diff --git a/kwant/builder.py b/kwant/builder.py
index 1215e1991a0118ed61dac38b46794101d1e81426..bd86c2531e0ac160e0801082083aae96f7690361 100644
--- a/kwant/builder.py
+++ b/kwant/builder.py
@@ -454,7 +454,7 @@ class SelfEnergyLead(Lead):
interface : sequence of `Site` instances
"""
def __init__(self, selfenergy_func, interface):
- self._selfenergy_func = selfenergy_func
+ self.selfenergy_func = selfenergy_func
self.interface = tuple(interface)
def finalized(self):
@@ -462,7 +462,7 @@ class SelfEnergyLead(Lead):
return self
def selfenergy(self, energy, args=()):
- return self._selfenergy_func(energy, args)
+ return self.selfenergy_func(energy, args)
class ModesLead(Lead):
diff --git a/kwant/lattice.py b/kwant/lattice.py
index 470ff6885bd23bac57e5dee771f8ca23da4f2ac3..f415cec2a599ff177a1c198588f8fc29d4ebc4b3 100644
--- a/kwant/lattice.py
+++ b/kwant/lattice.py
@@ -98,8 +98,8 @@ class Polyatomic(object):
# Sequence of primitive vectors of the lattice.
self._prim_vecs = prim_vecs
# Precalculation of auxiliary arrays for real space calculations.
- self._reduced_vecs, self._transf = lll.lll(prim_vecs)
- self._voronoi = ta.dot(lll.voronoi(self._reduced_vecs), self._transf)
+ self.reduced_vecs, self.transf = lll.lll(prim_vecs)
+ self.voronoi = ta.dot(lll.voronoi(self.reduced_vecs), self.transf)
def shape(self, function, start):
"""Return a key for all the lattice sites inside a given shape.
@@ -158,7 +158,7 @@ class Polyatomic(object):
raise ValueError('Dimensionality of start position does not '
'match the space dimensionality.')
lats = self.sublattices
- deltas = list(self._voronoi)
+ deltas = list(self.voronoi)
#### Flood-fill ####
sites = []
@@ -421,11 +421,11 @@ class Monatomic(builder.SiteFamily, Polyatomic):
self.offset = offset
# Precalculation of auxiliary arrays for real space calculations.
- self._reduced_vecs, self._transf = lll.lll(prim_vecs)
- self._voronoi = ta.dot(lll.voronoi(self._reduced_vecs), self._transf)
+ self.reduced_vecs, self.transf = lll.lll(prim_vecs)
+ self.voronoi = ta.dot(lll.voronoi(self.reduced_vecs), self.transf)
self.dim = dim
- self._lattice_dim = len(prim_vecs)
+ self.lattice_dim = len(prim_vecs)
if name != '':
msg = "Monatomic lattice {0}, vectors {1}, origin {2}"
@@ -442,7 +442,7 @@ class Monatomic(builder.SiteFamily, Polyatomic):
def normalize_tag(self, tag):
tag = ta.array(tag, int)
- if len(tag) != self._lattice_dim:
+ if len(tag) != self.lattice_dim:
raise ValueError("Dimensionality mismatch.")
return tag
@@ -455,8 +455,8 @@ class Monatomic(builder.SiteFamily, Polyatomic):
An array with sites coordinates.
"""
# TODO (Anton): transform to tinyarrays, once ta indexing is better.
- return np.dot(lll.cvp(pos - self.offset, self._reduced_vecs, n),
- self._transf.T)
+ return np.dot(lll.cvp(pos - self.offset, self.reduced_vecs, n),
+ self.transf.T)
def closest(self, pos):
"""
@@ -497,7 +497,6 @@ class TranslationalSymmetry(builder.Symmetry):
"""
def __init__(self, *periods):
self.periods = ta.array(periods)
- self._periods = self.periods
if self.periods.ndim != 2:
# TODO: remove the second part of the following message once
# everybody got used to it.
@@ -539,18 +538,18 @@ class TranslationalSymmetry(builder.Symmetry):
ValueError
If lattice `fam` is incompatible with given periods.
"""
- dim = self._periods.shape[1]
+ dim = self.periods.shape[1]
if fam in self.site_family_data:
raise KeyError('Family already processed, delete it from '
'site_family_data first.')
inv = np.linalg.pinv(fam.prim_vecs)
- bravais_periods = np.dot(self._periods, inv)
+ bravais_periods = np.dot(self.periods, inv)
# Absolute tolerance is correct in the following since we want an error
# relative to the closest integer.
if not np.allclose(bravais_periods, np.round(bravais_periods),
rtol=0, atol=1e-8) or \
not np.allclose([fam.vec(i) for i in bravais_periods],
- self._periods):
+ self.periods):
msg = 'Site family {0} does not have commensurate periods with ' +\
'symmetry {1}.'
raise ValueError(msg.format(fam, self))
@@ -655,7 +654,7 @@ class TranslationalSymmetry(builder.Symmetry):
The resulting symmetry has all the period vectors opposite to the
original and an identical fundamental domain.
"""
- result = TranslationalSymmetry(*self._periods)
+ result = TranslationalSymmetry(*self.periods)
result.site_family_data = self.site_family_data
result.is_reversed = not self.is_reversed
result.periods = -self.periods
diff --git a/kwant/linalg/mumps.py b/kwant/linalg/mumps.py
index 79eaa949169cd01afa1ab51f45e8658440fa917a..170a2523df42d534c9fe805ae52a51775db07e28 100644
--- a/kwant/linalg/mumps.py
+++ b/kwant/linalg/mumps.py
@@ -23,8 +23,6 @@ orderings = { 'amd' : 0, 'amf' : 2, 'scotch' : 3, 'pord' : 4, 'metis' : 5,
ordering_name = [ 'amd', 'user-defined', 'amf',
'scotch', 'pord', 'metis', 'qamd']
-_possible_orderings = None
-
def possible_orderings():
"""Return the ordering options that are available in the current
@@ -41,13 +39,12 @@ def possible_orderings():
A list of installed orderings that can be used in the `ordering` option
of MUMPS.
"""
- global _possible_orderings
- if not _possible_orderings:
+ if not possible_orderings.cached:
# Try all orderings on a small test matrix, and check which one was
# actually used.
- _possible_orderings = ['auto']
+ possible_orderings.cached = ['auto']
for ordering in [0, 2, 3, 4, 5, 6]:
data = np.asfortranarray([1, 1], dtype=np.complex128)
row = np.asfortranarray([1, 2], dtype=_mumps.int_dtype)
@@ -60,9 +57,11 @@ def possible_orderings():
instance.call()
if instance.infog[7] == ordering:
- _possible_orderings.append(ordering_name[ordering])
+ possible_orderings.cached.append(ordering_name[ordering])
+
+ return possible_orderings.cached
- return _possible_orderings
+possible_orderings.cached = None
error_messages = {
diff --git a/kwant/linalg/tests/test_mumps.py b/kwant/linalg/tests/test_mumps.py
index a316be12d0af43c3b6f8545424dceebc682f0ad5..597b24d35351038c38f7646a006e9d3cc4351de9 100644
--- a/kwant/linalg/tests/test_mumps.py
+++ b/kwant/linalg/tests/test_mumps.py
@@ -8,9 +8,9 @@
try:
from kwant.linalg.mumps import MUMPSContext, schur_complement
- _no_mumps = False
+ no_mumps = False
except ImportError:
- _no_mumps = True
+ no_mumps = True
from kwant.lattice import honeycomb
from kwant.builder import Builder, HoppingKind
@@ -19,7 +19,7 @@ import numpy as np
import scipy.sparse as sp
from _test_utils import _Random, assert_array_almost_equal
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_lu_with_dense():
def _test_lu_with_dense(dtype):
rand = _Random()
@@ -48,7 +48,7 @@ def test_lu_with_dense():
_test_lu_with_dense(np.complex128)
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_schur_complement_with_dense():
def _test_schur_complement_with_dense(dtype):
rand = _Random()
@@ -60,7 +60,7 @@ def test_schur_complement_with_dense():
_test_schur_complement_with_dense(np.complex128)
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_error_minus_9(r=10):
"""Test if MUMPSError -9 is properly caught by increasing memory"""
diff --git a/kwant/plotter.py b/kwant/plotter.py
index 1a5bf39a19f4976a6b25639577dd013e6fdd241e..8bc192a15e274f510c7ebf63398828a504326753 100644
--- a/kwant/plotter.py
+++ b/kwant/plotter.py
@@ -68,7 +68,7 @@ if mpl_enabled:
self.reflen = reflen
def set_linewidths(self, linewidths):
- self._linewidths_orig = nparray_if_array(linewidths)
+ self.linewidths_orig = nparray_if_array(linewidths)
def draw(self, renderer):
if self.reflen is not None:
@@ -79,7 +79,7 @@ if mpl_enabled:
else:
factor = 1
- super(LineCollection, self).set_linewidths(self._linewidths_orig *
+ super(LineCollection, self).set_linewidths(self.linewidths_orig *
factor)
return super(LineCollection, self).draw(renderer)
@@ -89,13 +89,13 @@ if mpl_enabled:
super(PathCollection, self).__init__(paths, sizes=sizes, **kwargs)
self.reflen = reflen
- self._linewidths_orig = nparray_if_array(self.get_linewidths())
+ self.linewidths_orig = nparray_if_array(self.get_linewidths())
- self._transforms = [matplotlib.transforms.Affine2D().scale(x) for x
+ self.transforms = [matplotlib.transforms.Affine2D().scale(x) for x
in sizes]
def get_transforms(self):
- return self._transforms
+ return self.transforms
def get_transform(self):
Affine2D = matplotlib.transforms.Affine2D
@@ -112,7 +112,7 @@ if mpl_enabled:
# Note: only works for aspect ratio 1!
factor = (self.axes.transData.frozen().to_values()[0] /
self.figure.dpi * 72.0 * self.reflen)
- self.set_linewidths(self._linewidths_orig * factor)
+ self.set_linewidths(self.linewidths_orig * factor)
return collections.Collection.draw(self, renderer)
@@ -156,10 +156,10 @@ if mpl_enabled:
def __init__(self, segments, reflen=None, zorder=0, **kwargs):
super(Line3DCollection, self).__init__(segments, **kwargs)
self.reflen = reflen
- self._zorder3d = zorder
+ self.zorder3d = zorder
def set_linewidths(self, linewidths):
- self._linewidths_orig = nparray_if_array(linewidths)
+ self.linewidths_orig = nparray_if_array(linewidths)
def do_3d_projection(self, renderer):
super(Line3DCollection, self).do_3d_projection(renderer)
@@ -168,7 +168,7 @@ if mpl_enabled:
# "-" due to the different logic in the 3d plotting, we still
# want larger zorder values to be plotted on top of smaller
# ones.
- return -self._zorder3d
+ return -self.zorder3d
def draw(self, renderer):
if self.reflen:
@@ -185,7 +185,7 @@ if mpl_enabled:
factor = 1
super(Line3DCollection, self).set_linewidths(
- self._linewidths_orig * factor)
+ self.linewidths_orig * factor)
super(Line3DCollection, self).draw(renderer)
@@ -203,38 +203,38 @@ if mpl_enabled:
self.set_3d_properties(zs=offsets[:, 2], zdir="z")
self.reflen = reflen
- self._zorder3d = zorder
+ self.zorder3d = zorder
- self._paths_orig = np.array(paths, dtype='object')
- self._linewidths_orig = nparray_if_array(self.get_linewidths())
- self._linewidths_orig2 = self._linewidths_orig
- self._array_orig = nparray_if_array(self.get_array())
- self._facecolors_orig = nparray_if_array(self.get_facecolors())
- self._edgecolors_orig = nparray_if_array(self.get_edgecolors())
+ self.paths_orig = np.array(paths, dtype='object')
+ self.linewidths_orig = nparray_if_array(self.get_linewidths())
+ self.linewidths_orig2 = self.linewidths_orig
+ self.array_orig = nparray_if_array(self.get_array())
+ self.facecolors_orig = nparray_if_array(self.get_facecolors())
+ self.edgecolors_orig = nparray_if_array(self.get_edgecolors())
Affine2D = matplotlib.transforms.Affine2D
- self._orig_transforms = np.array([Affine2D().scale(x) for x in
+ self.orig_transforms = np.array([Affine2D().scale(x) for x in
sizes], dtype='object')
- self._transforms = self._orig_transforms
+ self.transforms = self.orig_transforms
def set_array(self, array):
- self._array_orig = nparray_if_array(array)
+ self.array_orig = nparray_if_array(array)
super(Path3DCollection, self).set_array(array)
def set_color(self, colors):
- self._facecolors_orig = nparray_if_array(colors)
- self._edgecolors_orig = self._facecolors_orig
+ self.facecolors_orig = nparray_if_array(colors)
+ self.edgecolors_orig = self.facecolors_orig
super(Path3DCollection, self).set_color(colors)
def set_edgecolors(self, colors):
colors = matplotlib.colors.colorConverter.to_rgba_array(colors)
- self._edgecolors_orig = nparray_if_array(colors)
+ self.edgecolors_orig = nparray_if_array(colors)
super(Path3DCollection, self).set_edgecolors(colors)
def get_transforms(self):
# this is exact only for an isometric projection, for the
# perspective projection used in mplot3d it's an approximation
- return self._transforms
+ return self.transforms
def get_transform(self):
Affine2D = matplotlib.transforms.Affine2D
@@ -253,7 +253,7 @@ if mpl_enabled:
# numpy complains about zero-length index arrays
if len(xs) == 0:
- return -self._zorder3d
+ return -self.zorder3d
proj = mplot3d.proj3d.proj_transform_clip
vs = np.array(proj(xs, ys, zs, renderer.M)[:3])
@@ -263,41 +263,41 @@ if mpl_enabled:
self.set_offsets(vs[:2, indx].T)
- if len(self._paths_orig) > 1:
- paths = np.resize(self._paths_orig, (vs.shape[1],))
+ if len(self.paths_orig) > 1:
+ paths = np.resize(self.paths_orig, (vs.shape[1],))
self.set_paths(paths[indx])
- if len(self._orig_transforms) > 1:
- self._transforms = np.resize(self._orig_transforms,
+ if len(self.orig_transforms) > 1:
+ self.transforms = np.resize(self.orig_transforms,
(vs.shape[1],))
- self._transforms = self._transforms[indx]
+ self.transforms = self.transforms[indx]
- lw_orig = self._linewidths_orig
+ lw_orig = self.linewidths_orig
if (isinstance(lw_orig, np.ndarray) and len(lw_orig) > 1):
- self._linewidths_orig2 = np.resize(lw_orig,
+ self.linewidths_orig2 = np.resize(lw_orig,
(vs.shape[1],))[indx]
# Note: here array, facecolors and edgecolors are
# guaranteed to be 2d numpy arrays or None. (And
# array is the same length as the coordinates)
- if self._array_orig is not None:
+ if self.array_orig is not None:
super(Path3DCollection,
- self).set_array(self._array_orig[indx])
+ self).set_array(self.array_orig[indx])
- if (self._facecolors_orig is not None and
- self._facecolors_orig.shape[0] > 1):
- shape = list(self._facecolors_orig.shape)
+ if (self.facecolors_orig is not None and
+ self.facecolors_orig.shape[0] > 1):
+ shape = list(self.facecolors_orig.shape)
shape[0] = vs.shape[1]
super(Path3DCollection, self).set_facecolors(
- np.resize(self._facecolors_orig, shape)[indx])
+ np.resize(self.facecolors_orig, shape)[indx])
- if (self._edgecolors_orig is not None and
- self._edgecolors_orig.shape[0] > 1):
- shape = list(self._edgecolors_orig.shape)
+ if (self.edgecolors_orig is not None and
+ self.edgecolors_orig.shape[0] > 1):
+ shape = list(self.edgecolors_orig.shape)
shape[0] = vs.shape[1]
super(Path3DCollection, self).set_edgecolors(
- np.resize(self._edgecolors_orig,
+ np.resize(self.edgecolors_orig,
shape)[indx])
else:
self.set_offsets(vs[:2].T)
@@ -316,7 +316,7 @@ if mpl_enabled:
proj = mplot3d.proj3d.proj_transform_clip
cz = proj(*(list(np.dot(corners, bbox)) + [renderer.M]))[2]
- return -self._zorder3d + vs[2].mean() / cz.ptp()
+ return -self.zorder3d + vs[2].mean() / cz.ptp()
def draw(self, renderer):
if self.reflen:
@@ -325,7 +325,7 @@ if mpl_enabled:
factor = proj_len * (args[0] +
args[3]) * 0.5 * 72.0 / self.figure.dpi
- self.set_linewidths(self._linewidths_orig2 * factor)
+ self.set_linewidths(self.linewidths_orig2 * factor)
super(Path3DCollection, self).draw(renderer)
diff --git a/kwant/solvers/common.py b/kwant/solvers/common.py
index a6bdecdaed1f9a693bc82ac9ced86211b9731ab6..e8655648ca1f9f661038d82a470056924c7aed50 100644
--- a/kwant/solvers/common.py
+++ b/kwant/solvers/common.py
@@ -560,11 +560,11 @@ class BlockResult(object):
self.lead_info = lead_info
self.out_leads = out_leads
self.in_leads = in_leads
- self._sizes = np.array(sizes)
- self._in_offsets = np.zeros(len(self.in_leads) + 1, int)
- self._in_offsets[1 :] = np.cumsum(self._sizes[self.in_leads])
- self._out_offsets = np.zeros(len(self.out_leads) + 1, int)
- self._out_offsets[1 :] = np.cumsum(self._sizes[self.out_leads])
+ self.sizes = np.array(sizes)
+ self.in_offsets = np.zeros(len(self.in_leads) + 1, int)
+ self.in_offsets[1 :] = np.cumsum(self.sizes[self.in_leads])
+ self.out_offsets = np.zeros(len(self.out_leads) + 1, int)
+ self.out_offsets[1 :] = np.cumsum(self.sizes[self.out_leads])
def block_coords(self, lead_out, lead_in):
"""
@@ -576,16 +576,16 @@ class BlockResult(object):
"""Return a slice with the rows in the block corresponding to lead_out.
"""
lead_out = self.out_leads.index(lead_out)
- return slice(self._out_offsets[lead_out],
- self._out_offsets[lead_out + 1])
+ return slice(self.out_offsets[lead_out],
+ self.out_offsets[lead_out + 1])
def in_block_coords(self, lead_in):
"""
Return a slice with the columns in the block corresponding to lead_in.
"""
lead_in = self.in_leads.index(lead_in)
- return slice(self._in_offsets[lead_in],
- self._in_offsets[lead_in + 1])
+ return slice(self.in_offsets[lead_in],
+ self.in_offsets[lead_in + 1])
def submatrix(self, lead_out, lead_in):
"""Return the matrix elements from lead_in to lead_out."""
diff --git a/kwant/solvers/tests/test_mumps.py b/kwant/solvers/tests/test_mumps.py
index fff9cdc1539eef56e8b44b428d621751ec12d2a5..c0f4007841e3a809521352dd1be6aeaf595ce05d 100644
--- a/kwant/solvers/tests/test_mumps.py
+++ b/kwant/solvers/tests/test_mumps.py
@@ -12,9 +12,9 @@ try:
from kwant.solvers.mumps import \
smatrix, greens_function, ldos, wave_function, options, reset_options
import _test_sparse
- _no_mumps = False
+ no_mumps = False
except ImportError:
- _no_mumps = True
+ no_mumps = True
opt_list=[{},
@@ -25,7 +25,7 @@ opt_list=[{},
{'nrhs' : 2, 'ordering' : 'amd', 'sparse_rhs' : True}]
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_output():
for opts in opt_list:
reset_options()
@@ -33,7 +33,7 @@ def test_output():
_test_sparse.test_output(smatrix)
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_one_lead():
for opts in opt_list:
reset_options()
@@ -41,7 +41,7 @@ def test_one_lead():
_test_sparse.test_one_lead(smatrix)
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_smatrix_shape():
for opts in opt_list:
reset_options()
@@ -49,14 +49,14 @@ def test_smatrix_shape():
_test_sparse.test_smatrix_shape(smatrix)
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_two_equal_leads():
for opts in opt_list:
reset_options()
options(**opts)
_test_sparse.test_two_equal_leads(smatrix)
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_graph_system():
for opts in opt_list:
reset_options()
@@ -64,7 +64,7 @@ def test_graph_system():
_test_sparse.test_graph_system(smatrix)
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_singular_graph_system():
for opts in opt_list:
reset_options()
@@ -72,7 +72,7 @@ def test_singular_graph_system():
_test_sparse.test_singular_graph_system(smatrix)
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_tricky_singular_hopping():
for opts in opt_list:
reset_options()
@@ -80,7 +80,7 @@ def test_tricky_singular_hopping():
_test_sparse.test_tricky_singular_hopping(smatrix)
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_selfenergy():
for opts in opt_list:
reset_options()
@@ -88,7 +88,7 @@ def test_selfenergy():
_test_sparse.test_selfenergy(greens_function, smatrix)
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_selfenergy_reflection():
for opts in opt_list:
reset_options()
@@ -96,7 +96,7 @@ def test_selfenergy_reflection():
_test_sparse.test_selfenergy_reflection(greens_function, smatrix)
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_very_singular_leads():
for opts in opt_list:
reset_options()
@@ -104,7 +104,7 @@ def test_very_singular_leads():
_test_sparse.test_very_singular_leads(smatrix)
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_ldos():
for opts in opt_list:
reset_options()
@@ -112,7 +112,7 @@ def test_ldos():
_test_sparse.test_ldos(ldos)
-@skipif(_no_mumps)
+@skipif(no_mumps)
def test_wavefunc_ldos_consistency():
for opts in opt_list:
options(**opts)