generate.py

-import os
-import yaml
-from mako.lookup import TemplateLookup
-import pyrtek, pyrtek.rst, pyrtek.mako
-
-
-mako_filter = pyrtek.mako.Filter(TemplateLookup(['../templates']))
-rst_filter = pyrtek.rst.Filter()
-
-filters = {'mako': mako_filter,
-          'rst': rst_filter,
-          'default': pyrtek.chain_filters(rst_filter, mako_filter)}
-
-default_meta = {'__filter__': 'default',
-                '__template__': 'default.mako'}
-
-# rexp, repl, priority, func
-rules = [(r'(.*)\.txt$', r'\1.html', 0,
-          lambda s, d: pyrtek.Text(s, d, filters, default_meta))]
-
-
-def main():
-    # Load catalog, if it exists.
-    try:
-        with open('catalog.yaml') as f:
-            catalog = yaml.load(f)
-    except IOError:
-        catalog = {}
-
-    # The following block of code is executed inside the content directory.
-    saved_cwd = os.getcwd();
-    os.chdir('content')
-    try:
-        catalog = pyrtek.build(pyrtek.expand_rules(rules), catalog)
-    finally:
-        os.chdir(saved_cwd)
-
-    # Save catalog.
-    with open('catalog.yaml', 'w') as f:
-        yaml.dump(catalog, f)
-
-
-if __name__ == '__main__':
-    main()

htaccess-apache

+<IfModule mod_mime.c>
+AddType image/svg+xml svg svgz
+AddEncoding gzip svgz
+</IfModule>
+
+# Do not treat Python files as CGI scripts.
+<FilesMatch \.py$>
+  SetHandler default-handler
+</FilesMatch>
+
+RewriteEngine on
+
+# We don't need more than that.
+RewriteOptions MaxRedirects=2
+
+# Redirect /foo/index.html to /foo/
+RewriteRule ^(|.*/)index\.html$ /$1 [R=301,L]
+
+# Redirect /foo/bar.html to /foo/bar only if a html file was requested by the
+# browser.  Without the condition the following rewrite rule leads to a
+# redirection loop.
+RewriteCond %{THE_REQUEST} ^[A-Z]{3,9}\ /.*\.html\ HTTP/
+RewriteRule ^(.*)\.html$ /$1 [R=301,L]
+
+# Rewrite /foo/bar to /foo/bar.html if the latter exists.
+RewriteCond %{REQUEST_FILENAME}.html -f
+RewriteRule ^(.*[^/])$ /$1.html [L]
+
+# Remove trailing slash if the requested directory does not exist.
+RewriteCond %{REQUEST_FILENAME} !-d
+RewriteRule ^(.*)/$  /$1 [R=301,L]
+
+Redirect 302 /contact /doc/latest/pre/authors
+Redirect 302 /authors /doc/latest/pre/authors
+Redirect 302 /citing /doc/latest/pre/citing
+Redirect 302 /cite /doc/latest/pre/citing
+Redirect 302 /license /doc/latest/pre/license
+Redirect 302 /download /install
+
+# Redirect old tutorial URLs to new ones.
+# The tutorial numbers refer to the tutorial enumeration in Kwant 1.2.x
+Redirect 302 /doc/1/tutorial/tutorial1 /doc/1/tutorial/first_steps
+Redirect 302 /doc/1/tutorial/tutorial2 /doc/1/tutorial/spin_potential_shape
+Redirect 302 /doc/1/tutorial/tutorial3 /doc/1/tutorial/spectrum
+Redirect 302 /doc/1/tutorial/tutorial4 /doc/1/tutorial/graphene
+Redirect 302 /doc/1/tutorial/tutorial5 /doc/1/tutorial/superconductor
+Redirect 302 /doc/1/tutorial/tutorial6 /doc/1/tutorial/plotting

imgsrc/workflow/billiard.py

+import kwant
+import matplotlib.pyplot as pyplot
+from scipy import misc
+import numpy as np
+
+# shape.png is an image containing the system shape colored in black.  Here we
+# read the image from this file, create an empty scattering region, and add to
+# it the sites with coordinates of pixels that we encounter in the image.
+im = misc.imread('billiard-shape.png')[:, :, 0]
+sys = kwant.Builder()
+lat = kwant.lattice.square()
+for pos in np.argwhere(im != 255):
+    sys[lat(pos[1], -pos[0])] = 4
+
+def wire_shape(period, center, r, ymin, ymax):
+    """Return sites from a bounded segment of an infinite wire."""
+    direction = np.array(period / np.linalg.norm(period))
+    def wire_shape(pos):
+        rel_pos = center - pos
+        projection = direction * np.dot(direction, rel_pos) - rel_pos
+        return sum(projection**2) <= r**2 and ymin < pos[1] < ymax
+    return lat.shape(wire_shape, center)
+
+# Directions of the leads, positions of the centers of the lead segments to be
+# attached, and the boundaries of these segments in y-directions.
+wire_dir = [(-1., -1.), (3., -4.), (2., 4.)]
+wire_center = [(166, -236), (216, -106), (246, -86)]
+ylims = [(-400, -200), (-440, -100), (-100, 60)]
+
+# Add segments of leads to the scattering region, and attach leads themselves.
+for direction, center, ylim in zip(wire_dir, wire_center, ylims):
+    sys[wire_shape(direction, np.array(center), 50, *ylim)] = 4
+    lead = kwant.Builder(kwant.TranslationalSymmetry(direction))
+    lead[lat.wire(center, 50)] = 4
+    lead[lat.neighbors()] = -1
+    sys.attach_lead(lead)
+
+# Finally add hoppings to the system, get its wave function, and plot.
+sys[lat.neighbors()] = -1
+sys = sys.finalized()
+wfs = kwant.wave_function(sys, energy=0.14)(0)[0]
+kwant.plotter.map(sys, abs(wfs), oversampling=1, cmap="PuBu")

posts/improved-interface-for-mailing-list.rst

+.. title: Improved web interface for the mailing list
+.. slug: improved-interface-for-mailing-list
+.. date: 2020-05-28 20:00:00 UTC
+.. category: 
+.. type: text
+
+The Kwant mailing list has been migrated to a new server that provides a much-improved web interface.
+
+.. TEASER_END
+
+In May 2020, thanks to the friendly people at python.org,
+kwant-discuss was migrated to a server running Mailman 3.
+The list remains a mailing list (existing subscriptions continue),
+but now also offers a modern web interface that is similar to a web forum.
+The complete archives were migrated and are now searchable.
+Please see the `“community” section </community>`_ of this site for usage information.
+The `old address of the list <kwant-discuss@kwant-project.org>`_ remains usable: any messages are simply redirected to the new one.

posts/kwant-extensions.rst

+.. title: List of Kwant extensions added to website
+.. slug: kwant-extensions
+.. date: 2018-03-28 11:56:55 UTC
+.. tags:
+.. category:
+.. link:
+.. description:
+.. type: text
+
+We have added a `new section to the website </extensions.html>`_
+that showcases useful extensions to Kwant that have been made by members of the
+community.
+
+.. TEASER_END
+
+While we welcome contributions to the core Kwant package, we realize that
+it can be a lot of work to implement something that is both robust enough
+and of sufficiently general interest to be added to Kwant directly.
+
+Nevertheless there is a body of existing software that extends Kwant in ways
+that could be useful to others in the Kwant community. We hope that providing
+a central place for listing these extensions will make them more discoverable
+by others.
+
+If you have extended Kwant in some way, please get in touch via the
+`kwant-devel <mailto:kwant-devel@kwant-project.org>`_ mailing list!
+
+Happy Kwanting,
+
+Kwant team

posts/kwant-faq-intro.rst

+.. title: Kwant adds an FAQ to the documentation
+.. slug: kwant-faq-intro
+.. date: 2017-06-29 07:07:23 UTC
+.. tags: 
+.. category: 
+.. link: 
+.. description: 
+.. type: text
+
+The Kwant team in Grenoble is currently hosting a masters student, Paul Clisson,
+who has taken the initiative and written a "Frequently Asked
+Questions" (FAQ) section to complement the existing Kwant tutorial; thanks Paul!
+
+.. TEASER_END
+
+A preliminary version of of the FAQ is already available
+`here <https://test.kwant-project.org/doc/doc-faq/tutorial/FAQ>`_. Any and all
+user feedback is valuable to us, so tell us what you think! You can either join
+the `discussion on the mailing
+list <https://www.mail-archive.com/kwant-discuss@kwant-project.org/msg01313.html>`_
+or comment on the open `merge
+request <https://gitlab.kwant-project.org/kwant/kwant/merge_requests/148>`_ on
+the Kwant gitlab.
+
+Happy Kwanting,
+
+Kwant team

posts/release-of-kwant-13.rst

+.. title: Release of Kwant 1.3
+.. slug: release-of-kwant-13
+.. date: 2017-05-24 21:17:10 UTC
+.. category: release-announcement
+.. type: text
+
+After more than one year of development, we are extremely pleased to announce the release of Kwant 1.3.
+
+.. TEASER_END
+
+Kwant 1.3 supports
+
+* discretizing of continuum Hamiltonians,
+* calculating and displaying local densities and currents,
+* declaring and using symmetries and conservation laws,
+* calculating bulk properties using the kernel polynomial method,
+* finalizing builders with multiple translational symmetries,
+
+and has many other improvements that are detailed in the `what's new in Kwant 1.3 </doc/1/pre/whatsnew/1.3>`_ document.
+
+The `installation instructions </install.html>`_ have been updated to explain how to install Kwant 1.3 on computers running GNU/Linux, Mac OS, and Windows.  Note that thanks to the package manager Conda it is now much easier to install Kwant under Mac OS and on Unix accounts without root privileges.
+
+The new version is practically 100% backwards-compatible with scripts written for previous versions of Kwant 1.x.
+
+The Kwant team is happy to welcome Joseph Weston as a member.  We are also grateful to the many contributors without whom this release would not be nearly as good:
+
+* Jörg Behrmann
+* Bas Nijholt
+* Michał Nowak
+* Viacheslav Ostroukh
+* Pablo Pérez Piskunow
+* Tómas Örn Rosdahl
+* Sebastian Rubbert
+* Rafał Skolasiński
+* Adrien Sorgniard
+
+We would like to hear your feedback at kwant-discuss@kwant-project.org.

posts/release-of-kwant-14.rst

+.. title: Release of Kwant 1.4
+.. slug: release-of-kwant-14
+.. date: 2019-03-06 11:46:18 UTC
+.. category: release-announcement
+.. type: text
+
+We are pleased to announce the release of Kwant 1.4, the result of a year and a half of development.
+
+.. TEASER_END
+
+Highlights of the new release:
+
+* Adding magnetic field to systems, even in complicated cases, is now specially supported.
+* The KPM module can now calculate conductivities.
+* The `Qsymm library <https://gitlab.kwant-project.org/qt/qsymm>`_ for Hamiltonian symmetry analysis has been integrated.
+* The handling of system parameters has been improved and optimized.
+* Plotting has been improved, most notably through the addition of a routine that plots densities with interpolation.
+* Installing Kwant on Windows is now much easier thanks to Conda packages.
+
+All these and other improvements that are detailed in the `what's new in Kwant 1.4 </doc/1/pre/whatsnew/1.4>`_ document.  The new version is practically 100% backwards-compatible with scripts written for previous versions of Kwant 1.x.
+
+The following people contributed code to this release:
+
+* Anton Akhmerov
+* Paul Clisson
+* Christoph Groth
+* Thomas Kloss
+* Bas Nijholt
+* Pablo Pérez Piskunow
+* Tómas Örn Rosdahl
+* Rafał Skolasiński
+* Dániel Varjas
+* Joseph Weston
+
+We would like to hear your feedback at kwant-discuss@kwant-project.org.

posts/release-of-tkwant-1-0.rst

+.. title: Release of TKwant 1.0
+.. slug: release-of-tkwant-1-0
+.. date: 2020-09-08 15:00:00 UTC
+.. category: release-announcement
+.. type: text
+
+We are pleased to announce the first release of TKwant,
+a Kwant extension for time-resolved quantum transport.
+
+.. TEASER_END
+
+A system is defined in TKwant in the same way as in Kwant except that some terms in the Hamiltonian may depend on the time parameter. Any system that can be studied in Kwant can be studied with TKwant as well. Typical problems where TKwant can be used include the propagation of voltage pulses, spectroscopy of interferometers, Floquet topological insulators, time resolved Andreev reflection and more.
+
+An introduction to TKwant can be found in `TKwant paper <https://arxiv.org/abs/2009.03132>`_. The software itself and
+its tutorials are available on the `TKwant website <https://tkwant.kwant-project.org/>`_.

pyrtek/__init__.py

-import os, os.path
-import re
-import abc
-import logging
-import yaml
-
-log = logging.getLogger(__name__)
-
-class Item(object):
-    __metaclass__ = abc.ABCMeta
-
-    @abc.abstractproperty
-    def name(self):
-        pass
-
-    def isuptodate(self, oldmeta, catalog):
-        return False
-
-    def render(self, catalog):
-        """Render the item, return re-generated metadata."""
-        pass
-
-
-class Text(Item):
-    def __init__(self, source, dest, filters, default_meta={}):
-        self.source = source
-        self.dest = dest
-        self.filters = filters
-        self.default_meta = default_meta
-
-    def __repr__(self):
-        return '<{0}({1}, {2}, ...)>'.format(
-            self.__class__.__name__, self.source, self.dest)
-
-    @property
-    def name(self):
-        return self.dest
-
-    def render(self, catalog):
-        meta = self.default_meta.copy()
-
-        # Initialize data and metadata from source file.
-        with open(self.source) as f:
-            data = f.read().decode('utf-8')
-        if data.startswith('---\n'):
-            meta_yaml, data = data.split('\n---\n', 1)
-            meta.update(yaml.safe_load(meta_yaml[4:]))
-
-        # Appply filter.
-        try:
-            filter_name = meta['__filter__']
-        except KeyError:
-            log.error('{0}: No __filter__ defined.'.format(self.source))
-        else:
-            try:
-                filter = self.filters[filter_name]
-            except KeyError:
-                log.error('{0}: No filter {0}.'.format(filter_name))
-            else:
-                data, meta = filter(data, meta, self.dest, catalog)
-
-        # Write filtered data to destination file.
-        with open(self.dest, 'w') as f:
-            f.write(data.encode('utf-8'))
-
-        return meta
-
-
-def build(items, old_catalog={}):
-    catalog = {}
-
-    for item in items:
-        name = item.name
-        meta = old_catalog.get(name)
-        if meta is None or not item.isuptodate(meta, catalog):
-            meta = item.render(catalog)
-        if name in catalog:
-            log.warning('{0} already present.'.format(name))
-        catalog[name] = meta
-
-    return catalog
-
-
-def chain_filters(*filters):
-    def chained(data, meta, name, catalog):
-        for filter in filters:
-            data, meta = filter(data, meta, name, catalog)
-        return data, meta
-
-    return chained
-
-
-def expand_rules(rules):
-    rules = [(rexp if hasattr(rexp, 'match') else re.compile(rexp),
-             repl, priority, func)
-             for rexp, repl, priority, func in rules]
-
-    priority_item_seq = []
-    for root, dirs, files in os.walk('.'):
-        for file in files:
-            # For security, do not follow symlinks.
-            source = os.path.join(root, file)
-            if os.path.islink(os.path.join(root, file)):
-                log.warn('Ignoring symlink: {0}'.format(source))
-                continue
-            for rexp, repl, priority, func in rules:
-                if not rexp.match(source):
-                    continue
-                dest = rexp.sub(repl, source)
-                priority_item_seq.append((priority, func(source, dest)))
-
-    priority_item_seq.sort(key=lambda p_i: p_i[0])
-    return [i for p, i in priority_item_seq]

pyrtek/mako.py

-import logging
-
-log = logging.getLogger(__name__)
-
-class Filter(object):
-    def __init__(self, lookup):
-        self.lookup = lookup
-
-    def __call__(self, data, meta, name, catalog):
-        try:
-            template_name = meta['__template__']
-        except KeyError:
-            log.error('{0}: No __template__ defined.'.format(name))
-            return None, meta
-
-        # TODO: surround with try-block
-        template = self.lookup.get_template(template_name)
-        data = template.render(body=data, name=name, meta=meta, catalog=catalog)
-
-        return data, meta

pyrtek/rst.py

-import logging
-import docutils.core, docutils.nodes, docutils.io, docutils as du
-
-log = logging.getLogger(__name__)
-
-class Filter(object):
-    def __call__(self, data, meta, name, catalog):
-        doctree = du.core.publish_doctree(data)
-        parts = du.core.publish_parts(doctree, reader_name='doctree',
-                                      source_class=du.io.DocTreeInput,
-                                      writer_name='html')
-        data = parts['html_body']
-        meta.setdefault('title', parts['title'])
-        meta.setdefault('subtitle', parts['subtitle'])
-        return data, meta

serve.py

-# Taken from
-# http://www.linuxjournal.com/content/tech-tip-really-simple-http-server-python
-
-import os
-import BaseHTTPServer
-from SimpleHTTPServer import SimpleHTTPRequestHandler
-
-
-HandlerClass = SimpleHTTPRequestHandler
-ServerClass  = BaseHTTPServer.HTTPServer
-Protocol     = "HTTP/1.0"
-
-server_address = ('127.0.0.1', 8000)
-
-HandlerClass.protocol_version = Protocol
-httpd = ServerClass(server_address, HandlerClass)
-
-sa = httpd.socket.getsockname()
-print "Serving HTTP on", sa[0], "port", sa[1], "..."
-os.chdir('content')
-httpd.serve_forever()

templates/base.mako

-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"
-"http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" lang="en">
-
-<head>
-<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
-<link href="/common/kwant.css" rel="stylesheet" type="text/css" />
-<title><%block name="title">kwant: quantum transport simulation package</%block></title>
-<link rel="icon" href="/common/kwant_icon.png" type="image/png" />
-<%block name="extra_head" />\
-</head>
-
-<body>
-<div id="header" class="meta">
-  <a href="/"><img alt="kwant_logo.png" src="/common/kwant_logo.png" /></a>
-<h3 class="hidden_structure">Navigation</h3>
-<ul class="navigation">
-  <li><a href="/">home</a></li>
-  <li><a href="/install.html">install</a></li>
-  <li><a href="/docs/">documentation</a></li>
-  <li><a href="/citing.html">citing</a></li>
-  <li><a href="/contribute.html">contribute</a></li>
-  <li><a href="/contact.html">contact</a></li>
-</ul>
-</div>
-
-${next.body()}\
-<%block name="tail"></%block>\
-</body>
-
-</html>

templates/default.mako

-<%inherit file="base.mako"/>\
-<%block name="title">${meta['title']} - kwant</%block>\
-${body}\

themes/kwant/assets/css/custom.css

+h1 {
+    text-align: center;
+}
+
+footer {
+    text-align: center;
+    margin-top: 1em;
+    padding-top: 0.3em;
+    border-top-style: solid;
+    border-top-color: #EEEEEE;
+    border-top-width: medium;
+}
+
+.nomargin {
+    margin-left: 0px;
+    margin-right: 0px;
+}
+
+/* Enable hyphenation. */
+body {
+    text-align:justify;
+    -webkit-hyphens: auto;
+    -moz-hyphens: auto;
+    -ms-hyphens: auto;
+    -o-hyphens: auto;
+    hyphens: auto;
+}
+tt, pre {
+    -webkit-hyphens: none;
+    -moz-hyphens: none;
+    -ms-hyphens: none;
+    -o-hyphens: none;
+    hyphens: none;
+}
+
+/* Navbar styling */
+
+.navbar-nav>li {
+    display: table-cell;
+    text-align: center;
+}
+
+.navbar-nav > li > a:hover {
+    text-decoration:underline;
+}
+
+.navbar-brand {
+    float: none;
+}
+
+.navbar-collapse {
+  text-align:center;
+}
+
+.navbar-nav {
+    display:inline-block;
+    float:none;
+}
+
+/* Index page workflow image styling */
+
+.workflow-image {
+    padding-bottom: 20px;
+}
+
+/* Post list styling */
+
+ul.post-list {
+    list-style-type: none;
+    padding-left: 0;
+}
+
+li.post-list-item {
+    padding-bottom: 5px;
+}
+
+li.post-list-item .post-item-title {
+    display: inline;
+    font-size: 1.1em;
+}
+
+/* Kwant uses list */
+#kwant-uses-list {
+    list-style-type: none;
+    padding-left: 0;
+}
+
+#kwant-uses-list > li {
+    padding: .5em 0 .4em;
+    border-bottom: 1px solid #caccce;
+}
+
+.entry-title {
+    display: inline;
+}
+
+.postindex article.post-text {
+    border-bottom: 1px solid #caccce;
+    margin-bottom: .5em;
+}
+
+/* documentation links */
+
+ul.docs-list {
+    padding-left: 0 ;
+    line-height: 2.5em ;
+}
+
+ul.docs-list ul {
+    padding-left: 20px;
+}
+
+ul.docs-list > li {
+    display: flex ;
+}
+
+ul.docs-list > li li {
+    display:inline ;
+}
+
+
+
+ul.inline-list {
+    display: inline ;
+    padding-left: 10px ;
+}
+
+ul.inline-list li{
+    display: inline ;
+}
+
+
+
+/* give button-like appearance to links, adapted from python.org */
+
+.button-links a{
+    display: inline ;
+    vertical-align: baseline ;
+    width: auto ;
+    cursor: pointer ;
+    margin-bottom: .5em ;
+    padding: .4em .75em .35em ;
+    text-align: left ;
+    white-space: nowrap ;
+    border-radius: 6px ;
+    background-color: #eeeeee ;
+    text-decoration: none ;
+}
+
+.button-links a:hover {
+    background-color: #dddddd ;
+}
+
+/* target the "stable version" link. This is a massive hack, but we're
+   not web developers */
+ul.docs-list > li:first-child > ul:nth-child(2) > li:first-child > a {
+    background-color: #0077cc ;
+    color: #eeeeee ;
+}
+
+ul.docs-list > li:first-child > ul:nth-child(2) > li:first-child > a:hover {
+    background-color: #0055aa ;
+}