From a2c62218e5d1889eeb0396c873415e7f36245e2d Mon Sep 17 00:00:00 2001
From: Christoph Groth <christoph.groth@cea.fr>
Date: Sun, 28 Apr 2013 09:38:49 +0200
Subject: [PATCH] rename self_energy to selfenergy
---
doc/source/reference/kwant.physics.rst | 2 +-
doc/source/whatsnew/0.3.rst | 2 ++
examples/square.py | 6 +++---
examples/tests/test_square.py | 4 ++--
kwant/builder.py | 16 ++++++++--------
kwant/physics/leads.py | 6 +++---
kwant/physics/tests/test_leads.py | 24 ++++++++++++------------
kwant/physics/tests/test_noise.py | 4 ++--
kwant/solvers/common.py | 2 +-
kwant/solvers/tests/_test_sparse.py | 8 ++++----
kwant/solvers/tests/test_mumps.py | 8 ++++----
kwant/solvers/tests/test_sparse.py | 8 ++++----
kwant/system.py | 8 ++++----
13 files changed, 50 insertions(+), 48 deletions(-)
diff --git a/doc/source/reference/kwant.physics.rst b/doc/source/reference/kwant.physics.rst
index 90128888..38de2fee 100644
--- a/doc/source/reference/kwant.physics.rst
+++ b/doc/source/reference/kwant.physics.rst
@@ -10,4 +10,4 @@ Leads
Bands
modes
- self_energy
+ selfenergy
diff --git a/doc/source/whatsnew/0.3.rst b/doc/source/whatsnew/0.3.rst
index d9c5add3..5ee9c7ae 100644
--- a/doc/source/whatsnew/0.3.rst
+++ b/doc/source/whatsnew/0.3.rst
@@ -28,6 +28,8 @@ Some renames
------------
* site groups are now called site families. This affects all the names that
used to contain "group" or "groups".
+* ``self_energy`` has been renamed to ``selfenergy`` in all cases, most notably
+ in `kwant.physics.selfenergy`.
* ``wave_func`` has been renamed to `~kwant.solvers.default.wave_function`,
* ``MonatomicLattice`` has been renamed to `~kwant.lattice.Monatomic`,
* ``PolyatomicLattice`` has been renamed to `~kwant.lattice.Polyatomic`.
diff --git a/examples/square.py b/examples/square.py
index 14e0bd27..dbfd7e82 100644
--- a/examples/square.py
+++ b/examples/square.py
@@ -6,7 +6,7 @@ from __future__ import division
import numpy as np
from matplotlib import pyplot
import kwant
-from kwant.physics.selfenergy import square_self_energy
+from kwant.physics.selfenergy import square_selfenergy
__all__ = ['System' ]
@@ -16,8 +16,8 @@ class Lead(object):
self.t = t
self.potential = potential
- def self_energy(self, fermi_energy):
- return square_self_energy(self.width, self.t, self.potential,
+ def selfenergy(self, fermi_energy):
+ return square_selfenergy(self.width, self.t, self.potential,
fermi_energy)
class System(kwant.system.FiniteSystem):
diff --git a/examples/tests/test_square.py b/examples/tests/test_square.py
index e49d67ff..9abfbbb1 100644
--- a/examples/tests/test_square.py
+++ b/examples/tests/test_square.py
@@ -26,12 +26,12 @@ def test_hamiltonian():
assert_almost_equal(m, m_herm)
assert_almost_equal(m_herm, sys.hamiltonian(j, i))
-def test_self_energy():
+def test_selfenergy():
sys = square.System((2, 4), 1)
for lead in xrange(len(sys.lead_interfaces)):
n_orb = sum(
sys.num_orbitals(site) for site in sys.lead_interfaces[lead])
- se = sys.self_energy(lead, 0)
+ se = sys.selfenergy(lead, 0)
assert_equal(len(se.shape), 2)
assert_equal(se.shape[0], se.shape[1])
assert_equal(se.shape[0], n_orb)
diff --git a/kwant/builder.py b/kwant/builder.py
index 53b3bd62..38f05118 100644
--- a/kwant/builder.py
+++ b/kwant/builder.py
@@ -388,10 +388,10 @@ class Lead(object):
Notes
-----
The finalized lead must at least have a single method
- ``self_energy(energy)`` but it can be a full
+ ``selfenergy(energy)`` but it can be a full
`kwant.system.InfiniteSystem` as well.
- The method ``self_energy`` of the finalized lead must return a square
+ The method ``selfenergy`` of the finalized lead must return a square
matrix of appropriate size.
The order of interface sites is assumed to be preserved during
@@ -444,21 +444,21 @@ class SelfEnergy(Lead):
Parameters
----------
- self_energy_func : function
+ selfenergy_func : function
Function which returns the self energy matrix for the interface sites
given the energy and optionally a list of extra arguments.
interface : sequence of `Site` instances
"""
- def __init__(self, self_energy_func, interface):
- self._self_energy_func = self_energy_func
+ def __init__(self, selfenergy_func, interface):
+ self._selfenergy_func = selfenergy_func
self.interface = tuple(interface)
def finalized(self):
"""Trivial finalization: the object is returned itself."""
return self
- def self_energy(self, energy, args=()):
- return self._self_energy_func(energy, args)
+ def selfenergy(self, energy, args=()):
+ return self._selfenergy_func(energy, args)
class ModesLead(Lead):
@@ -482,7 +482,7 @@ class ModesLead(Lead):
def modes(self, energy, args=()):
return self._modes_func(energy, args)
- def self_energy(self, energy, args=()):
+ def selfenergy(self, energy, args=()):
modes = self.modes(energy, args)
return physics.selfenergy(modes=modes)
diff --git a/kwant/physics/leads.py b/kwant/physics/leads.py
index 370e4eca..a9a630e9 100644
--- a/kwant/physics/leads.py
+++ b/kwant/physics/leads.py
@@ -17,7 +17,7 @@ from .. import linalg as kla
dot = np.dot
-__all__ = ['self_energy', 'modes', 'Modes']
+__all__ = ['selfenergy', 'modes', 'Modes']
Linsys = namedtuple('Linsys', ['eigenproblem', 'v', 'extract', 'project'])
@@ -503,7 +503,7 @@ def modes(h_onslice, h_hop, tol=1e6):
return Modes(vecs, vecslmbdainv, nmodes, v)
-def self_energy(lead_modes, tol=1e6):
+def selfenergy(lead_modes, tol=1e6):
"""
Compute the self-energy generated by a lead.
@@ -539,7 +539,7 @@ def self_energy(lead_modes, tol=1e6):
return la.solve(vecslmbdainv.T, vecs.T).T
-def square_self_energy(width, hopping, fermi_energy):
+def square_selfenergy(width, hopping, fermi_energy):
"""
Calculate analytically the self energy for a square lattice.
diff --git a/kwant/physics/tests/test_leads.py b/kwant/physics/tests/test_leads.py
index 96054f86..e182fa8c 100644
--- a/kwant/physics/tests/test_leads.py
+++ b/kwant/physics/tests/test_leads.py
@@ -11,7 +11,7 @@ import numpy as np
from numpy.testing import assert_almost_equal
from kwant.physics import leads
-modes_se = lambda h, t: leads.self_energy(leads.modes(h, t))
+modes_se = lambda h, t: leads.selfenergy(leads.modes(h, t))
def h_slice(t, w, e):
h = (4 * t - e) * np.identity(w)
@@ -25,7 +25,7 @@ def test_analytic_numeric():
t = 0.78 # hopping element
e = 1.3 # Fermi energy
- assert_almost_equal(leads.square_self_energy(w, t, e),
+ assert_almost_equal(leads.square_selfenergy(w, t, e),
modes_se(h_slice(t, w, e), -t * np.identity(w)))
@@ -48,8 +48,8 @@ def test_regular_fully_degenerate():
h_onslice[w:, w:] = h_onslice_s
g = np.zeros((2*w, 2*w), dtype=complex)
- g[:w, :w] = leads.square_self_energy(w, t, e)
- g[w:, w:] = leads.square_self_energy(w, t, e)
+ g[:w, :w] = leads.square_selfenergy(w, t, e)
+ g[w:, w:] = leads.square_selfenergy(w, t, e)
assert_almost_equal(g, modes_se(h_onslice, h_hop))
@@ -78,8 +78,8 @@ def test_regular_degenerate_with_crossing():
h_onslice[w:, w:] = -h_onslice_s
g = np.zeros((2*w, 2*w), dtype=complex)
- g[:w, :w] = leads.square_self_energy(w, t, e)
- g[w:, w:] = -np.conj(leads.square_self_energy(w, t, e))
+ g[:w, :w] = leads.square_selfenergy(w, t, e)
+ g[w:, w:] = -np.conj(leads.square_selfenergy(w, t, e))
assert_almost_equal(g, modes_se(h_onslice, hop))
@@ -104,7 +104,7 @@ def test_singular():
h_onslice[:w, w:] = h_hop_s
h_onslice[w:, :w] = h_hop_s
h_onslice[w:, w:] = h_onslice_s
- g = leads.square_self_energy(w, t, e)
+ g = leads.square_selfenergy(w, t, e)
print np.round(g, 5) / np.round(modes_se(h_onslice, h_hop), 5)
assert_almost_equal(g, modes_se(h_onslice, h_hop))
@@ -132,7 +132,7 @@ def test_singular_but_square():
h_onslice[w:, w:] = h_onslice_s
g = np.zeros((2*w, 2*w), dtype=complex)
- g[:w, :w] = leads.square_self_energy(w, t, e)
+ g[:w, :w] = leads.square_selfenergy(w, t, e)
assert_almost_equal(g, modes_se(h_onslice, h_hop))
def test_singular_fully_degenerate():
@@ -163,8 +163,8 @@ def test_singular_fully_degenerate():
h_onslice[3*w:4*w, 3*w:4*w] = h_onslice_s
g = np.zeros((2*w, 2*w), dtype=complex)
- g[:w, :w] = leads.square_self_energy(w, t, e)
- g[w:, w:] = leads.square_self_energy(w, t, e)
+ g[:w, :w] = leads.square_selfenergy(w, t, e)
+ g[w:, w:] = leads.square_selfenergy(w, t, e)
assert_almost_equal(g, modes_se(h_onslice, h_hop))
@@ -197,8 +197,8 @@ def test_singular_degenerate_with_crossing():
h_onslice[3*w:4*w, 3*w:4*w] = -h_onslice_s
g = np.zeros((2*w, 2*w), dtype=complex)
- g[:w, :w] = leads.square_self_energy(w, t, e)
- g[w:, w:] = -np.conj(leads.square_self_energy(w, t, e))
+ g[:w, :w] = leads.square_selfenergy(w, t, e)
+ g[w:, w:] = -np.conj(leads.square_selfenergy(w, t, e))
assert_almost_equal(g, modes_se(h_onslice, h_hop))
diff --git a/kwant/physics/tests/test_noise.py b/kwant/physics/tests/test_noise.py
index bf5f1d58..4a9c25bf 100644
--- a/kwant/physics/tests/test_noise.py
+++ b/kwant/physics/tests/test_noise.py
@@ -43,9 +43,9 @@ class LeadWithOnlySelfEnergy(object):
def __init__(self, lead):
self.lead = lead
- def self_energy(self, energy, args=()):
+ def selfenergy(self, energy, args=()):
assert args == ()
- return self.lead.self_energy(energy)
+ return self.lead.selfenergy(energy)
def test_twoterminal():
diff --git a/kwant/solvers/common.py b/kwant/solvers/common.py
index 55a09560..7ec7b61c 100644
--- a/kwant/solvers/common.py
+++ b/kwant/solvers/common.py
@@ -224,7 +224,7 @@ class SparseSolver(object):
# See comment about zero-shaped sparse matrices at the top.
rhs.append(np.zeros((lhs.shape[1], 0)))
else:
- sigma = lead.self_energy(energy, args)
+ sigma = lead.selfenergy(energy, args)
lead_info.append(sigma)
indices = np.r_[tuple(slice(offsets[i], offsets[i + 1])
for i in interface)]
diff --git a/kwant/solvers/tests/_test_sparse.py b/kwant/solvers/tests/_test_sparse.py
index 38460be5..16c6ac90 100644
--- a/kwant/solvers/tests/_test_sparse.py
+++ b/kwant/solvers/tests/_test_sparse.py
@@ -21,9 +21,9 @@ class LeadWithOnlySelfEnergy(object):
def __init__(self, lead):
self.lead = lead
- def self_energy(self, energy, args=()):
+ def selfenergy(self, energy, args=()):
assert args == ()
- return self.lead.self_energy(energy)
+ return self.lead.selfenergy(energy)
# Test output sanity: that an error is raised if no output is requested,
@@ -273,7 +273,7 @@ def test_tricky_singular_hopping(solve):
# Test equivalence between self-energy and scattering matrix representations.
# Also check that transmission works.
-def test_self_energy(solve):
+def test_selfenergy(solve):
np.random.seed(4)
system = kwant.Builder()
left_lead = kwant.Builder(kwant.TranslationalSymmetry((-1,)))
@@ -316,7 +316,7 @@ def test_self_energy(solve):
assert_almost_equal(t_should_be, sol.transmission(1, 0))
-def test_self_energy_reflection(solve):
+def test_selfenergy_reflection(solve):
np.random.seed(4)
system = kwant.Builder()
left_lead = kwant.Builder(kwant.TranslationalSymmetry((-1,)))
diff --git a/kwant/solvers/tests/test_mumps.py b/kwant/solvers/tests/test_mumps.py
index 01f7d6cc..2b1b8b15 100644
--- a/kwant/solvers/tests/test_mumps.py
+++ b/kwant/solvers/tests/test_mumps.py
@@ -81,19 +81,19 @@ def test_tricky_singular_hopping():
@skipif(_no_mumps)
-def test_self_energy():
+def test_selfenergy():
for opts in opt_list:
reset_options()
options(**opts)
- _test_sparse.test_self_energy(solve)
+ _test_sparse.test_selfenergy(solve)
@skipif(_no_mumps)
-def test_self_energy_reflection():
+def test_selfenergy_reflection():
for opts in opt_list:
reset_options()
options(**opts)
- _test_sparse.test_self_energy_reflection(solve)
+ _test_sparse.test_selfenergy_reflection(solve)
@skipif(_no_mumps)
diff --git a/kwant/solvers/tests/test_sparse.py b/kwant/solvers/tests/test_sparse.py
index 9f3edd69..46b58a16 100644
--- a/kwant/solvers/tests/test_sparse.py
+++ b/kwant/solvers/tests/test_sparse.py
@@ -39,12 +39,12 @@ def test_tricky_singular_hopping():
_test_sparse.test_tricky_singular_hopping(solve)
-def test_self_energy():
- _test_sparse.test_self_energy(solve)
+def test_selfenergy():
+ _test_sparse.test_selfenergy(solve)
-def test_self_energy_reflection():
- _test_sparse.test_self_energy_reflection(solve)
+def test_selfenergy_reflection():
+ _test_sparse.test_selfenergy_reflection(solve)
def test_very_singular_leads():
diff --git a/kwant/system.py b/kwant/system.py
index 5e557d2b..cfc1e413 100644
--- a/kwant/system.py
+++ b/kwant/system.py
@@ -69,7 +69,7 @@ class FiniteSystem(System):
------------------
leads : sequence of lead objects
Each lead has to provide a method
- ``self_energy(energy, args)`` or ``modes(energy, args)``.
+ ``selfenergy(energy, args)`` or ``modes(energy, args)``.
lead_interfaces : sequence of sequences of integers
Each sub-sequence contains the indices of the system sites to which the
lead is connected.
@@ -78,7 +78,7 @@ class FiniteSystem(System):
-----
The length of `leads` must be equal to the length of `lead_interfaces`.
- For lead ``n``, the method leads[n].self_energy must return a square matrix
+ For lead ``n``, the method leads[n].selfenergy must return a square matrix
whose size is ``sum(self.num_orbitals(neighbor)`` for neighbor in
self.lead_interfaces[n])``. The output format for ``leads[n].modes`` is more
complicated, and it should match the output of `~kwant.physics.modes`.
@@ -161,10 +161,10 @@ class InfiniteSystem(System):
ham.flat[::ham.shape[0] + 1] -= energy
return physics.modes(ham, self.inter_slice_hopping(args=args))
- def self_energy(self, energy, args=()):
+ def selfenergy(self, energy, args=()):
"""Return self-energy of a lead.
The returned matrix has the shape (n, n), where n is
``sum(self.num_orbitals(i) for i in range(self.slice_size))``.
"""
- return physics.self_energy(self.modes(energy, args=()))
+ return physics.selfenergy(self.modes(energy, args=()))
--
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