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content/citing.txt
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Citing kwant
============
While kwant is not publicly released yet, we hope that once it is, it will be
used for research. If kwant contributes to a project that leads to a scientific
publication, please acknowledge this fact by citing the project. The kwant
paper has not been published yet, but will be announced at this place once
published: please check.
The principal developers of kwant are:
* Christoph W. Groth (SPSMS-INAC-CEA Grenoble)
* Michael Wimmer (Leiden University)
* `Anton R. Akhmerov <http://antonakhmerov.org>`__ (Harvard University, Leiden University)
* Xavier Waintal (SPSMS-INAC-CEA Grenoble)
We provide Kwant as free software under a BSD license as a
service to the physics community. If you have used Kwant for work that has lead
to a scientific publication, please mention this explicitly in the text body.
In addition, we ask you to cite the main paper that introduces Kwant:
The reference will be provided here once it is available (soon).
If you have profited from the quantum transport functionality of Kwant, please
also cite the upcoming paper that describes the relevant algorithms. The
reference will also be added here once it is available.
Kwant owes much of its current performance to the use of the `MUMPS
<http://graal.ens-lyon.fr/MUMPS/>`_ library for solving systems of sparse linear
equations. If you have done high-performance calculations, we suggest citing
P. R. Amestoy, I. S. Duff, J. S. Koster, J. Y. L’Excellent, SIAM. J. Matrix
Anal. & Appl. **23** (1), 15 (2001).
Finally, if you use the routine for generation of circular ensembles of random
matrices, please cite
\F. Mezzadri, Notices Am. Math. Soc. **54**, 592 (2007).
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============================================
Contributing to Kwant and reporting problems
============================================
We see Kwant not just as a package with fixed functionality, but rather as a
framework for implementing different physics-related algorithms using a common
set of concepts and, if possible, a shared interface. We have designed it
leaving room for growth, and plan to keep extending it.
External contributions to Kwant are highly welcome. You can help to advance the
project not only by writing code, but also by reporting bugs, and
fixing/improving the documentation. A mailing list TODO: add link (also
usable through a web interface (TODO: add link) ) is available for discussions.
If you have some code that works well with Kwant, or extends it in some useful
way, please consider sharing it. Any external contribution will be clearly
marked as such, and relevant papers will be added to the list of `suggested
acknowledgements </citing.html>`_. The complete development history is
available through a `web interface <http://git.kwant-project.org/kwant>`_.
Reporiting bugs
---------------
If you encounter a problem with Kwant, first try to reproduce it with as simple
a system as possible. Double-check with the documentation that what you observe
is actually a bug in Kwant. If you think it is, please check whether the problem
is already known by searching the mailing list. (TODO: tell how).
If the problem is not known yet, please email a bug report to the `Kwant mailing
list <mailto:kwant-discuss@kwant-project.org>`_. A report should contain:
* The versions of software you are using (Kwant, Python, operating system, etc.)
* A description of the problem, i.e. what exactly goes wrong.
* Enough information to reproduce the bug, preferably in the form of a simple
script.
How to contribute
-----------------
We use the version control system `Git <http://git-scm.com/>`_ to coordinate the
development of Kwant. If you are new to Git, we invite you to learn its basics.
(There's a plethora of information available on the Web.) Kwant's Git
repository contains not only the source code, but also all of the reference
documentation and the tutorial.
It is best to base your work on the latest version of Kwant::
git clone http://git.kwant-project.org/kwant
Then you can modify the code, and build Kwant and the documentation as described
in the `installation instructions </install.html>`_.
Some things to keep in mind:
* Please keep the code consistent by adhering to the prevailing naming and
formatting conventions. We generally follow the `"Style Guide for Python
Code" <http://www.python.org/dev/peps/pep-0008/>`_ For docstrings, we follow
`NumPy's "Docstring Standard"
<http://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt>`_ and
`Python's "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.
A useful trick for working on the source code is to build in-place so that there
is no need to re-install after each change. 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 that 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.
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Download
========
Thank you for your interest in kwant. We expect to release it to the public in
summer 2013. Please use the form below if you would like to get a notification
once kwant is available. We will only use the provided email address to send
the announcement.
.. raw:: html
<form action="/mail.php" method="POST">
<p>Your name</p>
<input type="text" name="name">
<p>Your email address</p>
<input type="text" name="email">
<p>Optional comment</p>
<textarea name="comment" rows="6" cols="40"></textarea>
<br />
<br />
<input type="submit" value="Inform me once kwant is available">
</form>
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Install
=======
Kwant can be installed either using some prepared packages (on GNU/Linux, Mac OS
X, and Windows), or it can be built and installed from source.
In general, installation from packages is advisable, especially for novice
users. Expert users may find it helpful to build Kwant from source, as this
will also allow them to customize Kwant to use certain optimized versions of
libraries.
Ubuntu (and derivatives)
------------------------
Execute the following commands::
sudo apt-add-repository ppa:kwant-project/ppa
sudo apt-get update
sudo apt-get install python-kwant
This should provide Kwant for all the versions of Ubuntu >= 12.04.
Debian GNU/Linux (and derivatives)
----------------------------------
The easiest way to install Kwant on a Debian system is using the pre-built
packages we provide. Our packages are known to work with Debian "wheezy" and
Debian "jessie", but they may also work on many other recent Debian-derived
sytems as well. (For example the following works with recent Ubuntu
installations as well.)
The lines prefixed with ``sudo`` have to be run as root.
1. Add the following lines to ``/etc/apt/sources.list``::
deb http://kwant-project.org/debian/ stable main
deb-src http://kwant-project.org/debian/ stable main
2. (Optional) Add the OpenPGP key used to sign the repositories by executing::
sudo apt-key adv --keyserver pgp.mit.edu --recv-key C3F147F5980F3535
(Feel free to verify the validity of this key using the web of trust!)
3. Update the package data, and install Kwant::
sudo apt-get update
sudo apt-get install python-kwant python-kwant-doc
The `python-kwant-doc` package is optional and installs the HTML
documentation of Kwant in the directory ``/usr/share/doc/python-kwant-doc``.
Windows
-------
There are multiple distributions of scientific Python software for Windows that
provide the prerequisites for Kwant. We recommend to use the packages kindly
provided by Christoph Gohlke. To install Kwant on Windows
1. Determine whether you have a 32-bit or 64-bit Windows installation by
following these `instructions <http://support.microsoft.com/kb/827218>`_.
2. Download and install Python 2.7 for the appropriate architecture (32-bit or
64-bit) from the official `Python download site
<http://www.python.org/download/>`_.
3. Download and install ``scipy-stack``, ``tinyarray``, and ``kwant`` for Python
2.7 from `Christoph Gohlke's page
<http://www.lfd.uci.edu/~gohlke/pythonlibs/>`_. Once again you should choose
the architecture that is appropriate for your system. ("win32" means 32-bit,
"amd64" means 64-bit -- even if you have a processor from Intel.) If the
download from Gohlke's site is slow, try to download from our `mirror
<http://downloads.kwant-project.org/gohlke-mirror/>`_.
You may see a warning that says "The publisher could not be verified. Do you
want to run this software?". Select "Run".
Mac OSX
-------
There is a number of different package managers for bringing software
from the Unix/Linux world to Mac OSX. Since the community is quite
split, we provide Kwant and its dependencies both via the `MacPorts
<http://www.macports.org>`_ and `homebrew <http://brew.sh>`_ systems.
Mac OSX: MacPorts
-----------------
MacPorts is a full-fledged package manager that recreates a whole Linux-like
environment on your Mac. It requires little choices to be made by the user,
and allows for the simplest way to install Kwant.
In order to install Kwant, you have to
1. Install a recent version of MacPorts, as explained in the
`installation instructions of MacPorts
<http://www.macports.org/install.php>`_.
In particular, as explained there, you will have to install also a
few prerequisites, namely
* the Xcode developer tools (compiler suite for Mac OSX) from
`<http://developer.apple.com/downloads>`_. You need an Apple ID to
download: Note that if you have one already from using the App store
on the Mac/Ipad/Iphone/... you can use this one. You will also need the
command line tools: Within Xcode 4, you have to download them by going to
`Xcode->Preferences`, click on `Download`, go to `Components`,
select `Command Line Tools` and click on `Install`. Alternatively, you can
also directly download the command line tools from the
Apple developer website.
* if you have MacOSX 10.8 or higher, the X11 server from the
`XQuartz project <http://xquartz.macosforge.org>`_.
2. After the installation, open a terminal and execute ::
echo http://downloads.kwant-project.org/macports/ports.tar |\
sudo tee -a /opt/local/etc/macports/sources.conf >/dev/null
(this adds the Kwant MacPorts download link
`<http://downloads.kwant-project.org/macports/ports.tar>`_ at the end of the
``sources.conf`` file.)
3. Execute ::
sudo port selfupdate
4. Now, install Kwant and its prerequisites ::
sudo port install py27-kwant
5. Finally, we choose python 2.7 to be the default python ::
sudo port select --set python python27
After that, you will need to close and reopen the terminal to
have all changes in effect.
Notes:
* If you have problems with macports because your institution's firewall
blocks macports (more precisely, the `rsync` port), resulting in
errors from ``sudo port selfupdate``, follow
`these instructions <https://trac.macports.org/wiki/howto/PortTreeTarball>`_.
* Of course, if you already have macports installed, you can skip step 1
and continue with step 2.
Mac OS X: homebrew
------------------
homebrew is a recent addition to the package managers on Mac OSX. It is
more lightweight, tries to be as minimalistic as possible and give the user
more freedom. Because of that, it requires a little more experience on
the user side compared to MacPorts. The requirements are moderate though,
if you know how to add directories to the ``$PATH`` variable for your shell,
you are safe.
1. Open a terminal and install homebrew as described on the `homebrew
homepage <http://brew.sh>`_ (instructions are towards the end of
the page)
2. Run ::
brew doctor
and follow its directions. It will ask for a few prerequisites to be
installed, in particular
* the Xcode developer tools (compiler suite for Mac OSX) from
`<http://developer.apple.com/downloads>`_. You need an Apple ID to
download: Note that if you have one already from using the App store
on the Mac/Ipad/Iphone/... you can use this one. Note that downloading
the command line tools (not the full Xcode suite) suffices. If you have
the full Xcode suite installed, you might need to download the command
line tools manually if you have version 4 or higher. In this case
go to `Xcode->Preferences`, click on `Download`, go to `Components`,
select `Command Line Tools` and click on `Install`.
* although `brew doctor` might not complain about it right away,
while we're at it, you should also install the X11 server from the
`XQuartz project <http://xquartz.macosforge.org>`_ if you have Mac
OSX 10.8 or higher.
3. Add permanently ``/usr/local/bin`` before ``/usr/bin/`` in the ``$PATH$``
environment variable of your shell, for example by adding ::
export PATH=/usr/local/bin:$PATH
at the end of your ``.bash_profile`` or ``.profile``. Then close
the terminal Terminal and reopen it again.
4. Install a few prerequisites ::
brew install gfortran python
5. Add additional repositories ::
brew tap homebrew/science
brew tap samueljohn/python
brew tap michaelwimmer/kwant
6. Install Kwant and its prerequisites ::
pip install nose
brew install numpy scipy matplotlib
brew install kwant
Notes:
- If something does not work as expected, use ``brew doctor`` for
instructions (it will find conflicts and things like that).
- As mentioned, homebrew allows for quite some freedom. In particular,
if you are an expert, you don't need necessarily to install
numpy/scipy/matplotlib from homebrew, but can use your own installation.
The only prerequisite is that they are importable from python. (the
Kwant installation will in any case complain if they are not)
- In principle, you need not install the homebrew python, but could use
Apple's already installed python. Homebrew's python is more up-to-date,
though.
Building and installing from source
-----------------------------------
See complete `building instructions
</docs/build/html/pre/install.html#building-and-installing-from-source>`_.
templates/base.mako
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<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="/download.html">download</a></li>
<li><a href="/contact.html">contact</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>
......
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