allow computations even if a discrete symmetry is broken

Closes #236 and #242

See merge request kwant/kwant!257

Previously if there were more site families than colours in the
matplotlib cycle, then plotting would raise an exception. Now
we cycle through the colours indefinitely.

Closes #257

This was fixed on stable, but due to interim changes and a badly
solved merge conflict, the fix was not applied to master.

This has a lower chance to give an impression that the substitution
happens in-place.

Closes gitlab issue #237

The 'mpl_available' flag was relegated to '_plotter' in
the development version, but the check in the test was still
referring to 'plotter'. The change 'plotter → _plotter' was
made on the development version, so this fix does not need to
be backported to the stable branch.

Currently we test against 5 environments: Ubuntu LTS, Debian stable,
minimum required dependency versions from conda forge, minimum
required dependencies without extras (sympy and matplotlib), and latest
dependency versions from conda forge.

Dániel Varjas authored 7 years ago and Joseph Weston committed 6 years ago

Improve the logic of 'cvp', now it provably works in all cases.
Add 'reduced' option to 'linalg.lll.voronoi', this eliminates
superfluous Voronoi vectors that do not have a corresponding face
of the Voronoi cell, or this face would be smaller than 'rtol'.

Simplify 'lattice.Polyatomic.neighbors' by providing the option
to group equidistant vectors 'group_by_length' in 'linalg.lll.cvp'.

See !165 for details.

Closes #163.

builder.fill: Make starting sites that are not in the template a warning, and improve the warning message in this case.

See merge request kwant/kwant!244

We raise a warning and remove the sites from 'start', so as to avoid
cryptic 'KeyError's later.

Also take an early exit if there are no starting sites in the template,
to avoid a spurious warning about all starting sites already being
present in the target.

Closes #224.

This is the standard way to re-raise errors and makes the messages
easier to follow.

Simplifications and optimizations of how parameters are handled

Closes #228

See merge request kwant/kwant!243

Christoph Groth authored 6 years ago and Joseph Weston committed 6 years ago

Co-authored-by: Joseph Weston <joseph@weston.cloud>

Christoph Groth authored 6 years ago and Joseph Weston committed 6 years ago

With this, wrapping parameter-substituted value functions is no longer
necessary and any overhead of using builder parameter substitutions
disappears.

Co-authored-by: Joseph Weston <joseph@weston.cloud>

Christoph Groth authored 6 years ago and Joseph Weston committed 6 years ago

Co-authored-by: Joseph Weston <joseph@weston.cloud>

Christoph Groth authored 6 years ago and Joseph Weston committed 6 years ago

and without default values.

Co-authored-by: Joseph Weston <joseph@weston.cloud>

Christoph Groth authored 6 years ago and Joseph Weston committed 6 years ago

This requires changes to other modules, but these were kept to a
minimum.  The most important one is that
builder._FinalizedBuilderMixin.hamiltonian() now always calls value
functions using *args.

So it's no longer necessary to provide the REFNAME environment variable.
Also the link template string format is now more general to support at
least gitlab github and cgit.

Previously we masked points that are further than a "typical" distance
from any site. This was determined as the minimal nearest-neighbor
distance from 10 arbitrarily chosen sites. Now we mask points where
the bump function is zero (as it has finite support).

Closes #219.