Closes #182

version 1.3.2

This commit fixes the bug in phs_symmetrization when it fails to produce ph eigenstates
with PH^2 = +1 when one of the wave functions is mapped exactly onto another one by PH,
as in this case the PH symmetrized wf's from the two are identical. This is the case
with wfs = np.eye(2) and  particle_hole = sigma[1], the second vector returned is an
eigenstate with eigenvalue -1 not +1. In general this can be even worse, if there are
multiple such vector pairs some vectors may not be ph eigenstates at all.

The new code uses an improved version of the matrix square root method from
Applied Mathematics and Computation 234 (2014) 380-384.

Tests are modified to clear up the random unitary generation process (using kwant.rmt).
Tests are now guaranteed to feed orthonormal set of vectors to phs_symmetrization().
Add extra tests for the fully off-diagonal case where the old method fails.

Previously, in order to not to fix the matplotlib backend, we required
users to import matplotlib.pyplot before calling any Kwant plotting
functions.  This did not have the desired effect, since we did import
`matplotlib.backends` and that also fixes the backend.

Now, both backends and pyplot are imported at the last possible moment
and a warning is emitted if this fixes the backend.

The problem was introduced in commit 7c802539.

Closes #47.

Previously it was never made explicit that the current
returned from an operator is ordered like the system graph, or
that the density is ordered as the sites of the system.

Closes #172.

Backport deprecation warning fixes from 'master' to 'stable'
(these changes should have been applied to 'stable' directly).

The lead does not have connected unit cells and serves no purpose.
We also remove the check for the number of 'collections' in the
resulting plots, as now both 'syst_2d' and 'syst_3d' produce
systems with 2 leads.

Improve mode documentation.

See !190 for details.

Previously the fact that the positive direction of mode
velocity is determined by the translational symmetry vector
of the system was not made clear in the relevant docstrings.

Closes #143.

Previously it was never explicitly stated that the wavefunctions
returned by modes() are only defined over the unit cell of the
infinite system. This was confusing, as syst.sites contains
not only the unit cell sites, but also the connected sites in
neighboring cells.

Closes #178.

As of version 1.1.1 Sympy does not include MutableDenseMatrix
in 'all_classes', so expressions containing such terms did not trigger
the warning in kwant.continuum.sympify when 'locals' are provided.

Closes #180.

Previously, when plotting a 3D system with 'site_size' provided
explicity as a sequence, a ValueError would be raised when using
'%matplotlib inline' or '%matplotlib notebook' from a Jupyter
notebook. We do not add a test for this, because that would require
depending on Jupyter.

Closes #39.

This backend does not require a display to be connected,
which is good for tests.

Closes #83.

The lattice constant is never changed from 1, and in addition can be
varied independently of the 't' and 'α' parameters; This should not
be the case if the model is meant to be derived from a discretization
of a continuum model. We remove the lattice constant to limit confusion.

For a spin-orbit term of the form '-iασ_y∂_x' the hopping
for 'HoppingKind((1, 0), lat)' (*from* 'x' *to* 'x + a')
is 'iασ_y/2'.

Closes #175.

Previously, an erroneous current was shown at *zero* magnetic field,
which was due to a choice of degenerate eigenvalue. Now we evaluate
the current and density at finite magnetic field, to demonstrate
the intended effect.

Closes #150.

Rafal Skolasinski authored 7 years ago and Joseph Weston committed 7 years ago

A regression in Sympy causes symbols that are invalid
identifiers to be created, e.g. '-B_x'. While we cannot
fix Sympy's behaviour, we can at least shield our users
from its quirks.

Closes #179.

Previously, the wording of the explanatory comment above
discretized hopping functions was confusing. Now we
are clear about where the hopping originates.

Fixes #173.

Improve error message when creating invalid HoppingKinds

Closes #147, see !183.

The test was using a 2D delta with a 3D site family. This was
not previously raising an error because the HoppingKind in question
was not used for anything (just to test its equality to other
HoppingKinds).

Set correct stack level when issuing warnings, and when
calling API functionality that itself raises warnings.

See #161 and !181.

Some API functions call other API functions that report warnings.
We need to increase the stacklevel so that the user sees their
own line of code in the warning message.

Now the line in the *calling* code will be displayed, which is
more useful for users.

Closes #177.

Kwant no longer needs linking against Lapack directly, as
we use the Lapack provided by Scipy.

Previously, the numpy 'include_dirs' would be shadowed by
any 'include_dirs' provided in 'build.conf'. We want to avoid
burdening people with remembering to specify the numpy 'include_dirs'
every time, and if custom numpy headers is the desired behaviour, these
can still be specified in 'build.conf', and will take precedence.