doc/source/_static/kwant.css

-@import "default.css";
-
-/**
- * Spacing fixes
-
-
-div.body p, div.body dd, div.body li {
-  line-height: 125%;
-}
-
-ul.simple {
-    margin-top: 0;
-    margin-bottom: 0;
-    padding-top: 0;
-    padding-bottom: 0;
-}
-*/
-
-/* spacing around blockquoted fields in parameters/attributes/returns */
-/*Essential. Otherwise there is way too much space around*/
-td.field-body > blockquote {
-    margin-top: 0.1em;
-    margin-bottom: 0.5em;
-}
-
-/* THE NEXT TWO ARE EVENTUALLY IMPORTANT I THINK */
-/* spacing around example code
-div.highlight > pre {
-    padding: 2px 5px 2px 5px;
-}
-*/
-
-/* spacing in see also definition lists
-dl.last > dd {
-    margin-top: 1px;
-    margin-bottom: 5px;
-    margin-left: 30px;
-}
-*/
-/* hide overflowing content in the sidebar
-div.sphinxsidebarwrapper p.topless {
-    overflow: hidden;
-}
-*/
-
-/**
- * Hide dummy toctrees
-
-
-ul {
-  padding-top: 0;
-  padding-bottom: 0;
-  margin-top: 0;
-  margin-bottom: 0;
-}
-ul li {
-  padding-top: 0;
-  padding-bottom: 0;
-  margin-top: 0;
-  margin-bottom: 0;
-}
-ul li a.reference {
-  padding-top: 0;
-  padding-bottom: 0;
-  margin-top: 0;
-  margin-bottom: 0;
-}
-
-*/
-
-/**
- * Make high-level subsections easier to distinguish from top-level ones
-
-div.body h3 {
-  background-color: transparent;
-}
-
-div.body h4 {
-  border: none;
-  background-color: transparent;
-}
-*/
-
-/**
- * Scipy colors
-
-body {
-  background-color: rgb(100,135,220);
-}
-
-div.document {
-  background-color: rgb(230,230,230);
-}
-
-div.sphinxsidebar {
-  background-color: rgb(230,230,230);
-}
-
-div.related {
-  background-color: rgb(100,135,220);
-}
-
-div.sphinxsidebar h3 {
-  color: rgb(0,102,204);
-}
-
-div.sphinxsidebar h3 a {
-  color: rgb(0,102,204);
-}
-
-div.sphinxsidebar h4 {
-  color: rgb(0,82,194);
-}
-
-div.sphinxsidebar p {
-  color: black;
-}
-
-div.sphinxsidebar a {
-  color: #355f7c;
-}
-
-div.sphinxsidebar ul.want-points {
-  list-style: disc;
-}
-*/
-
-.field-list th {
-  color: rgb(0,50,150);
-  background-color: #EEE8AA;
-  white-space: nowrap; /*Essential. Otherwise the colons can break
-			 into a new line*/
-}
-
-
-
-/**
- * Extra admonitions
-
-
-div.tip {
-  background-color: #ffffe4;
-  border: 1px solid #ee6;
-}
-
-div.plot-output {
-  clear-after: both;
-}
-
-div.plot-output .figure {
-  float: left;
-  text-align: center;
-  margin-bottom: 0;
-  padding-bottom: 0;
-}
-
-div.plot-output .caption {
-  margin-top: 2;
-  padding-top: 0;
-}
-
-div.plot-output p.admonition-title {
-  display: none;
-}
-
-div.plot-output:after {
-  content: "";
-  display: block;
-  height: 0;
-  clear: both;
-}
-*/
-
-
-/*
-div.admonition-example {
-    background-color: #e4ffe4;
-    border: 1px solid #ccc;
-}*/
-
-
-/**
- * Styling for field lists
- */
-
-table.field-list th {
-  border-left: 2px solid #999 !important;
-  padding-left: 5px;
-}
-
-table.field-list {
-  border-collapse: separate; /*Essential. Otherwise Parameters and Returns
-			       are sharing one solid colored field. That looks
-			       weird.*/
-  border-spacing: 10px;
-}
-
-/**
- * Styling for footnotes
-
-
-table.footnote td, table.footnote th {
-  border: none;
-}
-*/
-
-div.specialnote-title {
-    font-size: 105%;
-    font-weight: bold;
-    font-color: #3B4D3C;
-    background-color: #DCE4DC;
-    padding: 1em;
-    padding-top: 0.4em;
-    padding-bottom: 0.4em;
-    margin-top: 1em;
-    margin-bottom: 0px;
-    border-width: 1px;
-    border-color: #546C55;
-    border-style: solid;
-}
-
-div.specialnote-body {
-    background-color: #DCE4DC;
-    padding: 1em;
-    padding-top: 0.1em;
-    padding-bottom: 0.4em;
-    margin-top: 0px;
-    border-width: 1px;
-    border-top-width: 0px;
-    border-color: #546C55;
-    border-style: solid;
-}

doc/source/_static/mathconf.js

+MathJax.Hub.Config({
+    TeX: {
+        Macros: {
+            bra: ['{\\left\\langle #1\\right|}',1],
+            ket: ['{\\left| #1\\right\\rangle}',1],
+            braket: ['\\left\\langle#1|#2\\right\\rangle', 2],
+            ri: '\\text{i}',
+            rd: '\\text{d}'
+        }
+    }
+});

doc/source/_static/sidebar.js

+/*
+ * sidebar.js
+ * ~~~~~~~~~~
+ *
+ * This script makes the Sphinx sidebar collapsible.
+ *
+ * .sphinxsidebar contains .sphinxsidebarwrapper.  This script adds in
+ * .sphixsidebar, after .sphinxsidebarwrapper, the #sidebarbutton used to
+ * collapse and expand the sidebar.
+ *
+ * When the sidebar is collapsed the .sphinxsidebarwrapper is hidden and the
+ * width of the sidebar and the margin-left of the document are decreased.
+ * When the sidebar is expanded the opposite happens.  This script saves a
+ * per-browser/per-session cookie used to remember the position of the sidebar
+ * among the pages.  Once the browser is closed the cookie is deleted and the
+ * position reset to the default (expanded).
+ *
+ * :copyright: Copyright 2007-2011 by the Sphinx team.
+ * :license: BSD, see LICENSE.txt for details.
+ *
+ */
+
+$(function() {
+  // global elements used by the functions.
+  // the 'sidebarbutton' element is defined as global after its
+  // creation, in the add_sidebar_button function
+  var bodywrapper = $('.bodywrapper');
+  var sidebar = $('.sphinxsidebar');
+  var sidebarwrapper = $('.sphinxsidebarwrapper');
+
+  // original margin-left of the bodywrapper and width of the sidebar
+  // with the sidebar expanded
+  var bw_margin_expanded = bodywrapper.css('margin-left');
+  var ssb_width_expanded = sidebar.width();
+
+  // margin-left of the bodywrapper and width of the sidebar
+  // with the sidebar collapsed
+  var bw_margin_collapsed = '.8em';
+  var ssb_width_collapsed = '.8em';
+
+  // colors used by the current theme
+  var dark_color = '#AAAAAA';
+  var light_color = '#CCCCCC';
+
+  function sidebar_is_collapsed() {
+    return sidebarwrapper.is(':not(:visible)');
+  }
+
+  function toggle_sidebar() {
+    if (sidebar_is_collapsed())
+      expand_sidebar();
+    else
+      collapse_sidebar();
+  }
+
+  function collapse_sidebar() {
+    sidebarwrapper.hide();
+    sidebar.css('width', ssb_width_collapsed);
+    bodywrapper.css('margin-left', bw_margin_collapsed);
+    sidebarbutton.css({
+        'margin-left': '0',
+        'height': bodywrapper.height(),
+        'border-radius': '5px'
+    });
+    sidebarbutton.find('span').text('»');
+    sidebarbutton.attr('title', _('Expand sidebar'));
+    document.cookie = 'sidebar=collapsed';
+  }
+
+  function expand_sidebar() {
+    bodywrapper.css('margin-left', bw_margin_expanded);
+    sidebar.css('width', ssb_width_expanded);
+    sidebarwrapper.show();
+    sidebarbutton.css({
+        'margin-left': ssb_width_expanded-12,
+        'height': bodywrapper.height(),
+        'border-radius': '0 5px 5px 0'
+    });
+    sidebarbutton.find('span').text('«');
+    sidebarbutton.attr('title', _('Collapse sidebar'));
+    //sidebarwrapper.css({'padding-top':
+    //  Math.max(window.pageYOffset - sidebarwrapper.offset().top, 10)});
+    document.cookie = 'sidebar=expanded';
+  }
+
+  function add_sidebar_button() {
+    sidebarwrapper.css({
+        'float': 'left',
+        'margin-right': '0',
+        'width': ssb_width_expanded - 28
+    });
+    // create the button
+    sidebar.append(
+      '<div id="sidebarbutton"><span>&laquo;</span></div>'
+    );
+    var sidebarbutton = $('#sidebarbutton');
+    // find the height of the viewport to center the '<<' in the page
+    var viewport_height;
+    if (window.innerHeight)
+      viewport_height = window.innerHeight;
+    else
+      viewport_height = $(window).height();
+    var sidebar_offset = sidebar.offset().top;
+    var sidebar_height = Math.max(bodywrapper.height(), sidebar.height());
+    sidebarbutton.find('span').css({
+        'display': 'block',
+        'position': 'fixed',
+        'top': Math.min(viewport_height/2, sidebar_height/2 + sidebar_offset) - 10
+    });
+
+    sidebarbutton.click(toggle_sidebar);
+    sidebarbutton.attr('title', _('Collapse sidebar'));
+    sidebarbutton.css({
+        'border-radius': '0 5px 5px 0',
+        'color': '#444444',
+        'background-color': '#CCCCCC',
+        'font-size': '1.2em',
+        'cursor': 'pointer',
+        'height': sidebar_height,
+        'padding-top': '1px',
+        'padding-left': '1px',
+        'margin-left': ssb_width_expanded - 12
+    });
+
+    sidebarbutton.hover(
+      function () {
+          $(this).css('background-color', dark_color);
+      },
+      function () {
+          $(this).css('background-color', light_color);
+      }
+    );
+  }
+
+  function set_position_from_cookie() {
+    if (!document.cookie)
+      return;
+    var items = document.cookie.split(';');
+    for(var k=0; k<items.length; k++) {
+      var key_val = items[k].split('=');
+      var key = key_val[0];
+      if (key == 'sidebar') {
+        var value = key_val[1];
+        if ((value == 'collapsed') && (!sidebar_is_collapsed()))
+          collapse_sidebar();
+        else if ((value == 'expanded') && (sidebar_is_collapsed()))
+          expand_sidebar();
+      }
+    }
+  }
+
+  add_sidebar_button();
+  var sidebarbutton = $('#sidebarbutton');
+  set_position_from_cookie();
+});

doc/source/conf.py

 # -*- coding: utf-8 -*-
 #
-# kwant documentation build configuration file, created by
+# Kwant documentation build configuration file, created by
 # sphinx-quickstart on Tue Jan 11 09:39:28 2011.
 #
 # This file is execfile()d with the current directory set to its containing dir.
@@ -11,8 +11,23 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os
+import sys
+import os
+import string
+from distutils.util import get_platform
+
+package_path = os.path.abspath(
+    "../../build/lib.{0}-{1}.{2}"
+    .format(get_platform(), *sys.version_info[:2]))
+
+# Insert into sys.path so that we can import kwant here
+sys.path.insert(0, package_path)
+# Insert into PYTHONPATH so that jupyter-sphinx will pick it up
+os.environ['PYTHONPATH'] = ':'.join((package_path, os.environ.get('PYTHONPATH','')))
+
 import kwant
+import kwant.qsymm
+import kwant.continuum  # sphinx gets confused with lazy loading
 
 # -- General configuration -----------------------------------------------------
 
@@ -22,8 +37,9 @@ import kwant
 sys.path.insert(0, os.path.abspath('../sphinxext'))
 
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary',
-              'sphinx.ext.todo', 'sphinx.ext.pngmath', 'numpydoc',
-              'kwantdoc']
+              'sphinx.ext.todo', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon',
+              'sphinx.ext.linkcode', 'jupyter_sphinx', 'sphinx_togglebutton',
+              'sphinxcontrib.rsvgconverter']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['../templates']
@@ -38,22 +54,18 @@ source_suffix = '.rst'
 master_doc = 'index'
 
 # General information about the project.
-project = u'kwant'
-copyright = u'2011-2012, A. R. Akhmerov, C. W. Groth, X. Waintal, M. Wimmer'
+project = 'Kwant'
+copyright = '2011-2017, C. W. Groth (CEA), M. Wimmer, A. R. Akhmerov, X. Waintal (CEA), and others'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The full version, including alpha/beta/rc tags.
-release = kwant.version.version[:]
-
-for i, s in enumerate(release):
-    if s not in '0123456790.':
-        break
+release = kwant.__version__
 
 # The short X.Y version.
-version = release[:i]
+version = release[:len(release) - len(release.lstrip('012345679.'))].rstrip('.')
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -95,12 +107,20 @@ pygments_style = 'sphinx'
 # Do not show all class members automatically in the class documentation
 numpydoc_show_class_members = False
 
+# Jupyter Sphinx config
+
+jupyter_sphinx_thebelab_config = {
+    "binderOptions": {
+        "repo": "kwant-project/binder",
+        "ref": "master",
+    }
+}
+
 # -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  Major themes that come with
 # Sphinx are currently 'default' and 'sphinxdoc'.
-html_theme = 'default'
-html_style = 'kwant.css'
+html_theme = 'sphinx_book_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -119,7 +139,7 @@ html_style = 'kwant.css'
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+html_logo = "_static/kwant_logo.png"
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
@@ -169,26 +189,47 @@ html_domain_indices = False
 # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
 #html_file_suffix = ''
 
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'kwantdoc'
-
 
 # -- Options for LaTeX output --------------------------------------------------
 
-# The paper size ('letter' or 'a4').
-latex_paper_size = 'a4'
-
-# The font size ('10pt', '11pt' or '12pt').
-#latex_font_size = '10pt'
+latex_elements = {'papersize': 'a4paper',
+                  'release': '',
+                  'releasename': '',
+                  'preamble':
+r"""\makeatletter
+  \fancypagestyle{normal}{
+    \fancyhf{}
+    \fancyfoot[LE,RO]{{\py@HeaderFamily\thepage}}
+    \fancyfoot[LO]{{\py@HeaderFamily\nouppercase{\rightmark}}}
+    \fancyfoot[RE]{{\py@HeaderFamily\nouppercase{\leftmark}}}
+    \fancyhead[LE,RO]{{\py@HeaderFamily \@title}}
+    \renewcommand{\headrulewidth}{0.4pt}
+    \renewcommand{\footrulewidth}{0.4pt}
+  }
+\makeatother
+
+\newcommand{\bra}[1]{\left\langle#1\right|}
+\newcommand{\ket}[1]{\left|#1\right>}
+\newcommand{\braket}[2]{\left\langle#1|#2\right\rangle}
+\newcommand{\ri}{\text{i}}
+\newcommand{\rd}{\text{d}}
+
+\usepackage{unicode-math}
+"""}
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
+# We use "et al." as it is shorter and there's not much space left horizontally.
 latex_documents = [
-  ('index', 'kwant.tex', u'kwant Documentation',
-   u'A. R. Akhmerov, C. W. Groth, X. Waintal, M. Wimmer',
+  ('index', 'kwant.tex', 'Kwant {0} documentation'.format(release),
+   'C. W. Groth, M. Wimmer, A. R. Akhmerov, X. Waintal, et al.',
    'manual'),
 ]
 
+latex_engine = 'xelatex'
+
+latex_use_xindy = False  # Xindy not installable in CI environment
+
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
 #latex_logo = None
@@ -197,15 +238,9 @@ latex_documents = [
 # not chapters.
 #latex_use_parts = False
 
-# Additional stuff for the LaTeX preamble.
-#latex_preamble = ''
-
 # Documents to append as an appendix to all manuals.
 #latex_appendices = []
 
-# If false, no module index is generated.
-latex_use_modindex = False
-
 # This is needed too.
 latex_domain_indices = False
 
@@ -214,4 +249,86 @@ latex_domain_indices = False
 autosummary_generate = True
 
 autoclass_content = "both"
-autodoc_default_flags = ['show-inheritance']
+autodoc_default_options = {
+    'show-inheritance': True,
+}
+
+# -- Teach Sphinx to document bound methods like functions ---------------------
+import types
+from sphinx.ext import autodoc
+
+class BoundMethodDocumenter(autodoc.FunctionDocumenter):
+    objtype = "boundmethod"
+    directivetype = 'function'
+
+    @classmethod
+    def can_document_member(cls, member, membername, isattr, parent):
+        # Return True iff `member` is a bound method.  Taken from
+        # <https://stackoverflow.com/a/1260881>.
+        return (isinstance(member, types.MethodType) and
+                member.__self__ is not None and
+                not issubclass(member.__self__.__class__, type) and
+                member.__self__.__class__ is not type)
+
+    def format_args(self):
+        args = super(BoundMethodDocumenter, self).format_args()
+        left, sep, right = args.partition('self, ')
+        if left.endswith('('):
+            args = left + right
+        return args
+
+def setup(app):
+    app.add_autodocumenter(BoundMethodDocumenter)
+
+
+# By default linkcheck only tries once, but experience has shown us that this test is
+# very non-specific for detecting dead links. Trying a few times should significantly
+# lower the probability of false positives.
+linkcheck_retries = 5
+# Some websites (particularly IoP) take a long time to respond. The combination of
+# this timeout and the retries should make this check sufficiently specific.
+linkcheck_timeout = 10
+
+nitpick_ignore = [('py:class', 'Warning'), ('py:class', 'Exception'),
+                  ('py:class', 'object'), ('py:class', 'tuple'),
+                  ('py:class', 'kwant.operator._LocalOperator'),
+                  ('py:class', 'numpy.ndarray'),
+                  ('py:class', 'kwant.solvers.common.BlockResult'),
+                  ('py:class', 'kwant.builder._FinalizedBuilderMixin')]
+
+
+# -- Make Sphinx insert source code links --------------------------------------
+def linkcode_resolve(domain, info):
+    def find_source():
+        # try to find the file and line number, based on code from numpy:
+        # https://github.com/numpy/numpy/blob/master/doc/source/conf.py#L286
+        obj = sys.modules[info['module']]
+        for part in info['fullname'].split('.'):
+            obj = getattr(obj, part)
+        import inspect
+        fn = inspect.getsourcefile(obj)
+        fn = os.path.relpath(fn, start=os.path.dirname(kwant.__file__))
+        source, lineno = inspect.getsourcelines(obj)
+        return fn, lineno, lineno + len(source) - 1
+
+    if domain != 'py' or not info['module']:
+        return None
+    try:
+        filename = 'kwant/%s#L%d-%d' % find_source()
+    except Exception:
+        filename = info['module'].replace('.', '/') + '.py'
+
+    # The following relies on the documented format of kwant.__version__.
+    rel = release.rstrip('.dirty')
+    if '.dev' in rel:
+        try:
+            refname = rel[rel.index('+g') + 2:]
+        except ValueError:
+            return
+    else:
+        refname = 'v' + rel
+
+    templ = os.environ.get(
+        "SOURCE_LINK_TEMPLATE",
+        "https://gitlab.kwant-project.org/kwant/kwant/blob/$r/$f")
+    return string.Template(templ).safe_substitute(r=refname, f=filename)

doc/source/images/tutorial2c_sketch.svg → doc/source/figure/ab_ring_sketch.svg

@@ -3,7 +3,7 @@
 
 <svg
    xmlns:dc="http://purl.org/dc/elements/1.1/"
-   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:cc="https://creativecommons.org/ns#"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:svg="http://www.w3.org/2000/svg"
    xmlns="http://www.w3.org/2000/svg"

doc/source/images/tutorial2c_sketch2.svg → doc/source/figure/ab_ring_sketch2.svg

@@ -3,7 +3,7 @@
 
 <svg
    xmlns:dc="http://purl.org/dc/elements/1.1/"
-   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:cc="https://creativecommons.org/ns#"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:svg="http://www.w3.org/2000/svg"
    xmlns="http://www.w3.org/2000/svg"

doc/source/images/html.py

-# Default width of figures in pixels
-figwidth_px = 600
-# Width for smaller figures
-figwidth_small_px = 400

doc/source/images/latex.py

-pt_to_in = 1./72.
-
-# Default width of figures in pts
-figwidth_pt = 300
-
-# Width for smaller figures
-figwidth_small_pt = 200
-figwidth_small_in = figwidth_small_pt * pt_to_in
-
-# Sizes for matplotlib figures
-mpl_width_in = figwidth_pt * pt_to_in
-mpl_label_size = 10 # font sizes in points
-mpl_tick_size = 9

doc/source/images/tutorial1a.py

-# Physics background
-# ------------------
-#  Conductance of a quantum wire; subbands
-#
-# Kwant features highlighted
-# --------------------------
-#  - Builder for setting up transport systems easily
-#  - Making scattering region and leads
-#  - Using the simple sparse solver for computing Landauer conductance
-
-import kwant
-
-import latex, html
-
-# First, define the tight-binding system
-
-sys = kwant.Builder()
-
-# Here, we are only working with square lattices
-
-lat = kwant.lattice.Square()
-sys.default_site_group = lat
-
-t = 1.0
-W = 10
-L = 30
-
-# Define the scattering region
-
-for i in xrange(L):
-    for j in xrange(W):
-        sys[(i, j)] = 4 * t
-
-        # hoppig in y-direction
-        if j > 0 :
-            sys[(i, j), (i, j-1)] = - t
-
-        #hopping in x-direction
-        if i > 0:
-            sys[(i, j), (i-1, j)] = -t
-
-# Then, define the leads:
-
-# First the lead to the left
-
-# (Note: in the current version, TranslationalSymmetry takes a
-# realspace vector)
-sym_lead0 = kwant.TranslationalSymmetry([lat.vec((-1, 0))])
-lead0 = kwant.Builder(sym_lead0)
-lead0.default_site_group = lat
-
-for j in xrange(W):
-    lead0[(0, j)] = 4 * t
-
-    if j > 0:
-        lead0[(0, j), (0, j-1)] = - t
-
-    lead0[(1, j), (0, j)] = - t
-
-# Then the lead to the right
-
-sym_lead1 = kwant.TranslationalSymmetry([lat.vec((1, 0))])
-lead1 = kwant.Builder(sym_lead1)
-lead1.default_site_group = lat
-
-for j in xrange(W):
-    lead1[(0, j)] = 4 * t
-
-    if j > 0:
-        lead1[(0, j), (0, j-1)] = - t
-
-    lead1[(1, j), (0, j)] = - t
-
-# Then attach the leads to the system
-
-sys.attach_lead(lead0)
-sys.attach_lead(lead1)
-
-# finalize the system
-
-fsys = sys.finalized()
-
-# and plot it, to make sure it's proper
-
-kwant.plot(fsys, "tutorial1a_sys.pdf", width=latex.figwidth_pt)
-kwant.plot(fsys, "tutorial1a_sys.png", width=html.figwidth_px)
-
-# Now that we have the system, we can compute conductance
-
-energies = []
-data = []
-for ie in xrange(100):
-    energy = ie * 0.01
-
-    # compute the scattering matrix at energy energy
-    smatrix = kwant.solvers.sparse.solve(fsys, energy)
-
-    # compute the transmission probability from lead 0 to
-    # lead 1
-    energies.append(energy)
-    data.append(smatrix.transmission(1, 0))
-
-# Use matplotlib to write output
-# We should see conductance steps
-import pylab
-
-pylab.plot(energies, data)
-pylab.xlabel("energy [in units of t]",
-                 fontsize=latex.mpl_label_size)
-pylab.ylabel("conductance [in units of e^2/h]",
-                 fontsize=latex.mpl_label_size)
-fig = pylab.gcf()
-pylab.setp(fig.get_axes()[0].get_xticklabels(),
-           fontsize=latex.mpl_tick_size)
-pylab.setp(fig.get_axes()[0].get_yticklabels(),
-           fontsize=latex.mpl_tick_size)
-fig.set_size_inches(latex.mpl_width_in, latex.mpl_width_in*3./4.)
-fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-fig.savefig("tutorial1a_result.pdf")
-fig.savefig("tutorial1a_result.png", dpi=(html.figwidth_px/latex.mpl_width_in))

doc/source/images/tutorial2a.py

-# Physics background
-# ------------------
-#  Gaps in quantum wires with spin-orbit coupling and Zeeman splititng,
-#  as theoretically predicted in
-#   http://prl.aps.org/abstract/PRL/v90/i25/e256601
-#  and (supposedly) experimentally oberved in
-#   http://www.nature.com/nphys/journal/v6/n5/abs/nphys1626.html
-#
-# Kwant features highlighted
-# --------------------------
-#  - Numpy matrices as values in Builder
-
-import kwant
-import numpy
-
-import latex, html
-
-# define sigma-matrices for convenience
-sigma_0 = numpy.eye(2)
-sigma_x = numpy.array([[0, 1], [1, 0]])
-sigma_y = numpy.array([[0, -1j], [1j, 0]])
-sigma_z = numpy.array([[1, 0], [0, -1]])
-
-# First, define the tight-binding system
-
-sys = kwant.Builder()
-
-# Here, we are only working with square lattices
-
-# for simplicity, take lattice constant = 1
-a = 1
-lat = kwant.lattice.Square(a)
-
-t = 1.0
-alpha = 0.5
-e_z = 0.08
-W = 10
-L = 30
-
-# Define the scattering region
-
-def rectangle(pos):
-    (x, y) = pos
-    return ( -0.5 < x < L - 0.5 ) and ( -0.5 < y < W - 0.5 )
-
-sys[lat.shape(rectangle, (0, 0))] = 4 * t * sigma_0 + e_z * sigma_z
-# hoppings in x-direction
-sys[sys.possible_hoppings((1, 0), lat, lat)] = - t * sigma_0 - \
-    1j * alpha * sigma_y
-# hoppings in y-directions
-sys[sys.possible_hoppings((0, 1), lat, lat)] = - t * sigma_0 + \
-    1j * alpha * sigma_x
-
-# Then, define the leads:
-
-# First the lead to the left
-
-# (Note: in the current version, TranslationalSymmetry takes a
-# realspace vector)
-sym_lead0 = kwant.TranslationalSymmetry([lat.vec((-1, 0))])
-lead0 = kwant.Builder(sym_lead0)
-lead0.default_site_group = lat
-
-def lead_shape(pos):
-    (x, y) = pos
-    return (-1 < x < 1) and ( -0.5 < y < W - 0.5 )
-
-lead0[lat.shape(lead_shape, (0, 0))] = 4 * t * sigma_0 + e_z * sigma_z
-# hoppings in x-direction
-lead0[lead0.possible_hoppings((1, 0), lat, lat)] = - t * sigma_0 - \
-    1j * alpha * sigma_y
-# hoppings in y-directions
-lead0[lead0.possible_hoppings((0, 1), lat, lat)] = - t * sigma_0 + \
-    1j * alpha * sigma_x
-
-# Then the lead to the right
-# there we can use a special function that simply reverses the direction
-
-lead1 = lead0.reversed()
-
-# Then attach the leads to the system
-
-sys.attach_lead(lead0)
-sys.attach_lead(lead1)
-
-# finalize the system
-
-fsys = sys.finalized()
-
-# Now that we have the system, we can compute conductance
-
-energies = []
-data = []
-for ie in xrange(100):
-    energy = ie * 0.01 - 0.3
-
-    # compute the scattering matrix at energy energy
-    smatrix = kwant.solvers.sparse.solve(fsys, energy)
-
-    # compute the transmission probability from lead 0 to
-    # lead 1
-    energies.append(energy)
-    data.append(smatrix.transmission(1, 0))
-
-# Use matplotlib to write output
-# We should see conductance steps
-import pylab
-
-pylab.plot(energies, data)
-pylab.xlabel("energy [in units of t]",
-             fontsize=latex.mpl_label_size)
-pylab.ylabel("conductance [in units of e^2/h]",
-             fontsize=latex.mpl_label_size)
-fig = pylab.gcf()
-pylab.setp(fig.get_axes()[0].get_xticklabels(),
-           fontsize=latex.mpl_tick_size)
-pylab.setp(fig.get_axes()[0].get_yticklabels(),
-           fontsize=latex.mpl_tick_size)
-fig.set_size_inches(latex.mpl_width_in, latex.mpl_width_in*3./4.)
-fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-fig.savefig("tutorial2a_result.pdf")
-fig.savefig("tutorial2a_result.png",
-            dpi=(html.figwidth_px/latex.mpl_width_in))

doc/source/images/tutorial2b.py

-# Physics background
-# ------------------
-#  transmission through a quantum well
-#
-# Kwant features highlighted
-# --------------------------
-#  - Functions as values in Builder
-
-import kwant
-
-import latex, html
-
-# First, define the tight-binding system
-
-sys = kwant.Builder()
-
-# Here, we are only working with square lattices
-
-# for simplicity, take lattice constant = 1
-a = 1
-lat = kwant.lattice.Square(a)
-
-t = 1.0
-alpha = 0.5
-e_z = 0.08
-W = 10
-L = 30
-
-# Define the scattering region
-
-def rectangle(pos):
-    (x, y) = pos
-    return ( -0.5 < x < L - 0.5 ) and ( -0.5 < y < W - 0.5 )
-
-def potential(site):
-    (x, y) = site.pos
-    if 10 < x < 20:
-        return pot
-    else:
-        return 0
-
-def onsite(site):
-    return 4 * t + potential(site)
-
-sys[lat.shape(rectangle, (0, 0))] = onsite
-for hopping in lat.nearest:
-    sys[sys.possible_hoppings(*hopping)] = - t
-
-# Then, define the leads:
-
-# First the lead to the left
-
-# (Note: in the current version, TranslationalSymmetry takes a
-# realspace vector)
-sym_lead0 = kwant.TranslationalSymmetry([lat.vec((-1, 0))])
-lead0 = kwant.Builder(sym_lead0)
-lead0.default_site_group = lat
-
-def lead_shape(pos):
-    (x, y) = pos
-    return (-1 < x < 1) and ( -0.5 < y < W - 0.5 )
-
-lead0[lat.shape(lead_shape, (0, 0))] = 4 * t
-for hopping in lat.nearest:
-    lead0[lead0.possible_hoppings(*hopping)] = - t
-
-# Then the lead to the right
-# there we can use a special function that simply reverses the direction
-
-lead1 = lead0.reversed()
-
-# Then attach the leads to the system
-
-sys.attach_lead(lead0)
-sys.attach_lead(lead1)
-
-# finalize the system
-
-fsys = sys.finalized()
-
-# Now that we have the system, we can compute conductance
-
-energy = 0.2
-wellpot = []
-data = []
-for ipot in xrange(100):
-    pot = - ipot * 0.01
-
-    # compute the scattering matrix at energy energy
-    smatrix = kwant.solvers.sparse.solve(fsys, energy)
-
-    # compute the transmission probability from lead 0 to
-    # lead 1
-    wellpot.append(-pot)
-    data.append(smatrix.transmission(1, 0))
-
-# Use matplotlib to write output
-# We should see conductance steps
-import pylab
-
-pylab.plot(wellpot, data)
-pylab.xlabel("well depth [in units of t]",
-             fontsize=latex.mpl_label_size)
-pylab.ylabel("conductance [in units of e^2/h]",
-             fontsize=latex.mpl_label_size)
-fig = pylab.gcf()
-pylab.setp(fig.get_axes()[0].get_xticklabels(),
-           fontsize=latex.mpl_tick_size)
-pylab.setp(fig.get_axes()[0].get_yticklabels(),
-           fontsize=latex.mpl_tick_size)
-fig.set_size_inches(latex.mpl_width_in, latex.mpl_width_in*3./4.)
-fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-fig.savefig("tutorial2b_result.pdf")
-fig.savefig("tutorial2b_result.png",
-            dpi=(html.figwidth_px/latex.mpl_width_in))

doc/source/images/tutorial2c.py

-# Physics background
-# ------------------
-#  Flux-dependent transmission through a quantum ring
-#
-# Kwant features highlighted
-# --------------------------
-#  - More complex shapes with lattices
-#  - Allows for discussion of subtleties of `attach_lead` (not in the
-#    example, but in the tutorial main text)
-#  - Modifcations of hoppings/sites after they have been added
-
-from cmath import exp
-from math import pi
-import kwant
-
-import latex, html
-
-# First, define the tight-binding system
-
-sys = kwant.Builder()
-
-# Here, we are only working with square lattices
-
-# for simplicity, take lattice constant = 1
-a = 1
-lat = kwant.lattice.Square(a)
-
-t = 1.0
-W = 10
-r1 = 10
-r2 = 20
-
-# Define the scattering region
-# Now, we aim for a more compelx shape, namely a ring (or annulus)
-
-def ring(pos):
-    (x, y) = pos
-    rsq = x**2 + y**2
-    return ( r1**2 < rsq < r2**2)
-
-sys[lat.shape(ring, (0, 11))] = 4 * t
-for hopping in lat.nearest:
-    sys[sys.possible_hoppings(*hopping)] = - t
-
-# In order to introduce a flux through the ring, we introduce a phase
-# on the hoppings on the line cut through one of the arms
-
-# since we want to change the flux without modifying Builder repeatedly,
-# we define the modified hoppings as a function that takes the flux
-# as a global variable.
-
-def fluxphase(site1, site2):
-    return exp(1j * phi)
-
-# Now go through all the hoppings and modify those in the lower
-# arm of the ring that go from x=0 to x=1
-
-for (site1, site2) in sys.hoppings():
-    ix1, iy1 = site1.tag
-    ix2, iy2 = site2.tag
-
-    hopx = tuple(sorted((ix1, ix2)))
-
-    if hopx == (0, 1) and iy1 == iy2 and iy1 < 0:
-        sys[lat(hopx[1], iy1), lat(hopx[0], iy1)] = fluxphase
-
-# Then, define the leads:
-
-# First the lead to the left
-
-# (Note: in the current version, TranslationalSymmetry takes a
-# realspace vector)
-sym_lead0 = kwant.TranslationalSymmetry([lat.vec((-1, 0))])
-lead0 = kwant.Builder(sym_lead0)
-lead0.default_site_group = lat
-
-def lead_shape(pos):
-    (x, y) = pos
-    return (-1 < x < 1) and ( -W/2 < y < W/2  )
-
-lead0[lat.shape(lead_shape, (0, 0))] = 4 * t
-for hopping in lat.nearest:
-    lead0[lead0.possible_hoppings(*hopping)] = - t
-
-# Then the lead to the right
-# there we can use a special function that simply reverses the direction
-
-lead1 = lead0.reversed()
-
-# Then attach the leads to the system
-
-sys.attach_lead(lead0)
-sys.attach_lead(lead1)
-
-# finalize the system
-
-fsys = sys.finalized()
-
-# and plot it, to make sure it's proper
-
-kwant.plot(fsys, "tutorial2c_sys.pdf", width=latex.figwidth_pt)
-kwant.plot(fsys, "tutorial2c_sys.png", width=html.figwidth_px)
-
-# Now that we have the system, we can compute conductance
-
-energy = 0.15
-phases = []
-data = []
-for iphi in xrange(100):
-    phi = iphi * 0.01 * 3 * 2 * pi
-
-    # compute the scattering matrix at energy energy
-    smatrix = kwant.solve(fsys, energy)
-
-    # compute the transmission probability from lead 0 to
-    # lead 1
-    phases.append(phi / (2 * pi))
-    data.append(smatrix.transmission(1, 0))
-
-# Use matplotlib to write output
-# We should see conductance steps
-import pylab
-
-pylab.plot(phases, data)
-pylab.xlabel("flux [in units of the flux quantum]",
-             fontsize=latex.mpl_label_size)
-pylab.ylabel("conductance [in units of e^2/h]",
-             fontsize=latex.mpl_label_size)
-fig = pylab.gcf()
-pylab.setp(fig.get_axes()[0].get_xticklabels(),
-           fontsize=latex.mpl_tick_size)
-pylab.setp(fig.get_axes()[0].get_yticklabels(),
-           fontsize=latex.mpl_tick_size)
-fig.set_size_inches(latex.mpl_width_in, latex.mpl_width_in*3./4.)
-fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-fig.savefig("tutorial2c_result.pdf")
-fig.savefig("tutorial2c_result.png",
-            dpi=(html.figwidth_px/latex.mpl_width_in))
-
-# Finally, some plots needed for the notes
-
-sys = kwant.Builder()
-
-sys[lat.shape(ring, (0, 11))] = 4 * t
-for hopping in lat.nearest:
-    sys[sys.possible_hoppings(*hopping)] = - t
-
-sym_lead0 = kwant.TranslationalSymmetry([lat.vec((-1, 0))])
-lead0 = kwant.Builder(sym_lead0)
-lead0.default_site_group = lat
-
-def lead_shape(pos):
-    (x, y) = pos
-    return (-1 < x < 1) and ( 0.5 * W < y < 1.5 * W )
-
-lead0[lat.shape(lead_shape, (0, W))] = 4 * t
-for hopping in lat.nearest:
-    lead0[lead0.possible_hoppings(*hopping)] = - t
-
-# Then the lead to the right
-# there we can use a special function that simply reverses the direction
-
-lead1 = lead0.reversed()
-
-# Then attach the leads to the system
-
-sys.attach_lead(lead0)
-sys.attach_lead(lead1)
-
-# finalize the system
-
-fsys = sys.finalized()
-
-# and plot it, to make sure it's proper
-
-kwant.plot(fsys, "tutorial2c_note1.pdf", width=latex.figwidth_small_pt)
-kwant.plot(fsys, "tutorial2c_note1.png", width=html.figwidth_small_px)
-
-sys = kwant.Builder()
-
-sys[lat.shape(ring, (0, 11))] = 4 * t
-for hopping in lat.nearest:
-    sys[sys.possible_hoppings(*hopping)] = - t
-
-sym_lead0 = kwant.TranslationalSymmetry([lat.vec((-1, 0))])
-lead0 = kwant.Builder(sym_lead0)
-lead0.default_site_group = lat
-
-def lead_shape(pos):
-    (x, y) = pos
-    return (-1 < x < 1) and ( -W/2 < y < W/2  )
-
-lead0[lat.shape(lead_shape, (0, 0))] = 4 * t
-for hopping in lat.nearest:
-    lead0[lead0.possible_hoppings(*hopping)] = - t
-
-# Then the lead to the right
-# there we can use a special function that simply reverses the direction
-
-lead1 = lead0.reversed()
-
-# Then attach the leads to the system
-
-sys.attach_lead(lead0)
-sys.attach_lead(lead1, lat(0, 0))
-
-# finalize the system
-
-fsys = sys.finalized()
-
-# and plot it, to make sure it's proper
-
-kwant.plot(fsys, "tutorial2c_note2.pdf", width=latex.figwidth_small_pt)
-kwant.plot(fsys, "tutorial2c_note2.png", width=html.figwidth_small_px)

doc/source/images/tutorial3a.py

-# Physics background
-# ------------------
-#  band structure of a simple quantum wire in tight-binding approximation
-#
-# Kwant features highlighted
-# --------------------------
-#  - Computing the band structure of a finalized lead.
-
-import kwant
-import numpy as np
-from math import pi
-
-import latex, html
-
-a = 1
-lat = kwant.lattice.Square(a)
-
-t = 1.0
-W = 10
-
-# Define a lead:
-
-sym_lead = kwant.TranslationalSymmetry([lat.vec((-1, 0))])
-lead = kwant.Builder(sym_lead)
-lead.default_site_group = lat
-
-for j in xrange(W):
-    lead[(0, j)] = 4 * t
-
-    if j > 0:
-        lead[(0, j), (0, j-1)] = - t
-
-    lead[(1, j), (0, j)] = - t
-
-# Now compute the band structure
-
-# Only a finalized lead has the information about bandstructure
-flead = lead.finalized()
-
-momenta = np.arange(-pi, pi + .01, 0.02 * pi)
-energy_list = [flead.energies(k) for k in momenta]
-
-import pylab
-pylab.plot(momenta, energy_list)
-pylab.xlabel("momentum [in untis of (lattice constant)^-1]",
-             fontsize=latex.mpl_label_size)
-pylab.ylabel("energy [in units of t]",
-             fontsize=latex.mpl_label_size)
-fig = pylab.gcf()
-pylab.setp(fig.get_axes()[0].get_xticklabels(),
-           fontsize=latex.mpl_tick_size)
-pylab.setp(fig.get_axes()[0].get_yticklabels(),
-           fontsize=latex.mpl_tick_size)
-fig.set_size_inches(latex.mpl_width_in, latex.mpl_width_in*3./4.)
-fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-fig.savefig("tutorial3a_result.pdf")
-fig.savefig("tutorial3a_result.png",
-            dpi=(html.figwidth_px/latex.mpl_width_in))

doc/source/images/tutorial3b.py

-# Physics background
-# ------------------
-#  Fock-darwin spectrum of a quantum dot (energy spectrum in
-#  as a function of a magnetic field)
-#
-# Kwant features highlighted
-# --------------------------
-#  - Use of `hamiltonian_submatrix` in order to obtain a Hamiltonian
-#    matrix.
-
-
-from cmath import exp
-import kwant
-
-import latex, html
-
-# First, define the tight-binding system
-
-sys = kwant.Builder()
-
-# Here, we are only working with square lattices
-
-# for simplicity, take lattice constant = 1
-a = 1
-lat = kwant.lattice.Square(a)
-
-t = 1.0
-r = 10
-
-# Define the quantum dot
-
-def circle(pos):
-    (x, y) = pos
-    rsq = x**2 + y**2
-    return rsq < r**2
-
-def hopx(site1, site2):
-    y = site1.pos[1]
-    return - t * exp(-1j * B * y)
-
-sys[lat.shape(circle, (0, 0))] = 4 * t
-# hoppings in x-direction
-sys[sys.possible_hoppings((1, 0), lat, lat)] = hopx
-# hoppings in y-directions
-sys[sys.possible_hoppings((0, 1), lat, lat)] = - t
-
-# It's a closed system for a change, so no leads
-
-# finalize the system
-
-fsys = sys.finalized()
-
-# and plot it, to make sure it's proper
-
-kwant.plot(fsys, "tutorial3b_sys.pdf")
-kwant.plot(fsys, "tutorial3b_sys.png")
-
-# In the following, we compute the spectrum of the quantum dot
-# using dense matrix methods. This works in this toy example,
-# as the system is tiny. In a real example, one would want to use
-# sparse matrix methods
-
-import scipy.linalg as la
-
-Bs = []
-energies = []
-for iB in xrange(100):
-    B = iB * 0.002
-
-# Obtain the Hamiltonian as a dense matrix
-    ham_mat = fsys.hamiltonian_submatrix()
-
-    ev = la.eigh(ham_mat, eigvals_only=True)
-
-    Bs.append(B)
-    energies.append(ev[:15])
-
-import pylab
-
-pylab.plot(Bs, energies)
-pylab.xlabel("magnetic field [some arbitrary units]",
-             fontsize=latex.mpl_label_size)
-pylab.ylabel("energy [in units of t]",
-             fontsize=latex.mpl_label_size)
-fig = pylab.gcf()
-pylab.setp(fig.get_axes()[0].get_xticklabels(),
-           fontsize=latex.mpl_tick_size)
-pylab.setp(fig.get_axes()[0].get_yticklabels(),
-           fontsize=latex.mpl_tick_size)
-fig.set_size_inches(latex.mpl_width_in, latex.mpl_width_in*3./4.)
-fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-fig.savefig("tutorial3b_result.pdf")
-fig.savefig("tutorial3b_result.png",
-            dpi=(html.figwidth_px/latex.mpl_width_in))

doc/source/images/tutorial4.py

-# Physics background
-# ------------------
-#  Transport through a graphene quantum dot with a pn-junction
-#
-# Kwant features highlighted
-# --------------------------
-#  - Application of all the aspects of tutorials 1-3 to a more complicated
-#    lattice, namely graphene
-
-from __future__ import division # so that 1/2 == 0.5, and not 0
-from math import pi, sqrt
-import numpy as np
-
-import kwant
-import latex, html
-
-# For computing eigenvalues
-import scipy.sparse.linalg as sla
-
-# For plotting
-import pylab
-
-
-# Define the graphene lattice
-sin_30, cos_30 = (1/2, np.sqrt(3)/2)
-graphene = kwant.make_lattice([(1, 0), (sin_30, cos_30)],
-                              [(0, 0), (0, 1/np.sqrt(3))])
-a, b = graphene.sublattices
-
-
-def make_system(r=10, w=2.0, pot=0.1):
-
-    #### Define the scattering region. ####
-    # circular scattering region
-    def circle(pos):
-        x, y = pos
-        return x**2 + y**2 < r**2
-
-    sys= kwant.Builder()
-
-    # w: width and pot: potential maximum of the p-n junction
-    def potential(site):
-        (x, y) = site.pos
-        d = y * cos_30 + x * sin_30
-        return pot * np.tanh(d / w)
-
-    sys[graphene.shape(circle, (0,0))] = potential
-
-    # specify the hoppings of the graphene lattice in the
-    # format expected by possibe_hoppings()
-    hoppings = (((0, 0), b, a), ((0, 1), b, a), ((-1, 1), b, a))
-    for hopping in hoppings:
-        sys[sys.possible_hoppings(*hopping)] = - 1
-
-    # Modify the scattering region
-    del sys[a(0,0)]
-    sys[a(-2,1), b(2, 2)] = -1
-
-    # Keep a copy of the closed system without leads, for
-    # eigenvalue computations
-    closed_fsys = sys.finalized()
-
-    #### Define the leads. ####
-    # left lead
-    sym0 = kwant.TranslationalSymmetry([graphene.vec((-1, 0))])
-
-    def lead0_shape(pos):
-        x, y = pos
-        return (-1 < x < 1) and (-0.4 * r < y < 0.4 * r)
-
-    lead0 = kwant.Builder(sym0)
-    lead0[graphene.shape(lead0_shape, (0,0))] = - pot
-    for hopping in hoppings:
-        lead0[lead0.possible_hoppings(*hopping)] = - 1
-
-    # The second lead, going ot the top right
-    sym1 = kwant.TranslationalSymmetry([graphene.vec((0, 1))])
-
-    def lead1_shape(pos):
-        x, y = pos
-        u = x * sin_30 + y * cos_30
-        v = y * sin_30 - x * cos_30
-        return (-1 < u < 1) and (-0.4 * r < v < 0.4 * r)
-
-    lead1 = kwant.Builder(sym1)
-    lead1[graphene.shape(lead1_shape, (0,0))] = pot
-    for hopping in hoppings:
-        lead1[lead1.possible_hoppings(*hopping)] = - 1
-
-    # Attach the leads
-    sys.attach_lead(lead0)
-    sys.attach_lead(lead1)
-
-    return sys.finalized(), closed_fsys, lead0.finalized()
-
-
-def compute_evs(sys):
-    # Compute some eigenvalues of the closed system
-    sparse_mat = sys.hamiltonian_submatrix(sparse=True)
-
-    try:
-        # This requires scipy version >= 0.9.0
-        # Failure (i.e. insufficient scipy version) is not critical
-        # for the remainder of the tutorial, hence the try-block
-        evs = scipy.sparse.linalg.eigs(sparse_mat, 2)[0]
-        print evs
-    except:
-        pass
-
-
-def plot_conductance(fsys, energies):
-    # Compute transmission as a function of energy
-    data = []
-    for energy in energies:
-        smatrix = kwant.solve(fsys, energy)
-        data.append(smatrix.transmission(0, 1))
-
-    pylab.clf()
-    pylab.plot(energies, data)
-    pylab.xlabel("energy [in units of t]",
-                 fontsize=latex.mpl_label_size)
-    pylab.ylabel("conductance [in units of e^2/h]",
-                 fontsize=latex.mpl_label_size)
-    fig = pylab.gcf()
-    pylab.setp(fig.get_axes()[0].get_xticklabels(),
-               fontsize=latex.mpl_tick_size)
-    pylab.setp(fig.get_axes()[0].get_yticklabels(),
-               fontsize=latex.mpl_tick_size)
-    fig.set_size_inches(latex.mpl_width_in, latex.mpl_width_in*3./4.)
-    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-    fig.savefig("tutorial4_result.pdf")
-    fig.savefig("tutorial4_result.png",
-                dpi=(html.figwidth_px/latex.mpl_width_in))
-
-
-def plot_bandstructure(flead, momenta):
-    # Use the method ``energies`` of the finalized lead to compute
-    # the bandstructure
-    energy_list = [flead.energies(k) for k in momenta]
-
-    pylab.clf()
-    pylab.plot(momenta, energy_list)
-    pylab.xlabel("momentum [in untis of (lattice constant)^-1]",
-                 fontsize=latex.mpl_label_size)
-    pylab.ylabel("energy [in units of t]",
-                 fontsize=latex.mpl_label_size)
-    fig = pylab.gcf()
-    pylab.setp(fig.get_axes()[0].get_xticklabels(),
-               fontsize=latex.mpl_tick_size)
-    pylab.setp(fig.get_axes()[0].get_yticklabels(),
-               fontsize=latex.mpl_tick_size)
-    fig.set_size_inches(latex.mpl_width_in, latex.mpl_width_in*3./4.)
-    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-    fig.savefig("tutorial4_bs.pdf")
-    fig.savefig("tutorial4_bs.png",
-                dpi=(html.figwidth_px/latex.mpl_width_in))
-
-
-def main():
-    pot = 0.1
-    fsys, closed_fsys, flead = make_system(pot=pot)
-
-    # First, plot the closed system, and compute some eigenvalues
-
-    # To highlight the two sublattices of graphene, we plot one with
-    # a filled, and the other one with an open circle:
-    plotter_symbols = {a: kwant.plotter.Circle(r=0.3),
-                       b: kwant.plotter.Circle(r=0.3,
-                                               fcol=kwant.plotter.white,
-                                               lcol=kwant.plotter.black)}
-
-    kwant.plot(closed_fsys, a=1./sqrt(3.), symbols=plotter_symbols,
-               filename="tutorial4_sys1.pdf",
-               width=latex.figwidth_pt)
-    kwant.plot(closed_fsys, a=1./sqrt(3.), symbols=plotter_symbols,
-               filename="tutorial4_sys1.png",
-               width=html.figwidth_px)
-
-    # Then, plot the system with leads and compute the band structure
-    # of one of the (zigzag) leads, as well as the conductance
-
-    kwant.plot(fsys, a=1/sqrt(3.), symbols=plotter_symbols,
-               filename="tutorial4_sys2.png",
-               width=html.figwidth_px)
-    kwant.plot(fsys, a=1/sqrt(3.), symbols=plotter_symbols,
-               filename="tutorial4_sys2.pdf",
-               width=latex.figwidth_pt)
-
-    momenta = np.arange(-pi, pi + .01, 0.1 * pi)
-    plot_bandstructure(flead, momenta)
-
-    energies = np.arange(-2 * pot, 2 * pot, pot / 10.5)
-    plot_conductance(fsys, energies)
-
-
-# Call the main function if the script gets executed (as opposed to imported).
-# See <http://docs.python.org/library/__main__.html>.
-if __name__ == '__main__':
-    main()

doc/source/index.rst

-===================
-kwant documentation
-===================
-
-.. toctree::
-   :maxdepth: 1
-
-   README file (includes installation instructions) <readme>
-
-.. toctree::
-   :maxdepth: 2
-
-   tutorial/index.rst
+=============================
+Kwant |release| documentation
+=============================
 
 .. toctree::
    :maxdepth: 2
+   :numbered: 2
 
+   pre/index
+   tutorial/index
    reference/index
 
 * :ref:`genindex`