From cb8540823ddde113dd924245665b1d9fc4fccd61 Mon Sep 17 00:00:00 2001
From: Anton Akhmerov <anton.akhmerov@gmail.com>
Date: Sat, 20 Jul 2013 12:43:13 +0200
Subject: [PATCH] update docs, add whatsnew entry
---
doc/source/reference/kwant.physics.rst | 3 ++-
doc/source/reference/kwant.system.rst | 1 +
doc/source/whatsnew/1.0.rst | 14 ++++++++++++++
kwant/builder.py | 10 ++++++----
kwant/physics/leads.py | 14 +++++++-------
kwant/system.py | 16 ++++++++--------
6 files changed, 38 insertions(+), 20 deletions(-)
diff --git a/doc/source/reference/kwant.physics.rst b/doc/source/reference/kwant.physics.rst
index 7b202da0..2c457f56 100644
--- a/doc/source/reference/kwant.physics.rst
+++ b/doc/source/reference/kwant.physics.rst
@@ -12,4 +12,5 @@ Leads
modes
selfenergy
selfenergy_from_modes
- ModesTuple
+ PropagatingModes
+ StabilizedModes
diff --git a/doc/source/reference/kwant.system.rst b/doc/source/reference/kwant.system.rst
index 00065e6a..826eed55 100644
--- a/doc/source/reference/kwant.system.rst
+++ b/doc/source/reference/kwant.system.rst
@@ -20,3 +20,4 @@ the interface defined here.
System
InfiniteSystem
FiniteSystem
+ PrecalculatedLead
diff --git a/doc/source/whatsnew/1.0.rst b/doc/source/whatsnew/1.0.rst
index 13c8f574..597c3c93 100644
--- a/doc/source/whatsnew/1.0.rst
+++ b/doc/source/whatsnew/1.0.rst
@@ -159,6 +159,20 @@ solver, using the method `~kwant.system.FiniteSystem.precalculate`. This may
save time, when the linear system has to be solved many times with the same
lead parameters.
+Change of the modes and lead_info format
+----------------------------------------
+The `~kwant.physics.modes` now returns two objects:
+`~kwant.physics.PropagatingModes` and `~kwant.physics.StabilizedModes`. The
+first one contains the wave functions of all the propagating modes in real
+space, as well as their velocities and momenta. All these quantities were
+previously not directly available. The second object contains the propagating
+and evanescent modes in the compressed format expected by the sparse solver
+(previously this was the sole output of `~kwant.physics.modes`). Accordingly,
+the `lead_info` attribute of `~kwant.solvers.default.BlockResult` contains the
+real space information about the modes in the leads (a list of
+`~kwant.physics.PropagatingModes` objects).
+
+
Inclusion of contributed modules
--------------------------------
kwant now contains a sub-package :mod:`kwant.contrib` that contains various
diff --git a/kwant/builder.py b/kwant/builder.py
index 14fbd3cb..c53592e8 100644
--- a/kwant/builder.py
+++ b/kwant/builder.py
@@ -471,10 +471,12 @@ class ModesLead(Lead):
Parameters
----------
modes_func : function
- Function which returns the modes of the lead in the format specified
- in `~kwant.physics.ModesTuple` given the energy and optionally a list of
- extra arguments.
- interface : sequence of `Site` instances
+ Function which returns the modes of the lead as a tuple of
+ `~kwant.physics.PropagatingModes` and `~kwant.physics.StabilizedModes`
+ given the energy and optionally a list of extra arguments.
+ interface :
+ sequence of `Site` instances
+
"""
def __init__(self, modes_func, interface):
self._modes_func = modes_func
diff --git a/kwant/physics/leads.py b/kwant/physics/leads.py
index b9407f2c..313bd5a1 100644
--- a/kwant/physics/leads.py
+++ b/kwant/physics/leads.py
@@ -31,13 +31,7 @@ class PropagatingModes(object):
Instance variables
==================
wave_functions : numpy array
- The wave functions of the propagating modes. The first dimension
- corresponds to sites in a unit cell, the second one to the number of
- the mode. Each mode is normalized to carry unit current. If several
- modes have the same momentum and velocity, an arbitrary orthonormal
- basis in the subspace of these modes is chosed. The first half of the
- modes are incoming (having negative velocity), the second half is
- outgoing (having positive velocity). momenta : numpy array
+ The wave functions of the propagating modes.
momenta : numpy array
Momenta of the modes.
velocities : numpy array
@@ -49,6 +43,12 @@ class PropagatingModes(object):
modes have negative velocity, the second half have positive velocity. The
modes with negative velocity are ordered from larger to lower momenta, the
modes with positive velocity vice versa.
+
+ The first dimension of the `wave_functions` corresponds to sites in a unit
+ cell, the second one to the number of the mode. Each mode is normalized to
+ carry unit current. If several modes have the same momentum and velocity,
+ an arbitrary orthonormal basis in the subspace of these modes is
+ chosen.
"""
def __init__(self, wave_functions, velocities, momenta):
kwargs = locals()
diff --git a/kwant/system.py b/kwant/system.py
index c6843a99..2057e39e 100644
--- a/kwant/system.py
+++ b/kwant/system.py
@@ -14,7 +14,6 @@ __all__ = ['System', 'FiniteSystem', 'InfiniteSystem']
import abc
import types
from copy import copy
-import numpy as np
from . import physics, _system
@@ -73,12 +72,13 @@ class FiniteSystem(System):
For lead ``n``, the method leads[n].selfenergy must return a square matrix
whose size is ``sum(len(self.hamiltonian(site, site)) for site in
- self.lead_interfaces[n])``. The output format for ``leads[n].modes`` has to
- be as described in `~kwant.physics.ModesTuple`.
+ self.lead_interfaces[n])``. The output of ``leads[n].modes`` has to be a
+ tuple of `~kwant.physics.PropatatingModes, ~kwant.physics.StabilizedModes`.
Often, the elements of `leads` will be instances of `InfiniteSystem`. If
this is the case for lead ``n``, the sites ``lead_interfaces[n]`` match
the first ``len(lead_interfaces[n])`` sites of the InfiniteSystem.
+
"""
__metaclass__ = abc.ABCMeta
@@ -194,8 +194,8 @@ class InfiniteSystem(System):
def modes(self, energy=0, args=()):
"""Return mode decomposition of the lead
- See documentation of `~kwant.physics.ModesTuple` for the return
- format details.
+ See documentation of `~kwant.physics.PropagatingModes` and
+ `~kwant.physics.StabilizedModes` for the return format details.
"""
ham = self.cell_hamiltonian(args=args)
shape = ham.shape
@@ -209,8 +209,8 @@ class InfiniteSystem(System):
"""Return self-energy of a lead.
The returned matrix has the shape (s, s), where s is
- ``sum(len(self.hamiltonian(i, i))
- for i in range(self.graph.num_nodes - self.cell_size))``.
+ ``sum(len(self.hamiltonian(i, i)) for i in range(self.graph.num_nodes -
+ self.cell_size))``.
"""
ham = self.cell_hamiltonian(args=args)
shape = ham.shape
@@ -227,7 +227,7 @@ class PrecalculatedLead(object):
Parameters
----------
- modes : kwant.physics.ModesTuple
+ modes : (kwant.physics.PropagatingModes, kwant.physics.StabilizedModes)
Modes of the lead.
selfenergy : numpy array
Lead self-energy.
--
GitLab