development leading up to version 0.1

.gitignore

+*~
+MANIFEST
+*.pyc
+*.so
+/kwant/*/*.c
+/kwant/_static_version.py
+/build
+/dist
+/doc/build
+/doc/source/reference/generated/
+/doc/source/images/*.png
+/doc/source/images/*.pdf
+/doc/source/images/.*_flag

MANIFEST.in

+# This file specifies the files to be included in the source distribution
+# in addition to the default ones.
+
+recursive-include kwant *.pxd
+recursive-include kwant *.h
+recursive-include kwant test_*.py
+
+include TODO.txt
+recursive-include examples *.py
+
+include doc/other/*[a-zA-Z]
+include doc/Makefile
+recursive-include doc/source *.rst *.py *.svg
+recursive-include doc/source/_static *[a-zA-Z]
+recursive-include doc/templates *[a-zA-Z]
+prune doc/source/reference/generated
+recursive-include doc/sphinxext *.py *.txt *.in

README.txt

+=============================================================
+kwant, a package for numerical quantum transport calculations
+=============================================================
+
+Licence
+=======
+
+This software is NOT TO BE DISTRIBUTED, neither in part nor as a whole.
+
+The only exception to this is the ``doc/sphinxext`` subdirectory, which is free
+software.  (See the file ``LICENSE.txt`` in that subdirectory.)
+
+
+Installation
+============
+
+The prerequisites are
+
+ - More or less current versions of `Python <http://python.org>`_ and `SciPy
+   <http://scipy.org>`_.  Python 2.6 and scipy 0.7.2 should be enough.
+
+ - `Cython <http://cython.org/>`_ -- Version 0.13 works for us.
+
+optional:
+
+ - `pycairo <http://cairographics.org/pycairo/>`_ (for plotting)
+
+ - `matplotlib <http://matplotlib.sourceforge.net/>`_ (for some of the
+   examples)
+
+kwant can be build and installed using distutils, following standard python
+conventions.  To build and install, run the following commands in the root
+directory of the package. ::
+
+    python setup.py build
+    python setup.py install
+
+The second command has to be run as root (e.g. prefixing it with ``sudo``).  By
+default the package will be installed under ``/usr/local``.  You can change
+this using the ``--prefix`` option, e.g.::
+
+    python setup.py install --prefix=/opt
+
+If you would like to install kwant into your home directory only you can use ::
+
+    python setup.py install --home=~
+
+This does not require superuser priviledges.  If you install kwant in this way
+be sure to tell python where to find it.  This can be done by setting the
+``PYTHONPATH`` environment variable::
+
+    export PYTHONPATH=$HOME/lib/python
+
+You can make this setting permanent by adding this line to your the file
+``.bashrc`` in your home directory.
+
+To check successful installation try executing some examples in the
+``examples`` subdirectory.
+
+
+Documentation
+=============
+
+To build the documentation, kwant has to be installed as described in the
+previous section.  The `sphinx documentation generator
+<http://sphinx.pocoo.org/>`_ is required.
+
+HTML documentation can be built by entering the ``doc`` subdirectory of the
+kwant package and executing ``make html``.  PDF documentation is generated by
+executing ``make latex`` followed by a ``make all-pdf`` in ``doc/build/latex``.
+
+Because of some quirks of how sphinx works, it might be necessary to execute
+``make clean`` between building HTML and PDF documentation.  If this is not
+done, sphinx might mistakenly use PNG files for PDF output.
+
+Please consult the documentation for further information on how to use kwant.
+
+
+Hacking
+=======
+
+To work on the library itself it is useful to build it in-place.  This can be
+done with the following command ::
+
+    python setup.py build_ext -i
+
+The ``kwant`` subdirectory of the source distribution will be thus turned into
+a proper python package which can be imported.  To be able to import kwant from
+within python, one can either work in the root directory of the distribution
+(where the subdirectory ``kwant`` is located), or make a (symbolic) link from
+somewhere in the Python search path to the the package subdirectory.
+
+Some conventions to keep in mind:
+
+* Please keep the code consistent by adhering to the already used naming and
+  formatting conventions.  We generally follow the `"Style Guide for Python
+  Code" <http://www.python.org/dev/peps/pep-0008/>`_ and the `"Docstring
+  Conventions" <http://www.python.org/dev/peps/pep-0257/>`_.
+
+* Write tests for all the important functionality you add.  Be sure not to
+  break existing tests.
+
+
+Tests
+=====
+
+We use the `nose testing framework
+<http://somethingaboutorange.com/mrl/projects/nose/>`_.  To run the tests,
+execute the command ``nosetests`` from the root directory of the package after
+it has been built in place.

TODO.txt

+Roughly in order of importance.                                     -*-org-*-
+
+* Define a few benchmarks and check performance.  Optimize the code.
+
+* Write a fast tiny array module.
+  (If this turns out to be a performance bottleneck.)
+
+* Provide support for calculating and nicely plotting LDOS.
+  Make a tutorial example for this.
+
+* Allow attaching lead with further then nearest slice hoppings.
+  The most easy way to do this is increasing the period of the lead.
+
+* Optionally show site coordinates when plotting a system.
+
+* Add support for easily adding magnetic field to a system.
+
+* Generalize InfiniteSystem to multiple directions.
+
+* Add support for optimization of lead fundamental domains.
+
+* Write a module to generate "functional" random numbers.
+  This is a good starting point:
+  http://www.cs.umbc.edu/~olano/papers/GPUTEA.pdf
+
+* Write a RGF solver which uses graph/slicer.
+
+* Implement the C solver interface.
+
+* Wrap TB_SIM as a solver.
+
+* Wrap umfpack or some other sparse linear algebra library with Cython.
+  Use it directly in sparse solver.  This will allow to fine-tune the solution
+  of sparse systems.

doc/Makefile

+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+# In difference to the original Makefile, we convert all SVG files to PDF for
+# LaTeX output.  For HTML output, we don't create PNGs but rather use the SVG
+# files directly.
+IMAGESOURCES    = $(shell find source -name "*.svg")
+GENERATEDPDF    = $(patsubst %.svg, %.pdf, $(IMAGESOURCES))
+
+# Tutorial images.
+TUTORIAL1A_IMAGES = source/images/tutorial1a_result.png source/images/tutorial1a_result.pdf source/images/tutorial1a_sys.png source/images/tutorial1a_sys.pdf
+TUTORIAL2A_IMAGES = source/images/tutorial2a_result.png source/images/tutorial2a_result.pdf
+TUTORIAL2B_IMAGES = source/images/tutorial2b_result.png source/images/tutorial2b_result.pdf
+TUTORIAL2C_IMAGES = source/images/tutorial2c_result.png source/images/tutorial2c_result.pdf source/images/tutorial2c_sys.png source/images/tutorial2c_sys.pdf source/images/tutorial2c_note1.png source/images/tutorial2c_note1.pdf source/images/tutorial2c_note2.png source/images/tutorial2c_note2.pdf
+TUTORIAL3A_IMAGES = source/images/tutorial3a_result.png source/images/tutorial3a_result.pdf
+TUTORIAL3B_IMAGES = source/images/tutorial3b_result.png source/images/tutorial3b_result.pdf source/images/tutorial3b_sys.png source/images/tutorial3b_sys.pdf
+TUTORIAL4_IMAGES = source/images/tutorial4_result.png source/images/tutorial4_result.pdf source/images/tutorial4_sys1.png source/images/tutorial4_sys1.pdf source/images/tutorial4_sys2.png source/images/tutorial4_sys2.pdf source/images/tutorial4_bs.png source/images/tutorial4_bs.pdf
+ALL_TUTORIAL_IMAGES = $(TUTORIAL1A_IMAGES)  $(TUTORIAL2A_IMAGES) $(TUTORIAL2B_IMAGES) $(TUTORIAL2C_IMAGES) $(TUTORIAL3A_IMAGES) $(TUTORIAL3B_IMAGES) $(TUTORIAL4_IMAGES)
+
+.PHONY: help clean realclean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html      to make standalone HTML files"
+	@echo "  dirhtml   to make HTML files named index.html in directories"
+	@echo "  pickle    to make pickle files"
+	@echo "  json      to make JSON files"
+	@echo "  htmlhelp  to make HTML files and a HTML help project"
+	@echo "  qthelp    to make HTML files and a qthelp project"
+	@echo "  latex     to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  changes   to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck to check all external links for integrity"
+	@echo "  doctest   to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/* $(GENERATEDPDF)
+	-rm -rf source/reference/generated
+
+realclean: clean
+	-rm -f $(ALL_TUTORIAL_IMAGES) source/images/.*_flag
+
+html:	$(ALL_TUTORIAL_IMAGES)
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml: $(ALL_TUTORIAL_IMAGES)
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+pickle: $(ALL_TUTORIAL_IMAGES)
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:   $(ALL_TUTORIAL_IMAGES)
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp: $(ALL_TUTORIAL_IMAGES)
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp: $(ALL_TUTORIAL_IMAGES)
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/kwant.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/kwant.qhc"
+
+latex:  $(GENERATEDPDF) $(ALL_TUTORIAL_IMAGES)
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
+	      "run these through (pdf)latex."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+%.pdf: %.svg
+	inkscape --export-pdf=$@ $<
+
+# Generation of tutorial images.  This requires some serious make trickery, see
+# http://article.gmane.org/gmane.comp.gnu.make.general/5806
+$(TUTORIAL1A_IMAGES): source/images/.tutorial1a_flag
+	@:
+source/images/.tutorial1a_flag: source/images/tutorial1a.py
+	cd source/images/ && python tutorial1a.py
+	touch source/images/.tutorial1a_flag
+
+$(TUTORIAL2A_IMAGES): source/images/.tutorial2a_flag
+	@:
+source/images/.tutorial2a_flag: source/images/tutorial2a.py
+	cd source/images/ && python tutorial2a.py
+	touch source/images/.tutorial2a_flag
+
+$(TUTORIAL2B_IMAGES): source/images/.tutorial2b_flag
+	@:
+source/images/.tutorial2b_flag: source/images/tutorial2b.py
+	cd source/images/ && python tutorial2b.py
+	touch source/images/.tutorial2b_flag
+
+$(TUTORIAL2C_IMAGES): source/images/.tutorial2c_flag
+	@:
+source/images/.tutorial2c_flag: source/images/tutorial2c.py
+	cd source/images/ && python tutorial2c.py
+	touch source/images/.tutorial2c_flag
+
+$(TUTORIAL3A_IMAGES): source/images/.tutorial3a_flag
+	@:
+source/images/.tutorial3a_flag: source/images/tutorial3a.py
+	cd source/images/ && python tutorial3a.py
+	touch source/images/.tutorial3a_flag
+
+$(TUTORIAL3B_IMAGES): source/images/.tutorial3b_flag
+	@:
+source/images/.tutorial3b_flag: source/images/tutorial3b.py
+	cd source/images/ && python tutorial3b.py
+	touch source/images/.tutorial3b_flag
+
+$(TUTORIAL4_IMAGES): source/images/.tutorial4_flag
+	@:
+source/images/.tutorial4_flag: source/images/tutorial4.py
+	cd source/images/ && python tutorial4.py
+	touch source/images/.tutorial4_flag

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/togglediv.js

+function togglediv(id) {
+    var buttontext;
+
+    buttontext = $("#" + id + "-button").text();
+
+    if(buttontext == 'show') {
+        $("#" + id + "-button").text('hide');
+    }
+    else {
+        $("#" + id + "-button").text('show');
+    }
+
+    $("#" + id + "-body").slideToggle('swing');
+}

doc/source/conf.py

+# -*- coding: utf-8 -*-
+#
+# 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.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+import kwant
+
+# -- General configuration -----------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+
+sys.path.insert(0, os.path.abspath('../sphinxext'))
+
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary',
+              'sphinx.ext.todo', 'sphinx.ext.pngmath', 'numpydoc',
+              'kwantdoc']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['../templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8'
+
+# The master toctree document.
+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'
+
+# 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
+
+# The short X.Y version.
+version = release[:i]
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of documents that shouldn't be included in the build.
+#unused_docs = []
+
+# List of directories, relative to source directory, that shouldn't be searched
+# for source files.
+exclude_trees = []
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+default_role = "autolink"
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+# Do not show all class members automatically in the class documentation
+numpydoc_show_class_members = False
+
+# -- 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'
+
+# 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
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# 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
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+html_use_modindex = False
+
+# This is needed too.
+html_domain_indices = False
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# 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'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'kwant.tex', u'kwant Documentation',
+   u'A. R. Akhmerov, C. W. Groth, X. Waintal, M. Wimmer',
+   'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# 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
+
+# -- Options for autodoc -------------------------------------------------------
+# Generate stub pages for autosummary directives.
+autosummary_generate = True
+
+autoclass_content = "both"
+autodoc_default_flags = ['show-inheritance']

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/tutorial2c_sketch.svg

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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))