From eca8e38f8a3867eb64992ad2e2a95c7922e29573 Mon Sep 17 00:00:00 2001
From: Anton Akhmerov <anton.akhmerov@gmail.com>
Date: Sun, 28 Apr 2013 16:27:53 -0400
Subject: [PATCH] restore selfenergy to accept h, t, introduce
selfenergy_from_modes
---
doc/source/whatsnew/0.3.rst | 3 ---
kwant/builder.py | 2 +-
kwant/physics/leads.py | 38 +++++++++++++++++++++++++------
kwant/physics/tests/test_leads.py | 2 +-
kwant/system.py | 14 ++++++++----
5 files changed, 43 insertions(+), 16 deletions(-)
diff --git a/doc/source/whatsnew/0.3.rst b/doc/source/whatsnew/0.3.rst
index 3ce75445..eaaf78ce 100644
--- a/doc/source/whatsnew/0.3.rst
+++ b/doc/source/whatsnew/0.3.rst
@@ -133,6 +133,3 @@ responsibility.
The new class `~kwant.builder.ModesLead` allows to attach leads that have a
custom way of calculating their modes (e.g. ideal leads) directly to a
`~kwant.builder.Builder`.
-
-`~kwant.physics.selfenergy` now uses the output of `~kwant.physics.modes` as
-input instead of the slice Hamiltonian and inter-slice hopping.
diff --git a/kwant/builder.py b/kwant/builder.py
index 8dbc29a9..6869c547 100644
--- a/kwant/builder.py
+++ b/kwant/builder.py
@@ -481,7 +481,7 @@ class ModesLead(Lead):
def selfenergy(self, energy, args=()):
modes = self.modes(energy, args)
- return physics.selfenergy(modes=modes)
+ return physics.selfenergy_from_modes(modes=modes)
diff --git a/kwant/physics/leads.py b/kwant/physics/leads.py
index a9a630e9..dec942ef 100644
--- a/kwant/physics/leads.py
+++ b/kwant/physics/leads.py
@@ -503,20 +503,15 @@ def modes(h_onslice, h_hop, tol=1e6):
return Modes(vecs, vecslmbdainv, nmodes, v)
-def selfenergy(lead_modes, tol=1e6):
+def selfenergy_from_modes(lead_modes):
"""
- Compute the self-energy generated by a lead.
-
- The lead is described either by the unit-cell Hamiltonian h_onslice and the
- hopping matrix h_hop, or by its modes.
+ Compute the self-energy generated by lead modes.
Parameters
----------
lead_modes : Modes(vecs, vecslmbdainv, nmodes, v) a named tuple
The modes in the lead, as calculated by
`kwant.physics.modes`.
- tol : double
- Numerical tolerance used in several places.
Returns
-------
@@ -539,6 +534,35 @@ def selfenergy(lead_modes, tol=1e6):
return la.solve(vecslmbdainv.T, vecs.T).T
+def selfenergy(h_onslice, h_hop, tol=1e6):
+ """
+ Compute the self-energy generated by the lead.
+
+ Parameters
+ ----------
+ h_onslice : numpy array, real or complex, shape (N,N) The unit cell
+ Hamiltonian of the lead slice.
+ h_hop : numpy array, real or complex, shape (N,M)
+ The hopping matrix from a lead slice to the one on which self-energy
+ has to be calculated (and any other hopping in the same direction).
+ tol : float
+ Tolerance for numerical error.
+
+ Returns
+ -------
+ Sigma : numpy array, real or complex, shape (M,M)
+ The computed self-energy. Note that even if `h_onslice` and `h_hop`
+ are both real, `Sigma` will typically be complex. (More precisely, if
+ there is a propagating mode, `Sigma` will definitely be complex.)
+
+ Notes
+ -----
+ For simplicity this function internally calculates the modes first.
+ This may cause a small slowdown, and can be improved if necessary.
+ """
+ return selfenergy_from_modes(modes(h_onslice, h_hop, tol))
+
+
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 e182fa8c..0ec651be 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.selfenergy(leads.modes(h, t))
+modes_se = leads.selfenergy
def h_slice(t, w, e):
h = (4 * t - e) * np.identity(w)
diff --git a/kwant/system.py b/kwant/system.py
index fc5eb368..d07d54ed 100644
--- a/kwant/system.py
+++ b/kwant/system.py
@@ -148,10 +148,10 @@ class InfiniteSystem(System):
sparse=sparse, args=args)
def modes(self, energy, args=()):
- """Return self-energy of a lead.
+ """Return mode decomposition of the lead
- The returned matrix has the shape (n, n), where n is
- ``sum(self.num_orbitals(i) for i in range(self.slice_size))``.
+ See documentation of `~kwant.physics.Modes` for the return
+ format details.
"""
ham = self.slice_hamiltonian(args=args)
shape = ham.shape
@@ -167,4 +167,10 @@ class InfiniteSystem(System):
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.selfenergy(self.modes(energy, args=()))
+ ham = self.slice_hamiltonian(args=args)
+ shape = ham.shape
+ assert len(shape) == 2
+ assert shape[0] == shape[1]
+ # Subtract energy from the diagonal.
+ ham.flat[::ham.shape[0] + 1] -= energy
+ return physics.selfenergy(ham, self.inter_slice_hopping(args=args))
--
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