str(c)
         return kwant.digest.uniform(ta.array((sitea.tag, siteb.tag)), salt=salt)
 
-    lat = kwant.lattice.chain()
+    lat = kwant.lattice.chain(norbs=1)
 
     def make_system(sym=kwant.builder.NoSymmetry(), n=3):
         syst = kwant.Builder(sym)
@@ -1389,7 +1392,7 @@ def test_subs():
     assert lead.parameters == {'lead_a', 'lead_b', 'lead_c'}
 
 def test_attach_stores_padding():
-    lat = kwant.lattice.chain()
+    lat = kwant.lattice.chain(norbs=1)
     syst = kwant.Builder()
     syst[lat(0)] = 0
     lead = kwant.Builder(kwant.TranslationalSymmetry(lat.prim_vecs[0]))
@@ -1400,7 +1403,7 @@ def test_attach_stores_padding():
 
 
 def test_finalization_preserves_padding():
-    lat = kwant.lattice.chain()
+    lat = kwant.lattice.chain(norbs=1)
     syst = kwant.Builder()
     for i in range(10):
         syst[lat(i)] = 0
@@ -1416,3 +1419,28 @@ def test_finalization_preserves_padding():
     syst = syst.finalized()
     # The order is guaranteed because the paddings are sorted.
     assert [syst.sites[i] for i in syst.lead_paddings[0]] == padding[:-1]
+
+
+def test_add_peierls_phase():
+
+    lat = kwant.lattice.square(norbs=1)
+    syst = kwant.Builder()
+    syst[(lat(i, j) for i in range(5) for j in range(5))] = 4
+    syst[lat.neighbors()] = lambda a, b, t: -t
+
+    lead = kwant.Builder(kwant.TranslationalSymmetry((-1, 0)))
+    lead[(lat(0, j) for j in range(5))] = 4
+    lead[lat.neighbors()] = -1
+
+    syst.attach_lead(lead)
+    syst.attach_lead(lead.reversed())
+
+    syst, phase = builder.add_peierls_phase(syst)
+
+    assert isinstance(syst, builder.FiniteSystem)
+
+    params = phase(1, 0, 0)
+
+    assert all(p in params for p in ('phi', 'phi_lead0', 'phi_lead1'))
+
+    kwant.smatrix(syst, energy=0.1, params=dict(t=-1, **params))

kwant/tests/test_comprehensive.py

@@ -18,7 +18,7 @@ def test_qhe(W=16, L=8):
         x, y = pos
         return -L < x < L and abs(y) < W - 5.5 * math.exp(-x**2 / 5**2)
 
-    lat = kwant.lattice.square()
+    lat = kwant.lattice.square(norbs=1)
     syst = kwant.Builder()
 
     syst[lat.shape(central_region, (0, 0))] = onsite

kwant/tests/test_lattice.py

@@ -6,6 +6,7 @@
 # the file AUTHORS.rst at the top-level directory of this distribution and at
 # http://kwant-project.org/authors.
 
+import warnings
 from math import sqrt
 import numpy as np
 import tinyarray as ta
@@ -17,40 +18,42 @@ import pytest
 
 def test_closest():
     rng = ensure_rng(4)
-    lat = lattice.general(((1, 0), (0.5, sqrt(3)/2)))
+    lat = lattice.general(((1, 0), (0.5, sqrt(3)/2)), norbs=1)
     for i in range(50):
         point = 20 * rng.random_sample(2)
         closest = lat(*lat.closest(point)).pos
         assert np.linalg.norm(point - closest) <= 1 / sqrt(3)
-    lat = lattice.general(rng.randn(3, 3))
+    lat = lattice.general(rng.randn(3, 3), norbs=1)
     for i in range(50):
         tag = rng.randint(10, size=(3,))
         assert lat.closest(lat(*tag).pos) == tag
 
 
 def test_general():
-    for lat in (lattice.general(((1, 0), (0.5, 0.5))),
+    for lat in (lattice.general(((1, 0), (0.5, 0.5)), norbs=1),
                 lattice.general(((1, 0), (0.5, sqrt(3)/2)),
-                                     ((0, 0), (0, 1/sqrt(3))))):
+                                ((0, 0), (0, 1/sqrt(3))),
+                                norbs=1,
+                               )):
         for sl in lat.sublattices:
             tag = (-5, 33)
             site = sl(*tag)
             assert tag == sl.closest(site.pos)
 
     # Test 2D lattice with 1 vector.
-    lat = lattice.general([[1, 0]])
+    lat = lattice.general([[1, 0]], norbs=1)
     site = lat(0)
     raises(ValueError, lat, 0, 1)
 
 
 def test_neighbors():
-    lat = lattice.honeycomb(1e-10)
+    lat = lattice.honeycomb(1e-10, norbs=1)
     num_nth_nearest = [len(lat.neighbors(n)) for n in range(5)]
     assert num_nth_nearest == [2, 3, 6, 3, 6]
-    lat = lattice.general([(0, 1e8, 0, 0), (0, 0, 1e8, 0)])
+    lat = lattice.general([(0, 1e8, 0, 0), (0, 0, 1e8, 0)], norbs=1)
     num_nth_nearest = [len(lat.neighbors(n)) for n in range(5)]
     assert num_nth_nearest == [1, 2, 2, 2, 4]
-    lat = lattice.chain(1e-10)
+    lat = lattice.chain(1e-10, norbs=1)
     num_nth_nearest = [len(lat.neighbors(n)) for n in range(5)]
     assert num_nth_nearest == 5 * [1]
 
@@ -59,7 +62,7 @@ def test_shape():
     def in_circle(pos):
         return pos[0] ** 2 + pos[1] ** 2 < 3
 
-    lat = lattice.honeycomb()
+    lat = lattice.honeycomb(norbs=1)
     sites = list(lat.shape(in_circle, (0, 0))())
     sites_alt = list()
     sl0, sl1 = lat.sublattices
@@ -88,7 +91,7 @@ def test_wire():
     vecs = rng.randn(3, 3)
     vecs[0] = [1, 0, 0]
     center = rng.randn(3)
-    lat = lattice.general(vecs, rng.randn(4, 3))
+    lat = lattice.general(vecs, rng.randn(4, 3), norbs=1)
     syst = builder.Builder(lattice.TranslationalSymmetry((2, 0, 0)))
     def wire_shape(pos):
         pos = np.array(pos)
@@ -103,8 +106,8 @@ def test_wire():
 
 def test_translational_symmetry():
     ts = lattice.TranslationalSymmetry
-    f2 = lattice.general(np.identity(2))
-    f3 = lattice.general(np.identity(3))
+    f2 = lattice.general(np.identity(2), norbs=1)
+    f3 = lattice.general(np.identity(3), norbs=1)
     shifted = lambda site, delta: site.family(*ta.add(site.tag, delta))
 
     raises(ValueError, ts, (0, 0, 4), (0, 5, 0), (0, 0, 2))
@@ -112,7 +115,7 @@ def test_translational_symmetry():
     raises(ValueError, sym.add_site_family, f2)
 
     # Test lattices with dimension smaller than dimension of space.
-    f2in3 = lattice.general([[4, 4, 0], [4, -4, 0]])
+    f2in3 = lattice.general([[4, 4, 0], [4, -4, 0]], norbs=1)
     sym = ts((8, 0, 0))
     sym.add_site_family(f2in3)
     sym = ts((8, 0, 1))
@@ -150,7 +153,7 @@ def test_translational_symmetry():
                         (site, shifted(site, hop)))
 
     # Test act for hoppings belonging to different lattices.
-    f2p = lattice.general(2 * np.identity(2))
+    f2p = lattice.general(2 * np.identity(2), norbs=1)
     sym = ts(*(2 * np.identity(2)))
     assert sym.act((1, 1), f2(0, 0), f2p(0, 0)) == (f2(2, 2), f2p(1, 1))
     assert sym.act((1, 1), f2p(0, 0), f2(0, 0)) == (f2p(1, 1), f2(2, 2))
@@ -160,7 +163,7 @@ def test_translational_symmetry():
     # generated symmetry with proper vectors.
     rng = ensure_rng(30)
     vec = rng.randn(3, 5)
-    lat = lattice.general(vec)
+    lat = lattice.general(vec, norbs=1)
     total = 0
     for k in range(1, 4):
         for i in range(10):
@@ -176,7 +179,7 @@ def test_translational_symmetry():
 
 def test_translational_symmetry_reversed():
     rng = ensure_rng(30)
-    lat = lattice.general(np.identity(3))
+    lat = lattice.general(np.identity(3), norbs=1)
     sites = [lat(i, j, k) for i in range(-2, 6) for j in range(-2, 6)
                           for k in range(-2, 6)]
     for i in range(4):
@@ -194,9 +197,9 @@ def test_translational_symmetry_reversed():
 
 
 def test_monatomic_lattice():
-    lat = lattice.square()
-    lat2 = lattice.general(np.identity(2))
-    lat3 = lattice.square(name='no')
+    lat = lattice.square(norbs=1)
+    lat2 = lattice.general(np.identity(2), norbs=1)
+    lat3 = lattice.square(name='no', norbs=1)
     assert len(set([lat, lat2, lat3, lat(0, 0), lat2(0, 0), lat3(0, 0)])) == 4
 
 @pytest.mark.parametrize('prim_vecs, basis', [
@@ -210,16 +213,22 @@ def test_monatomic_lattice():
 ])
 def test_lattice_constraints(prim_vecs, basis):
     with pytest.raises(ValueError):
-        lattice.general(prim_vecs, basis)
+        lattice.general(prim_vecs, basis, norbs=1)
 
 
 def test_norbs():
     id_mat = np.identity(2)
     # Monatomic lattices
-    assert lattice.general(id_mat).norbs == None
+    # Catch deprecation warning
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        assert lattice.general(id_mat).norbs == None
     assert lattice.general(id_mat, norbs=2).norbs == 2
     # Polyatomic lattices
-    lat = lattice.general(id_mat, basis=id_mat, norbs=None)
+    # Catch deprecation warning
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        lat = lattice.general(id_mat, basis=id_mat, norbs=None)
     for l in lat.sublattices:
         assert l.norbs == None
     lat = lattice.general(id_mat, basis=id_mat, norbs=2)
@@ -237,8 +246,14 @@ def test_norbs():
     raises(ValueError, lattice.general, id_mat, norbs=1.5)
     raises(ValueError, lattice.general, id_mat, id_mat, norbs=1.5)
     raises(ValueError, lattice.general, id_mat, id_mat, norbs=[1.5, 1.5])
+    # should raise ValueError if norbs is <= 0
+    raises(ValueError, lattice.general, id_mat, norbs=0)
+    raises(ValueError, lattice.general, id_mat, norbs=-1)
     # test that lattices with different norbs are compared `not equal`
-    lat = lattice.general(id_mat, basis=id_mat, norbs=None)
+    # Catch deprecation warning
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        lat = lattice.general(id_mat, basis=id_mat, norbs=None)
     lat1 = lattice.general(id_mat, basis=id_mat, norbs=1)
     lat2 = lattice.general(id_mat, basis=id_mat, norbs=2)
     assert lat != lat1
@@ -247,7 +262,7 @@ def test_norbs():
 
 
 def test_symmetry_act():
-    lat = lattice.square()
+    lat = lattice.square(norbs=1)
     sym = lattice.TranslationalSymmetry((1, 0), (0, 1))
     site = lat(0, 0)
     hopping = (lat(0, 0), lat(1, 0))

kwant/tests/test_operator.py

@@ -6,6 +6,7 @@
 # the file AUTHORS.rst at the top-level directory of this distribution and at
 # http://kwant-project.org/authors.
 
+import warnings
 import functools as ft
 from collections import deque
 import pickle
@@ -59,7 +60,10 @@ def test_operator_construction():
     N = len(fsyst.sites)
 
     # test construction failure if norbs not given
-    latnone = kwant.lattice.chain()
+    # Catch deprecation warning
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        latnone = kwant.lattice.chain()
     syst[latnone(0)] = 1
     for A in opservables:
         raises(ValueError, A, syst.finalized())
@@ -128,12 +132,35 @@ def test_operator_construction():
     fwhere = tuple(fsyst.id_by_site[s] for s in where)
     A = ops.Density(fsyst, where=where)
     assert np.all(np.asarray(A.where).reshape(-1) == fwhere)
+    # Test for passing integers as 'where'
+    A = ops.Density(fsyst, where=fwhere)
+    assert np.all(np.asarray(A.where).reshape(-1) == fwhere)
+    # Test passing invalid sites
+    with raises(ValueError):
+        ops.Density(fsyst, where=[lat(100)])
+    with raises(ValueError):
+        ops.Density(fsyst, where=[-1])
+    with raises(ValueError):
+        ops.Density(fsyst, where=[10000])
 
     where = [(lat(2, 2), lat(1, 2)), (lat(0, 0), lat(0, 1))]
     fwhere = np.asarray([(fsyst.id_by_site[a], fsyst.id_by_site[b])
               for a, b in where])
     A = ops.Current(fsyst, where=where)
     assert np.all(np.asarray(A.where) == fwhere)
+    # Test for passing integers as 'where'
+    A = ops.Current(fsyst, where=fwhere)
+    assert np.all(np.asarray(A.where) == fwhere)
+    # Test passing invalid hoppings
+    with raises(ValueError):
+        ops.Current(fsyst, where=[(lat(2, 2), lat(0, 0))])
+    with raises(ValueError):
+        ops.Current(fsyst, where=[(-1, 1)])
+    with raises(ValueError):
+        ops.Current(fsyst, where=[(len(fsyst.sites), 1)])
+    with raises(ValueError):
+        ops.Current(fsyst, where=[(fsyst.id_by_site[lat(2, 2)],
+                                   fsyst.id_by_site[lat(0, 0)])])
 
     # test construction with `where` given by a function
     tag_list = [(1, 0), (1, 1), (1, 2)]
@@ -304,7 +331,7 @@ def test_opservables_spin():
     down, up = kwant.wave_function(fsyst, energy=1., params=params)(0)
 
     x_hoppings = kwant.builder.HoppingKind((1,), lat)
-    spin_current_z = ops.Current(fsyst, sigmaz, where=x_hoppings(syst))
+    spin_current_z = ops.Current(fsyst, sigmaz, where=list(x_hoppings(syst)))
     _test(spin_current_z, up, params=params, per_el_val=1)
     _test(spin_current_z, down, params=params, per_el_val=-1)
 
@@ -366,12 +393,14 @@ def test_opservables_gauged():
                          (Us[i], sigmaz, Us[i].conjugate().transpose()))
 
     x_hoppings = kwant.builder.HoppingKind((1,), lat)
-    spin_current_gauge = ops.Current(fsyst, M_a, where=x_hoppings(syst))
+    spin_current_gauge = ops.Current(fsyst, M_a,
+                                     where=list(x_hoppings(syst)))
     _test(spin_current_gauge, up, per_el_val=1)
     _test(spin_current_gauge, down, per_el_val=-1)
     # check the reverse is also true
     minus_x_hoppings = kwant.builder.HoppingKind((-1,), lat)
-    spin_current_gauge = ops.Current(fsyst, M_a, where=minus_x_hoppings(syst))
+    spin_current_gauge = ops.Current(fsyst, M_a,
+                                     where=list(minus_x_hoppings(syst)))
     _test(spin_current_gauge, up, per_el_val=-1)
     _test(spin_current_gauge, down, per_el_val=1)
 
@@ -416,7 +445,7 @@ def test_arg_passing(A):
     lat1 = kwant.lattice.chain(norbs=1)
 
     syst = kwant.Builder()
-    syst[lat1(0)] = syst[lat1(1)] = lambda s0, a, b: s0.pos + a + b
+    syst[lat1(0)] = syst[lat1(1)] = lambda s0, a, b: s0.pos[0] + a + b
     syst[lat1.neighbors()] = lambda s0, s1, a, b: a - b
     fsyst = syst.finalized()
 

kwant/tests/test_plotter.py

@@ -91,7 +91,7 @@ def syst_2d(W=3, r1=3, r2=8):
 
 
 def syst_3d(W=3, r1=2, r2=4, a=1, t=1.0):
-    lat = kwant.lattice.general(((a, 0, 0), (0, a, 0), (0, 0, a)))
+    lat = kwant.lattice.general(((a, 0, 0), (0, a, 0), (0, 0, a)), norbs=1)
     syst = kwant.Builder()
 
     def ring(pos):
@@ -162,13 +162,29 @@ def test_plot_more_site_families_than_colors():
     # https://gitlab.kwant-project.org/kwant/kwant/issues/257
     ncolors = len(pyplot.rcParams['axes.prop_cycle'])
     syst = kwant.Builder()
-    lattices = [kwant.lattice.square(name=i) for i in range(ncolors + 1)]
+    lattices = [kwant.lattice.square(name=i, norbs=1)
+                for i in range(ncolors + 1)]
     for i, lat in enumerate(lattices):
         syst[lat(i, 0)] = None
     with tempfile.TemporaryFile('w+b') as out:
         plotter.plot(syst, file=out)
 
 
+@pytest.mark.skipif(not _plotter.mpl_available, reason="Matplotlib unavailable.")
+def test_plot_raises_on_bad_site_spec():
+    syst = kwant.Builder()
+    lat = kwant.lattice.square(norbs=1)
+    syst[(lat(i, j) for i in range(5) for j in range(5))] = None
+
+    # Cannot provide site_size as an array when syst is a Builder
+    with pytest.raises(TypeError):
+        plotter.plot(syst, site_size=[1] * 25)
+
+    # Cannot provide site_size as an array when syst is a Builder
+    with pytest.raises(TypeError):
+        plotter.plot(syst, site_symbol=['o'] * 25)
+
+
 def good_transform(pos):
     x, y = pos
     return y, x
@@ -237,7 +253,7 @@ def test_spectrum():
     def ham_2d(a, b, c):
         return np.eye(2) * (a**2 + b**2 + c**2)
 
-    lat = kwant.lattice.chain()
+    lat = kwant.lattice.chain(norbs=1)
     syst = kwant.Builder()
     syst[(lat(i) for i in range(3))] = lambda site, a, b: a + b
     syst[lat.neighbors()] = lambda site1, site2, c: c
@@ -361,7 +377,7 @@ def _border_is_0(field):
 def _test_border_0(interpolator):
     ## Test that current is always identically zero at box boundaries
     syst = kwant.Builder()
-    lat = kwant.lattice.square()
+    lat = kwant.lattice.square(norbs=1)
     syst[[lat(0, 0), lat(1, 0)]] = None
     syst[(lat(0, 0), lat(1, 0))] = None
     syst = syst.finalized()
@@ -488,7 +504,7 @@ def test_current_interpolation():
 
     ### Tests on a divergence-free current (closed system)
 
-    lat = kwant.lattice.general([(1, 0), (0.5, np.sqrt(3) / 2)])
+    lat = kwant.lattice.general([(1, 0), (0.5, np.sqrt(3) / 2)], norbs=1)
     syst = kwant.Builder()
     sites = [lat(0, 0), lat(1, 0), lat(0, 1), lat(2, 2)]
     syst[sites] = None

kwant/tests/test_system.py

@@ -17,7 +17,7 @@ from kwant._common import ensure_rng
 
 def test_hamiltonian_submatrix():
     syst = kwant.Builder()
-    chain = kwant.lattice.chain()
+    chain = kwant.lattice.chain(norbs=1)
     for i in range(3):
         syst[chain(i)] = 0.5 * i
     for i in range(2):
@@ -87,7 +87,7 @@ def test_hamiltonian_submatrix():
 def test_pickling():
     syst = kwant.Builder()
     lead = kwant.Builder(symmetry=kwant.TranslationalSymmetry([1.]))
-    lat = kwant.lattice.chain()
+    lat = kwant.lattice.chain(norbs=1)
     syst[lat(0)] = syst[lat(1)] = 0
     syst[lat(0), lat(1)] = 1
     lead[lat(0)] = syst[lat(1)] = 0

kwant/tests/test_wraparound.py

@@ -37,7 +37,8 @@ def _simple_syst(lat, E=0, t=1+1j, sym=None):
 
 def test_consistence_with_bands(kx=1.9, nkys=31):
     kys = np.linspace(-np.pi, np.pi, nkys)
-    for lat in [kwant.lattice.honeycomb(), kwant.lattice.square()]:
+    for lat in [kwant.lattice.honeycomb(norbs=1),
+                kwant.lattice.square(norbs=1)]:
         syst = _simple_syst(lat)
         wa_keep_1 = wraparound(syst, keep=1).finalized()
         wa_keep_none = wraparound(syst).finalized()
@@ -56,7 +57,7 @@ def test_consistence_with_bands(kx=1.9, nkys=31):
 
 
 def test_opposite_hoppings():
-    lat = kwant.lattice.square()
+    lat = kwant.lattice.square(norbs=1)
 
     for val in [1j, lambda a, b: 1j]:
         syst = kwant.Builder(kwant.TranslationalSymmetry((1, 1)))
@@ -74,7 +75,8 @@ def test_opposite_hoppings():
 def test_value_types(k=(-1.1, 0.5), E=2, t=1):
     k = dict(zip(('k_x', 'k_y', 'k_z'), k))
     sym_extents = [1, 2, 3]
-    lattices = [kwant.lattice.honeycomb(), kwant.lattice.square()]
+    lattices = [kwant.lattice.honeycomb(norbs=1),
+                kwant.lattice.square(norbs=1)]
     lat_syms = [
         (lat, kwant.TranslationalSymmetry(lat.vec((n, 0)), lat.vec((0, n))))
         for n, lat in itertools.product(sym_extents, lattices)
@@ -112,7 +114,7 @@ def test_value_types(k=(-1.1, 0.5), E=2, t=1):
 
 
 def test_signatures():
-    lat = kwant.lattice.square()
+    lat = kwant.lattice.square(norbs=1)
     syst = kwant.Builder(kwant.TranslationalSymmetry((-3, 0), (0, 1)))
     # onsites and hoppings that will be bound as sites
     syst[lat(-2, 0)] = 4
@@ -162,7 +164,7 @@ def test_signatures():
 
 
 def test_symmetry():
-    syst = _simple_syst(kwant.lattice.square())
+    syst = _simple_syst(kwant.lattice.square(norbs=1))
 
     matrices = [np.random.rand(2, 2) for i in range(4)]
     laws = (matrices, [(lambda a: m) for m in matrices])
@@ -190,10 +192,10 @@ def test_symmetry():
 
 @pytest.mark.skipif(not _plotter.mpl_available, reason="Matplotlib unavailable.")
 def test_plot_2d_bands():
-    chain = kwant.lattice.chain()
-    square = kwant.lattice.square()
-    cube = kwant.lattice.general([(1, 0, 0), (0, 1, 0), (0, 0, 1)])
-    hc = kwant.lattice.honeycomb()
+    chain = kwant.lattice.chain(norbs=1)
+    square = kwant.lattice.square(norbs=1)
+    cube = kwant.lattice.general([(1, 0, 0), (0, 1, 0), (0, 0, 1)], norbs=1)
+    hc = kwant.lattice.honeycomb(norbs=1)
 
     syst_1d = kwant.Builder(kwant.TranslationalSymmetry(*chain._prim_vecs))
     syst_1d[chain(0)] = 2
@@ -245,7 +247,7 @@ def test_fd_mismatch():
     # around in all directions, but could not be wrapped around when 'keep' is
     # provided.
     sqrt3 = np.sqrt(3)
-    lat = kwant.lattice.general([(sqrt3, 0), (-sqrt3/2, 1.5)])
+    lat = kwant.lattice.general([(sqrt3, 0), (-sqrt3/2, 1.5)], norbs=1)
     T = kwant.TranslationalSymmetry((sqrt3, 0), (0, 3))
 
     syst1 = kwant.Builder(T)
@@ -269,7 +271,8 @@ def test_fd_mismatch():
     ## Test that spectrum of non-trivial system (including above cases)
     ## is the same, regardless of the way in which it is wrapped around
     lat = kwant.lattice.general([(sqrt3, 0), (-sqrt3/2, 1.5)],
-                                [(sqrt3 / 2, 0.5), (0, 1)])
+                                [(sqrt3 / 2, 0.5), (0, 1)],
+                                norbs=1)
     a, b = lat.sublattices
     T = kwant.TranslationalSymmetry((3 * sqrt3, 0), (0, 3))
     syst = kwant.Builder(T)
@@ -302,7 +305,7 @@ def test_fd_mismatch():
     assert all(np.allclose(E, E[0]) for E in E_k)
 
     # Test square lattice with oblique unit cell
-    lat = kwant.lattice.general(np.eye(2))
+    lat = kwant.lattice.general(np.eye(2), norbs=1)
     translations = kwant.lattice.TranslationalSymmetry([2, 2], [0, 2])
     syst = kwant.Builder(symmetry=translations)
     syst[lat.shape(lambda site: True, [0, 0])] = 1
@@ -314,7 +317,7 @@ def test_fd_mismatch():
 
     # Test Rocksalt structure
     # cubic lattice that contains both sublattices
-    lat = kwant.lattice.general(np.eye(3))
+    lat = kwant.lattice.general(np.eye(3), norbs=1)
     # Builder with FCC translational symmetries.
     translations = kwant.lattice.TranslationalSymmetry([1, 1, 0], [1, 0, 1], [0, 1, 1])
     syst = kwant.Builder(symmetry=translations)
@@ -341,7 +344,7 @@ def test_fd_mismatch():
     def shape(site):
         return abs(site.tag[2]) < 4
 
-    lat = kwant.lattice.general(np.eye(3))
+    lat = kwant.lattice.general(np.eye(3), norbs=1)
     # First choice: primitive UC
     translations = kwant.lattice.TranslationalSymmetry([1, 1, 0], [1, -1, 0], [1, 0, 1])
     syst = kwant.Builder(symmetry=translations)

kwant/wraparound.py

@@ -20,36 +20,12 @@ from . import builder, system, plotter
 from .linalg import lll
 from .builder import herm_conj, HermConjOfFunc
 from .lattice import TranslationalSymmetry
-from ._common import get_parameters
+from ._common import get_parameters, memoize
 
 
 __all__ = ['wraparound', 'plot_2d_bands']
 
 
-def _hashable(obj):
-    return isinstance(obj, collections.abc.Hashable)
-
-
-def _memoize(f):
-    """Decorator to memoize a function that works even with unhashable args.
-
-    This decorator will even work with functions whose args are not hashable.
-    The cache key is made up by the hashable arguments and the ids of the
-    non-hashable args.  It is up to the user to make sure that non-hashable
-    args do not change during the lifetime of the decorator.
-
-    This decorator will keep reevaluating functions that return None.
-    """
-    def lookup(*args):
-        key = tuple(arg if _hashable(arg) else id(arg) for arg in args)
-        result = cache.get(key)
-        if result is None:
-            cache[key] = result = f(*args)
-        return result
-    cache = {}
-    return lookup
-
-
 def _set_signature(func, params):
     """Set the signature of 'func'.
 
@@ -103,7 +79,7 @@ def wraparound(builder, keep=None, *, coordinate_names='xyz'):
     format. It will be deprecated in the 2.0 release of Kwant.
     """
 
-    @_memoize
+    @memoize
     def bind_site(val):
         def f(*args):
             a, *args = args
@@ -113,7 +89,7 @@ def wraparound(builder, keep=None, *, coordinate_names='xyz'):
         _set_signature(f, get_parameters(val) + momenta)
         return f
 
-    @_memoize
+    @memoize
     def bind_hopping_as_site(elem, val):
         def f(*args):
             a, *args = args
@@ -128,7 +104,7 @@ def wraparound(builder, keep=None, *, coordinate_names='xyz'):
         _set_signature(f, params + momenta)
         return f
 
-    @_memoize
+    @memoize
     def bind_hopping(elem, val):
         def f(*args):
             a, b, *args = args
@@ -142,7 +118,7 @@ def wraparound(builder, keep=None, *, coordinate_names='xyz'):
         _set_signature(f, params + momenta)
         return f
 
-    @_memoize
+    @memoize
     def bind_sum(num_sites, *vals):
         """Construct joint signature for all 'vals'."""
 
@@ -386,10 +362,14 @@ def plot_2d_bands(syst, k_x=31, k_y=31, params=None,
     if not hasattr(syst, '_wrapped_symmetry'):
         raise TypeError("Expecting a system that was produced by "
                         "'kwant.wraparound.wraparound'.")
-    if not isinstance(syst, system.FiniteSystem):
+    if isinstance(syst, system.InfiniteSystem):
         msg = ("All symmetry directions must be wrapped around: specify "
                "'keep=None' when calling 'kwant.wraparound.wraparound'.")
         raise TypeError(msg)
+    if isinstance(syst, builder.Builder):
+        msg = ("Expecting a finalized system: remember to finalize your "
+               "system with 'syst.finalized()'.")
+        raise TypeError(msg)
 
     params = params or {}
     lat_ndim, space_ndim = syst._wrapped_symmetry.periods.shape

pytest.ini

 [pytest]
 testpaths = kwant
 flakes-ignore =
-    __init__.py UnusedImport
+    __init__.py UnusedImport ImportStarUsed ImportStarUsage
     kwant/_plotter.py UnusedImport
     graph/tests/test_scotch.py UndefinedName
-    graph/tests/test_dissection.py UndefinedName

setup.py

@@ -517,7 +517,7 @@ def maybe_add_numpy_include(exts):
 
 
 def main():
-    check_python_version((3, 5))
+    check_python_version((3, 6))
     check_versions()
 
     exts = collections.OrderedDict([
@@ -581,12 +581,12 @@ def main():
                     'build_ext': build_ext,
                     'test': test},
           ext_modules=exts,
-          install_requires=['numpy >= 1.11.0', 'scipy >= 0.17.0',
+          install_requires=['numpy >= 1.13.3', 'scipy >= 0.19.1',
                             'tinyarray >= 1.2'],
           extras_require={
               # The oldest versions between: Debian stable, Ubuntu LTS
-              'plotting': 'matplotlib >= 1.5.1',
-              'continuum': 'sympy >= 0.7.6',
+              'plotting': 'matplotlib >= 2.1.1',
+              'continuum': 'sympy >= 1.1.1',
               # qsymm is only packaged on PyPI
               'qsymm': 'qsymm >= 1.2.6',
           },