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.gitignore
View file @ 0d679b3e
......@@ -2,19 +2,14 @@
*.pyc
*.pyo
*.so
*.pyd
/kwant/*.c
/kwant/*/*.c
/build
/dist
/doc/build
/doc/source/reference/generated/
/doc/source/code/include/*.py
/doc/source/code/figure/*.png
/doc/source/code/figure/*.pdf
/doc/source/code/figure/.*_flag
/doc/source/code/figure/[a-zA-Z]*.py
/doc/source/code/figure/*.txt
/doc/source/code/download/
/doc/source/figure/*.pdf
/build.conf
/kwant.egg-info/
/MANIFEST.in
......@@ -22,3 +17,4 @@
.coverage
.eggs/
htmlcov/
.ipynb_checkpoints/
.gitlab-ci.yml
View file @ 0d679b3e
......@@ -7,32 +7,39 @@ stages:
- deploy
- release
before_script:
# Here and below, a workaround for gitlab runner not fetching tags
# See https://gitlab.com/gitlab-org/gitaly/-/issues/2221
- git config --global --add safe.directory /builds/kwant/kwant
- git fetch --tags
variables:
# rsync is used to send documentation to our web servers: we never send any
# secret information, and using 'ssh-keyscan' causes the CI server's IP to be blacklisted
IGNORE_HOSTKEY: "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null"
SSH_COMMAND: "ssh -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null"
# Turn off threading to avoid slowdowns
OPENBLAS_NUM_THREADS : 1
OMP_NUM_THREADS : 1
MKL_DYNAMIC : FALSE
MKL_NUM_THREADS : 1
## Building Docker environments
## Only runs when docker specifications change
.build-env: &build-env
.build-env:
stage: build-env
when: manual
image:
name: gcr.io/kaniko-project/executor:debug
entrypoint: [""]
artifacts:
untracked: true
expire_in: 1 hour
before_script:
- mkdir -p /root/.docker
- echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /root/.docker/config.json
- mkdir -p /kaniko/.docker
- echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json
- git config --global --add safe.directory /builds/kwant/kwant
- git fetch --tags
build-env:ubuntu:
<<: *build-env
only:
changes:
- docker/Dockerfile.ubuntu
extends: .build-env
script:
- /kaniko/executor
--context $CI_PROJECT_DIR/docker
......@@ -40,34 +47,15 @@ build-env:ubuntu:
--destination $CI_REGISTRY_IMAGE/ubuntu
build-env:debian:
<<: *build-env
only:
changes:
- docker/Dockerfile.debian
extends: .build-env
script:
- /kaniko/executor
--context $CI_PROJECT_DIR/docker
--dockerfile $CI_PROJECT_DIR/docker/Dockerfile.debian
--destination $CI_REGISTRY_IMAGE/debian
build-env:conda:
<<: *build-env
only:
changes:
- docker/Dockerfile.conda
- docker/*.yml
script:
- /kaniko/executor
--context $CI_PROJECT_DIR/docker
--dockerfile $CI_PROJECT_DIR/docker/Dockerfile.conda
--destination $CI_REGISTRY_IMAGE/conda
build-env:default:
<<: *build-env
only:
changes:
- docker/Dockerfile.conda
- docker/*.yml
extends: .build-env
script:
- /kaniko/executor
--context $CI_PROJECT_DIR/docker
......@@ -77,10 +65,10 @@ build-env:default:
## Build environment specifications
.build: &build
.build:
stage: build
script:
- echo -e "[DEFAULT]\ndefine_macros = CYTHON_TRACE=1" >build.conf
- echo -e "[DEFAULT]\ndefine_macros = CYTHON_TRACE=1 NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION" >build.conf
- ./setup.py build
- ./setup.py build_ext -i
artifacts:
......@@ -88,59 +76,73 @@ build-env:default:
expire_in: 2 hour
.stable-env: &stable_env
.stable-env:
before_script:
- source deactivate
- source activate kwant-stable
- eval "$(micromamba shell hook --shell bash)"
- micromamba activate kwant-stable
- git config --global --add safe.directory /builds/kwant/kwant
- git fetch --tags
.no-extras-env: &no_extras_env
.no-extras-env:
before_script:
- source deactivate
- source activate kwant-stable-no-extras
- eval "$(micromamba shell hook --shell bash)"
- micromamba activate kwant-stable-no-extras
- git config --global --add safe.directory /builds/kwant/kwant
- git fetch --tags
# Note that this is 'latest' as of when the image was last built
.latest-env: &latest_env
.latest-env:
before_script:
- source deactivate
- source activate kwant-latest
- eval "$(micromamba shell hook --shell bash)"
- micromamba activate kwant-latest
- git config --global --add safe.directory /builds/kwant/kwant
- git fetch --tags
.bleeding-edge-env: &bleeding_edge_env
.bleeding-edge-env:
before_script:
- source deactivate
- conda env update -f /kwant-latest.yml
- source activate kwant-latest
- eval "$(micromamba shell hook --shell bash)"
- micromamba activate kwant-latest
- micromamba update --all
- git config --global --add safe.directory /builds/kwant/kwant
- git fetch --tags
.ubuntu-env: &ubuntu_env
.ubuntu-env:
image: gitlab.kwant-project.org:5005/kwant/kwant/ubuntu
.debian-env: &debian_env
.debian-env:
image: gitlab.kwant-project.org:5005/kwant/kwant/debian
## Build Jobs
build:ubuntu:
<<: *build
<<: *ubuntu_env
extends:
- .build
- .ubuntu-env
build:debian:
<<: *build
<<: *debian_env
extends:
- .build
- .debian-env
build:stable:
<<: *build
<<: *stable_env
extends:
- .build
- .stable-env
build:no-extras:
<<: *build
<<: *no_extras_env
extends:
- .build
- .no-extras-env
build:latest:
<<: *build
<<: *latest_env
extends:
- .build
- .latest-env
build:bleeding-edge:
<<: *build
<<: *bleeding_edge_env
extends:
- .build
- .bleeding-edge-env
only:
- schedules
allow_failure: true
......@@ -159,7 +161,15 @@ check for dependencies installed:
allow_failure: true
.test: &test
.test:
stage: test
script:
- py.test -r w --flakes kwant --junitxml=tests.xml --durations=10
artifacts:
reports:
junit: tests.xml
.coverage:
stage: test
script:
- py.test -r w --cov=kwant --cov-report term --cov-report html --flakes kwant --junitxml=tests.xml --durations=10
......@@ -171,65 +181,98 @@ check for dependencies installed:
test:stable:
<<: *test
<<: *stable_env
extends:
- .test
- .stable-env
dependencies:
- build:stable
test:no-extras:
<<: *test
<<: *no_extras_env
extends:
- .test
- .no-extras-env
dependencies:
- build:no-extras
test:ubuntu:
<<: *test
<<: *ubuntu_env
extends:
- .test
- .ubuntu-env
dependencies:
- build:ubuntu
test:debian:
<<: *test
<<: *debian_env
extends:
- .test
- .debian-env
dependencies:
- build:debian
test:latest:
<<: *test
<<: *latest_env
extends:
- .test
- .latest-env
dependencies:
- build:latest
test:bleeding-edge:
<<: *test
<<: *bleeding_edge_env
extends:
- .test
- .bleeding-edge-env
dependencies:
- build:bleeding-edge
only:
- schedules
allow_failure: true
test:python-mumps:
extends:
- .test
- .latest-env
dependencies:
- build:latest
script:
- micromamba install -y -c conda-forge python-mumps
- py.test -r w --flakes kwant --junitxml=tests.xml --durations=10
coverage:latest:
extends:
- .coverage
- .latest-env
dependencies:
- build:latest
only:
- schedules
## Documentation building
build documentation:
<<: *latest_env
extends: .latest-env
dependencies:
- build:latest
stage: test
script:
- make -C doc realclean; make -C doc html SPHINXOPTS='-A website_deploy=True -n -W' SOURCE_LINK_TEMPLATE="$CI_PROJECT_URL"/blob/\$\$r/\$\$f
- pip install --editable . # Makefile executes from folders
- python -c 'from matplotlib import pyplot' # Pre-generate font cache
- pip install ipykernel # Temporary, should be removed after a jupyter-sphinx feedstock update.
- python -m ipykernel install --user --name kwant-latest # Register the kernel
- make -C doc clean; make -C doc html SPHINXOPTS='-A website_deploy=True -n -D jupyter_execute_default_kernel=kwant-latest' SOURCE_LINK_TEMPLATE="$CI_PROJECT_URL"/blob/\$\$r/\$\$f
artifacts:
paths:
- doc/build/html/
expire_in: 1 month
build PDF documentation:
<<: *latest_env
extends: .latest-env
dependencies:
- build:latest
stage: test
script:
- make -C doc latex SPHINXOPTS='-n -W'
- pip install --editable . # Makefile executes from folders
- python -c 'from matplotlib import pyplot' # Pre-generate font cache
- pip install ipykernel # Temporary, should be removed after a jupyter-sphinx feedstock update.
- python -m ipykernel install --user --name kwant-latest # Register the kernel
- make -C doc latex SPHINXOPTS='-n -D jupyter_execute_default_kernel=kwant-latest'
- cd doc/build/latex
- make all-pdf
artifacts:
......@@ -238,12 +281,15 @@ build PDF documentation:
expire_in: 1 month
check for broken links in doc:
<<: *latest_env
extends: .latest-env
dependencies:
- build:latest
stage: test
script:
- make -C doc linkcheck
- pip install --editable . # Makefile executes from folders
- pip install ipykernel # Temporary, should be removed after a jupyter-sphinx feedstock update.
- python -m ipykernel install --user --name kwant-latest # Register the kernel
- make -C doc linkcheck SPHINXOPTS='-n -D jupyter_execute_default_kernel=kwant-latest'
allow_failure: true
......@@ -252,19 +298,18 @@ check for broken links in doc:
upload coverage:
stage: deploy
only:
- branches@kwant/kwant
- schedules
dependencies:
- coverage:latest
environment:
name: coverage/$CI_BUILD_REF_NAME
url: https://kwant-project.org/coverage/$CI_BUILD_REF_SLUG
name: coverage/$CI_COMMIT_REF_NAME
url: https://kwant-project.org/coverage/$CI_COMMIT_REF_SLUG
on_stop: remove_coverage
before_script:
- mkdir -p ~/.ssh
- echo $MASTER_WEBSITE_KEY | base64 -d > ~/.ssh/id_rsa && chmod 600 ~/.ssh/id_rsa
script:
- mv htmlcov $CI_BUILD_REF_SLUG
- rsync -rlv -e "$IGNORE_HOSTKEY" --delete --relative $CI_BUILD_REF_SLUG kwant@kwant-project.org:coverage/
after_script:
- rm -rf ~/.ssh
- eval $(ssh-agent -s)
- echo $MASTER_WEBSITE_KEY | base64 -d | ssh-add -
- mv htmlcov $CI_COMMIT_REF_SLUG
- rsync -rlv -e "$SSH_COMMAND" --delete --relative $CI_COMMIT_REF_SLUG kwant@kwant-project.org:coverage/
remove_coverage:
......@@ -273,33 +318,27 @@ remove_coverage:
- branches@kwant/kwant
when: manual
environment:
name: coverage/$CI_BUILD_REF_NAME
name: coverage/$CI_COMMIT_REF_NAME
action: stop
before_script:
- mkdir -p ~/.ssh
- echo $MASTER_WEBSITE_KEY | base64 -d > ~/.ssh/id_rsa && chmod 600 ~/.ssh/id_rsa
script:
- eval $(ssh-agent -s)
- echo $MASTER_WEBSITE_KEY | base64 -d | ssh-add -
- mkdir empty/
- rsync -rlv -e "$IGNORE_HOSTKEY" --delete empty/ kwant@kwant-project.org:coverage/$CI_BUILD_REF_SLUG
after_script:
- rm -rf ~/.ssh
- rsync -rlv -e "$SSH_COMMAND" --delete empty/ kwant@kwant-project.org:coverage/$CI_COMMIT_REF_SLUG
upload documentation to the test server:
stage: deploy
environment:
name: docs review/$CI_BUILD_REF_NAME
url: https://test.kwant-project.org/doc/$CI_BUILD_REF_SLUG
name: docs review/$CI_COMMIT_REF_NAME
url: https://test.kwant-project.org/doc/$CI_COMMIT_REF_SLUG
on_stop: remove_docs
only:
- branches@kwant/kwant
before_script:
- mkdir -p ~/.ssh
- echo $TEST_WEBSITE_KEY | base64 -d > ~/.ssh/id_rsa && chmod 600 ~/.ssh/id_rsa
script:
- rsync -rlv -e "$IGNORE_HOSTKEY" --delete doc/build/html/* kwant@kwant-project.org:doc/$CI_BUILD_REF_SLUG
after_script:
- rm -rf ~/.ssh
- eval $(ssh-agent -s)
- echo $TEST_WEBSITE_KEY | base64 -d | ssh-add -
- rsync -rlv -e "$SSH_COMMAND" --delete doc/build/html/* kwant2@test.kwant-project.org:doc/$CI_COMMIT_REF_SLUG
remove_docs:
......@@ -308,16 +347,13 @@ remove_docs:
only:
- branches@kwant/kwant
environment:
name: docs review/$CI_BUILD_REF_NAME
name: docs review/$CI_COMMIT_REF_NAME
action: stop
before_script:
- mkdir -p ~/.ssh
- echo $TEST_WEBSITE_KEY | base64 -d > ~/.ssh/id_rsa && chmod 600 ~/.ssh/id_rsa
script:
- eval $(ssh-agent -s)
- echo $TEST_WEBSITE_KEY | base64 -d | ssh-add -
- mkdir empty
- rsync -arv -e "$IGNORE_HOSTKEY" --delete empty/ kwant@kwant-project.org:doc/$CI_BUILD_REF_SLUG/
after_script:
- rm -rf ~/.ssh
- rsync -arv -e "$SSH_COMMAND" --delete empty/ kwant2@test.kwant-project.org:doc/$CI_COMMIT_REF_SLUG/
upload dev version docs:
......@@ -325,25 +361,22 @@ upload dev version docs:
environment:
name: production
url: https://kwant-project.org/doc/dev
only:
- master@kwant/kwant
before_script:
- mkdir -p ~/.ssh
- echo $MASTER_WEBSITE_KEY | base64 -d > ~/.ssh/id_rsa && chmod 600 ~/.ssh/id_rsa
rules:
- if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PROJECT_PATH == "kwant/kwant"
script:
- rsync -rlv -e "$IGNORE_HOSTKEY" --delete doc/build/html/* kwant@kwant-project.org:doc/dev
after_script:
- rm -rf ~/.ssh
- eval $(ssh-agent -s)
- echo $MASTER_WEBSITE_KEY | base64 -d | ssh-add -
- rsync -rlv -e "$SSH_COMMAND" --delete doc/build/html/* kwant@kwant-project.org:doc/dev
## Build documentation for tagged releases
.tagged-version: &tagged_version
.tagged-version:
only:
- /^v[0-9]+\.[0-9]+.[0-9]+$/@kwant/kwant
gather release artifacts:
<<: *tagged_version
extends: .tagged-version
stage: release
script:
- ./setup.py sdist
......
.gitlab/issue_templates/release.md 0 → 100644
View file @ 0d679b3e
# Release %vX.Y.Z **UPDATE THIS**
This is a checklist based on the [release document](RELEASE.rst); consult it for more details.
## Preflight checks
- [ ] All the issues from this milestone are resolved
- [ ] Ensure that tests pass on [main](https://gitlab.kwant-project.org/kwant/kwant/tree/main) branch
- [ ] Documentation looks correct https://test.kwant-project.org/doc/main
- [ ] [Whatnew](doc/source/pre/whatsnew) is up to date
- [ ] `AUTHORS.rst` and `.mailmap` are up to date (run `git shortlog -s | sed -e "s/^ *[0-9\t ]*//"| xargs -i sh -c 'grep -q "{}" AUTHORS.rst || echo "{}"'`)
## Make a release, but do not publish it yet
- [ ] Tag the release
- [ ] Build the source tarball and inspect it
- [ ] Build the documentation
## Test packaging
These steps may be done in parallel
### Debian
- [ ] Follow the steps for building the Debian packages from [RELEASE.rst](RELEASE.rst)
### Conda
- [ ] Publish the release candidate source tarball "somewhere on the internet" (SOTI)
- [ ] open a PR to the [conda-forge/kwant-feedstock](https://github.com/conda-forge/kwant-feedstock/) repo on Github. Make sure to mark the PR as WIP so that it doesn't get merged in accidentally
- [ ] set the upstream tarball URL (in meta.yaml) to SOTI
- [ ] update the tarball hash in meta.yaml
- [ ] See if the package builds
## Publish the release
- [ ] push the tag
- [ ] upload the source tarball to PyPI
- [ ] upload the source tarball to the Kwant website
- [ ] publish the debian packages
- [ ] publish the ubuntu packages
- [ ] create a new version of the Kwant conda-forge feedstock, and open a pull request to upstream
- [ ] upload the documentation to the Kwant website
- [ ] update the Kwant website to say that Conda is the preferred way to install Kwant on Windows
## Announce the release
- [ ] Write a short post summarizing the highlights on the Kwant website
- [ ] post to the Kwant mailing list
## Working towards next release
- [ ] add a whatsnew file for the next release
- [ ] tag this release with an `a0` suffix
- [ ] push this tag to the official Kwant repository
- [ ] create a milestone for the next release
.mailmap
View file @ 0d679b3e
......@@ -2,6 +2,7 @@ Thomas Kloss <kloss@itp.uni-frankfurt.de>
<joseph@weston.cloud> <joseph.weston08@gmail.com>
<joseph@weston.cloud> <joseph.weston@cea.fr>
<joseph@weston.cloud> <me@josephweston.org>
<joseph@weston.cloud> <v-josewe@microsoft.com>
Tómas Örn Rosdahl <torosdahl@gmail.com>
<slavoutich@ostroukh.me> <ostroukh@lorentz.leidenuniv.nl>
<m.t.wimmer@tudelft.nl> <wimmer@lorentz.leidenuniv.nl>
......
AUTHORS.rst
View file @ 0d679b3e
......@@ -8,16 +8,20 @@ The principal developers of Kwant are
* `Christoph Groth <mailto:christoph.groth@cea.fr>`_ (CEA Grenoble)
* `Michael Wimmer <https://michaelwimmer.org>`_ (TU Delft)
* `Anton Akhmerov <http://antonakhmerov.org>`_ (TU Delft)
* `Xavier Waintal <http://inac.cea.fr/Pisp/xavier.waintal>`_ (CEA Grenoble)
* `Joseph Weston <http://josephweston.org>`_ (TU Delft)
* `Anton Akhmerov <https://antonakhmerov.org>`_ (TU Delft)
* `Xavier Waintal <https://www.pheliqs.fr/en/Pages/Portrait/Xavier-Waintal.aspx>`_ (CEA Grenoble)
* `Joseph Weston <https://joseph.weston.cloud>`_ (TU Delft)
Contributors to Kwant include
* Jörg Behrmann (FU Berlin)
* Pierre Carmier (CEA Grenoble)
* Paul Clisson (CEA Grenoble)
* `Dennis Heffels <mailto:d.heffels@fz-juelich.de>`_ (FZJ PGI-9)
* Mathieu Istas (CEA Grenoble)
* Daniel Jaschke (CEA Grenoble)
* Thomas Kloss (CEA Grenoble)
* Kelvin Loh (TNO)
* Bas Nijholt (TU Delft)
* Michał Nowak (TU Delft)
* Viacheslav Ostroukh (Leiden University)
......@@ -27,12 +31,11 @@ Contributors to Kwant include
* Rafał Skolasiński (TU Delft)
* Adrien Sorgniard (CEA Grenoble)
* Dániel Varjas (TU Delft)
* Thomas Kloss (CEA Grenoble)
* Pierre Carmier (CEA Grenoble)
* Kostas Vilkelis (TU Delft)
We thank Christoph Gohlke for the creation of installers for Microsoft Windows.
`CEA <http://www.cea.fr>`_ is the French Commissariat à l'énergie atomique et aux
`CEA <https://www.cea.fr>`_ is the French Commissariat à l'énergie atomique et aux
énergies alternatives. The CEA is the copyright holder for the contributions of
C. W. Groth, X. Waintal, and its other employees involved in Kwant.
......
CITING.rst
View file @ 0d679b3e
......@@ -15,7 +15,7 @@ cite the main paper that introduces Kwant:
C. W. Groth, M. Wimmer, A. R. Akhmerov, X. Waintal,
*Kwant: a software package for quantum transport*,
`New J. Phys. 16, 063065 (2014)
<https://iopscience.iop.org/1367-2630/16/6/063065/article>`_.
<https://doi.org/10.1088/1367-2630/16/6/063065>`_.
Other references we ask you to consider
......@@ -26,7 +26,7 @@ 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
<https://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
......
INSTALL.rst
View file @ 0d679b3e
......@@ -20,7 +20,7 @@ Obtaining the source code
Source distributions of Kwant (and Tinyarray) are available at the `downloads
section of the Kwant website <https://downloads.kwant-project.org/kwant/>`_ as well
as `PyPI <https://pypi.python.org/pypi/kwant>`_. The sources may be also
as `PyPI <https://pypi.org/project/kwant>`_. The sources may be also
cloned directly from the `official Kwant git repository
<https://gitlab.kwant-project.org/kwant/kwant>`_.
......@@ -29,33 +29,32 @@ Prerequisites
=============
Building Kwant requires
* `Python <https://www.python.org/>`_ 3.5 or above (Kwant 1.1 is the last
version to support Python 2),
* `NumPy <http://numpy.org/>`_ 1.11.0 or newer,
* `SciPy <https://www.scipy.org/>`_ 0.17.0 or newer,
* `LAPACK <http://netlib.org/lapack/>`_ and `BLAS <http://netlib.org/blas/>`_,
* `Python <https://www.python.org/>`_ 3.8 or above,
* `NumPy <https://numpy.org/>`_ 1.18.0 or newer,
* `SciPy <https://www.scipy.org/>`_ 1.3.0 or newer,
* `LAPACK <https://netlib.org/lapack/>`_ and `BLAS <https://netlib.org/blas/>`_,
(For best performance we recommend the free `OpenBLAS
<http://www.openblas.net/>`_ or the nonfree `MKL
<https://software.intel.com/en-us/intel-mkl>`_.)
* `Tinyarray <https://gitlab.kwant-project.org/kwant/tinyarray>`_ 1.2 or newer,
<https://www.openblas.net/>`_ or the nonfree `MKL
<https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html>`_.)
* `Tinyarray <https://gitlab.kwant-project.org/kwant/tinyarray>`_ 1.2.2 or newer,
a NumPy-like Python package optimized for very small arrays,
* An environment which allows to compile Python extensions written in C and
C++.
The following software is highly recommended though not strictly required:
* `matplotlib <http://matplotlib.org/>`_ 1.5.1 or newer, for the module `kwant.plotter` and the tutorial,
* `SymPy <http://sympy.org/>`_ 0.7.6 or newer, for the subpackage `kwant.continuum`.
* `matplotlib <https://matplotlib.org/>`_ 3.2.2 or newer, for the module `kwant.plotter` and the tutorial,
* `SymPy <https://sympy.org/>`_ 1.5.1 or newer, for the subpackage `kwant.continuum`.
* `Qsymm <https://pypi.org/project/qsymm/>`_ 1.2.6 or newer, for the subpackage `kwant.qsymm`.
* `MUMPS <http://graal.ens-lyon.fr/MUMPS/>`_, a sparse linear algebra library
* `MUMPS <https://mumps-solver.org/>`_, a sparse linear algebra library
that will in many cases speed up Kwant several times and reduce the memory
footprint. (Kwant uses only the sequential, single core version
of MUMPS. The advantages due to MUMPS as used by Kwant are thus independent
of the number of CPU cores of the machine on which Kwant runs.)
* The `py.test testing framework <http://pytest.org/>`_ 2.8 or newer for running the
* The `py.test testing framework <https://docs.pytest.org/>`_ 3.3.2 or newer for running the
tests included with Kwant.
In addition, to build a copy of Kwant that has been checked-out directly from
version control, you will also need `Cython <http://cython.org/>`_ 0.22 or
version control, you will also need `Cython <https://cython.org/>`_ 3.0 or
newer. You do not need Cython to build Kwant that has been unpacked from a
source .tar.gz-file.
......@@ -63,9 +62,8 @@ source .tar.gz-file.
Building and installing Kwant
=============================
Kwant can be built and installed following the `usual Python conventions
<https://docs.python.org/3/install/index.html>`_ by running the following
commands in the root directory of the Kwant distribution. ::
Kwant can be built and installed by running the following commands in the root
directory of the Kwant distribution. ::
python3 setup.py build
python3 setup.py install
......@@ -105,9 +103,9 @@ The sections bear the names of the extension modules, for example
``[DEFAULT]`` section that provides default values for all extensions, also
those not explicitly present in the file.
Possible keys are the keyword arguments for ``distutils.core.Extension`` (For a
Possible keys are the keyword arguments for ``setuptools.Extension`` (For a
complete list, see its `documentation
<https://docs.python.org/3/distutils/apiref.html#distutils.core.Extension>`_).
<https://setuptools.pypa.io/en/latest/userguide/ext_modules.html>`_).
The corresponding values are whitespace-separated lists of strings.
Example ``build.conf`` for compiling Kwant with C assertions and Cython's line
......@@ -128,7 +126,7 @@ The section ``[kwant.linalg._mumps]`` may be used to adapt the build process.
Example ``build.conf`` for linking Kwant against a self-compiled MUMPS, `SCOTCH
<http://www.labri.fr/perso/pelegrin/scotch/>`_ and `METIS
<https://www.labri.fr/perso/pelegrin/scotch/>`_ and `METIS
<http://glaros.dtc.umn.edu/gkhome/metis/metis/overview>`_::
[mumps]
......@@ -143,10 +141,13 @@ Building the documentation
==========================
To build the documentation, the `Sphinx documentation generator
<http://www.sphinx-doc.org/en/stable/>`_ is required with ``numpydoc`` extension
(version 0.5 or newer). If PDF documentation is to be built, the tools
from the `libRSVG <https://wiki.gnome.org/action/show/Projects/LibRsvg>`_ (Debian/Ubuntu package
``librsvg2-bin``) are needed to convert SVG drawings into the PDF format.
<https://www.sphinx-doc.org/en/stable/>`_ is required with ``numpydoc`` extension
(version 0.5 or newer), as well as ``jupyter-sphinx`` (version 0.2 or newer).
If PDF documentation is to be built, the tools
from the `libRSVG <https://wiki.gnome.org/action/show/Projects/LibRsvg>`_
(Debian/Ubuntu package ``librsvg2-bin``) and a Sphinx extension
``sphinxcontrib-svg2pdfconverter`` are needed to convert SVG drawings into the
PDF format.
As a prerequisite for building the documentation, Kwant must have been built
successfully using ``python3 setup.py build`` as described above (or Kwant must
......@@ -160,25 +161,6 @@ Because of some quirks of how Sphinx works, it might be necessary to execute
done, Sphinx may mistakenly use PNG files for PDF output or other problems may
appear.
When ``make html`` is run, modified tutorial example scripts are executed to
update any figures that might have changed. The machinery behind this works as
follows. The canonical source for a tutorial script, say ``graphene.py`` is
the file ``doc/source/images/graphene.py.diff``. This diff file contains the
information to recreate two versions of ``graphene.py``: a version that is
presented in the documentation (``doc/source/tutorial/graphene.py``), and a
version that is used to generate the figures for the documentation
(``doc/source/images/graphene.py``). Both versions are related but differ
e.g. in the details of the plotting. When ``make html`` is run, both versions
are extracted form the diff file.
The diff file may be modified directly. Another possible way of working is to
directly modify either the tutorial script or the figure generation script.
Then ``make html`` will use the command line tool `wiggle
<https://github.com/neilbrown/wiggle>`_ to propagate the modifications accordingly.
This will often just work, but may sometimes result in conflicts, in which case
a message will be printed. The conflicts then have to be resolved much like
with a version control system.
****************************
Hints for specific platforms
****************************
......@@ -211,72 +193,6 @@ By default the package will be installed under ``/usr/local``. Run ``python3
setup.py --help install`` for installation options.
Mac OS X: MacPorts
==================
The following instructions are valid for Kwant 1.1 with Python 2.7. They need
to be updated for Kwant 1.2. (Help is welcome.)
The required dependencies of Kwant are best installed with one of the packaging
systems. Here we only consider the case of `MacPorts
<https://www.macports.org>`_ in detail. Some remarks for homebrew are given
below.
1. Install a recent version of MacPorts, as explained in the `installation
instructions of MacPorts <https://www.macports.org/install.php>`_.
2. Install the required dependencies::
sudo port install gcc47 python27 py27-numpy py27-scipy py27-matplotlib mumps_seq
sudo port select --set python python27
3. Unpack Tinyarray, enter its directory, build and install::
python setup.py build
sudo python setup.py install
4. Unpack Kwant, go to the Kwant directory, and edit ``build.conf`` to read::
[mumps]
include_dirs = /opt/local/include
library_dirs = /opt/local/lib
libraries = zmumps_seq mumps_common_seq pord_seq esmumps scotch scotcherr mpiseq gfortran
5. Then, build and install Kwant. ::
CC=gcc-mp-4.7 LDSHARED='gcc-mp-4.7 -shared -undefined dynamic_lookup' python setup.py build
sudo python setup.py install
You might note that installing Kwant on Mac OS X is somewhat more involved than
installing on Linux. Part of the reason is that we need to mix Fortran and C
code in Kwant: While C code is usually compiled using Apple compilers,
Fortran code must be compiled with the Gnu Fortran compiler (there is
no Apple Fortran compiler). For this reason we force the Gnu compiler suite
with the environment variables ``CC`` and ``LDSHARED`` as shown above.
Mac OS X: homebrew
==================
The following instructions are valid for Kwant 1.1 with Python 2.7. They need
to be updated for Kwant 1.2. (Help is welcome.)
It is also possible to build Kwant using homebrew. The dependencies can be
installed as ::
brew install gcc python
brew tap homebrew/science
brew tap homebrew/python
brew tap kwant-project/kwant
pip install pytest pytest-runner six
brew install numpy scipy matplotlib
Note that during the installation you will be told which paths to add when you
want to compile/link against scotch/metis/mumps; you need to add these to the
build.conf file. Also, when linking against MUMPS, one needs also to link
against METIS (in addition to the libraries needed for MacPorts).
Microsoft Windows
=================
......
README.rst
View file @ 0d679b3e
......@@ -28,14 +28,11 @@ Kwant can calculate
Other computations involving tight-binding Hamiltonians can be implemented
easily.
See the `Kwant web site <http://kwant-project.org/>`_ for the latest stable
See the `Kwant website <https://kwant-project.org/>`_ for the latest stable
version. The current development version is available via the `Kwant gitlab
instance <https://gitlab.kwant-project.org/kwant/kwant>`_. Contributions are
welcome.
A `mailing list <http://kwant-project.org/community>`_ exists for general
A `mailing list <https://kwant-project.org/community>`_ exists for general
discussions related to Kwant. Please report bugs and other issues using the
`issue tracker <https://gitlab.kwant-project.org/kwant/kwant/issues>`_.
See also in this directory: `<INSTALL.rst>`_, `<LICENSE.rst>`_, `<AUTHORS.rst>`_,
`<CITING.rst>`_, `<CONTRIBUTE.rst>`_.
RELEASE.rst
View file @ 0d679b3e
......@@ -3,6 +3,10 @@ Making a Kwant release
This document guides a contributor through creating a release of Kwant.
Create a release issue
######################
Use the correct `issue template <gitlab.kwant-project.org/kwant/kwant/issues/new?issuable_template=release>`_, adjust it if necessary.
Preflight checks
################
......@@ -105,7 +109,9 @@ in /tmp and inspect that builds in isolation and that the tests run::
cd /tmp
tar xzf ~/src/kwant/dist/kwant-<version>.tar.gz
cd kwant-<version>
./setup.py test
./setup.py build
./setup.py build_ext -i
py.test
Build the documentation
......@@ -114,21 +120,23 @@ Building the documentation requires 'sphinx' and a Latex installation.
First build the HTML and PDF documentation::
./setup.py build
cd doc
make realclean
make html latex SPHINXOPTS='-A website_deploy=True -n -W'
cd doc/build/latex
make all-pdf
make -C doc realclean
make -C doc html latex
make -C doc/build/latex all-pdf
Then create a zipped version of the HTML documentation and name the PDF
consistently, storing them, for example, in the "dist" directory along with the
source tarballs::
ln -s `pwd`/doc/build/html /tmp/kwant-doc-<version>
(cd /tmp/; zip -r kwant-doc-<version>.zip kwant-doc-<version>)
mv /tmp/kwant-doc-<version>.zip dist
version=$(git describe | sed 's/^v//') # Assumes that we are on a tag.
ln -s `pwd`/doc/build/html /tmp/kwant-doc-$version
(cd /tmp/; zip -r kwant-doc-$version.zip kwant-doc-$version)
mv /tmp/kwant-doc-$version.zip dist
mv doc/build/latex/kwant.pdf dist/kwant-doc-$version.pdf
mv doc/build/latex/kwant.pdf dist/kwant-doc-<version>.pdf
Finally, rebuild the documentation for the website (including the web analysis javascript code)::
make -C doc html SPHINXOPTS='-A website_deploy=True -n -W'
Clone the repository of the Kwant Debian package
......@@ -274,6 +282,14 @@ current Debian testing)::
ARCH=i386 DIST=<dist> git-pbuilder update
ARCH=amd64 DIST=<dist> git-pbuilder update
Make sure that the working directory is completely clear::
git clean -id
(Note that pytest has the nasty habit of creating a hidden ``.pytest_cache``
directory which gitignores itself. The above command will not delete this
directory, but git-pbuilder will complain.)
Now build the packages. First the i386 package. The option "--git-tag" tags
and signs the tag if the build is successful. In a second step, the package is
built for amd64, but only the architecture-dependent files (not the
......@@ -324,7 +340,7 @@ Push the tag to the official Kwant repository::
PyPI
----
Install `twine <https://pypi.python.org/pypi/twine>`_ and run the following
Install `twine <https://pypi.org/project/twine>`_ and run the following
(this requires a file ~/.pypirc with a valid username and password: ask
Christoph Groth to add you as a maintainer on PyPI, if you are not already)::
......@@ -343,7 +359,7 @@ The following requires ssh access to ``kwant-project.org`` (ask Christoph
Groth). The tarball and its signature (generated by the twine command above) should be
uploaded to the downloads section of the website::
scp dist/kwant-<version>.tar.gz* kwant-project.org:webapps/downloads/kwant
scp dist/kwant-<version>.tar.gz* kwant:web/downloads/kwant
Debian packages
......@@ -368,7 +384,7 @@ sure to update the codenames and the versions)::
Version: 9.0
Architectures: i386 amd64 source
Components: main
Description: Unofficial Debian package repository of http://kwant-project.org/
Description: Unofficial Debian package repository of https://kwant-project.org/
SignWith: C3F147F5980F3535
Origin: Kwant project
......@@ -377,7 +393,7 @@ sure to update the codenames and the versions)::
Version: 10.0
Architectures: i386 amd64 source
Components: main
Description: Unofficial Debian package repository of http://kwant-project.org/
Description: Unofficial Debian package repository of https://kwant-project.org/
SignWith: C3F147F5980F3535
If the config had to be updated execute::
......@@ -433,7 +449,7 @@ We will also use the following script (prepare_ppa_upload)::
for release in $@; do
cp /tmp/changelog.$$ debian/changelog
DEBEMAIL=christoph.groth@cea.fr dch -b -v "$version~$release" -u low 'Ubuntu PPA upload'
sed -i -e "1,1 s/UNRELEASED/$release/" debian/changelog
sed -i -e "1,1 s/UNRELEASED/${release%[0-9]}/" debian/changelog
debuild -S -sa
done
......@@ -514,23 +530,20 @@ Ask Christoph Groth if you need to be granted access.
Upload the zipped HTML and PDF documentation::
scp dist/kwant-doc-<version>.zip kwant-project.org:webapps/downloads/doc
scp dist/kwant-doc-<version>.pdf kwant-project.org:webapps/downloads/doc
Point the symbolic links ``latest.zip`` and ``latest.pdf`` to these new files::
ssh kwant-project.org "cd webapps/downloads/doc; ln -s kwant-doc-<version>.zip latest.zip"
ssh kwant-project.org "cd webapps/downloads/doc; ln -s kwant-doc-<version>.pdf latest.pdf"
scp dist/kwant-doc-<version>.{zip,pdf} kwant:web/downloads/doc
Then upload the HTML documentation for the main website::
Upload the HTML documentation for the website::
rsync -rlv --delete doc/build/html/* kwant-project.org:webapps/kwant/doc/<short-version>
rsync -rlv --delete doc/build/html/* kwant:web/main/doc/<short-version>
where in the above ``<short-version>`` is just the major and minor version numbers.
Finally point the symbolic link ``<major-version>`` to ``<short-version>``::
Finally, create symbolic links for the website::
ssh kwant-project.org "cd webapps/kwant/doc; ln -s <major> <short-version>"
ssh kwant
for e in zip pdf; do ln -sf kwant-doc-<version>.$e webapps/downloads/doc/latest.$e; done
ln -nsf <short-version> webapps/kwant/doc/<major>
exit
Announce the release
......
conftest.py
View file @ 0d679b3e
......@@ -2,9 +2,9 @@
#
# This file is part of Kwant. It is subject to the license terms in the file
# LICENSE.rst found in the top-level directory of this distribution and at
# http://kwant-project.org/license. A list of Kwant authors can be found in
# https://kwant-project.org/license. A list of Kwant authors can be found in
# the file AUTHORS.rst at the top-level directory of this distribution and at
# http://kwant-project.org/authors.
# https://kwant-project.org/authors.
"""Pytest plugin to ignore packages that have uninstalled dependencies.
This ignores packages on test collection, which is required when the
......
doc/Makefile
View file @ 0d679b3e
# Makefile for Sphinx documentation
# Copyright 2011-2017 Kwant authors.
# Minimal makefile for Sphinx documentation
#
# This file is part of Kwant. It is subject to the license terms in the file
# LICENSE.rst found in the top-level directory of this distribution and at
# http://kwant-project.org/license. A list of Kwant authors can be found in
# the file AUTHORS.rst at the top-level directory of this distribution and at
# http://kwant-project.org/authors.
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
SOURCEDIR = source
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
# 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.
FIGURESOURCES = $(shell find source -name "*.svg")
GENERATEDPDF = $(patsubst %.svg,%.pdf,$(FIGURESOURCES))
# Figure generation from patched tutorial scripts
#
# As make does not support the generation of multiple targets by a single
# invocation of a (non-implicit) rule, we use a trick: We pretend to be
# generating a single (empty) flag file per invocation. The figure files are
# generated as well, but only as side-effects. Each flag file is used to
# remember the time at which the corresponding figure-generating script was run.
# This works perfectly unless the actual output files are deleted without
# deleting the corresponding flag file.
FIGSCRIPTS = $(patsubst %.diff,%,$(notdir $(wildcard source/code/figure/*.py.diff)))
FIGURES = $(patsubst %.py,source/code/figure/.%_flag,$(FIGSCRIPTS))
SCRIPTS = $(sort $(FIGSCRIPTS) $(notdir $(wildcard source/code/include/*.py)))
INCLUDES = $(patsubst %,source/code/include/%,$(SCRIPTS))
DOWNLOADS = $(patsubst %,source/code/download/%,$(SCRIPTS))
.PHONY: help clean realclean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest
# Put it first so that "make" without argument is like "make help".
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)"
@echo
@echo "Append SPHINXOPTS='-A website_deploy=True' to include web analytics code."
clean:
-rm -rf $(BUILDDIR)/* $(GENERATEDPDF)
-rm -rf source/reference/generated
realclean: clean
-rm -f $(FIGURES)
-rm -f $(patsubst %,source/code/include/%,$(FIGSCRIPTS))
-rm -f $(DOWNLOADS)
-rm -f $(patsubst %,source/code/figure/%,$(FIGSCRIPTS))
-rm -f $(patsubst %.py,source/code/figure/%_*.png,$(FIGSCRIPTS))
-rm -f $(patsubst %.py,source/code/figure/%_*.pdf,$(FIGSCRIPTS))
html: $(FIGURES) $(INCLUDES) $(DOWNLOADS)
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
dirhtml: $(FIGURES) $(INCLUDES) $(DOWNLOADS)
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
pickle: $(FIGURES) $(INCLUDES) $(DOWNLOADS)
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
json: $(FIGURES) $(INCLUDES) $(DOWNLOADS)
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
.PHONY: help Makefile
htmlhelp: $(FIGURES) $(INCLUDES) $(DOWNLOADS)
$(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: $(FIGURES) $(INCLUDES) $(DOWNLOADS)
$(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) $(FIGURES) $(INCLUDES) $(DOWNLOADS)
$(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 $(BUILDDIR)/doctest/output.txt."
%.pdf: %.svg
inkscape --export-pdf=$@ $<
#### Tutorial and figure script generation machinery ####
# See source/code/README for an explanation.
# Make tutorial scripts by extracting the (complete!) context of the "patches".
# We make sure not to use 'wiggle' here.
.SECONDARY:
source/code/include/%.py: source/code/figure/%.py.diff
@sed -n '/^[- ]/ s/^.//p' <$< >$@
@touch -r $< $@
source/code/download/%.py: source/code/include/%.py
@mkdir -p source/code/download
@grep -v '^#HIDDEN' <$< >$@
# Make the figure generation scripts by patching tutorial scripts. If the
# tutorial scripts haven't been modified, don't patch but directly extract the
# figure generation scripts. This means that 'wiggle' is only needed when the
# tutorial scripts have been modified.
.SECONDARY:
source/code/figure/%.py: source/code/include/%.py
@if [ $< -nt $@.diff ]; then \
cp $< $@; \
rm -f $@.porig; \
if ! wiggle --replace $@ $@.diff; then \
command -v wiggle >/dev/null 2>&1 && \
echo "Resolve conflicts by editing the files named below"; \
touch -d@0 $@; \
exit 1; \
fi \
else \
sed -n '/^[+ ]/ s/^.//p' <$@.diff >$@; \
touch -r $@.diff $@; \
fi
clean:
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
# Make the figure generation scripts also depend on the diffs.
define makedep
source/code/figure/$(1): source/code/figure/$(1).diff
endef
$(foreach name,$(FIGSCRIPTS),$(eval $(call makedep,$(name))))
latex:
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
# Run an figure generation script. When successful, and if the script is newer
# than the corresponding diff, recreate the latter. Note that the
# corresponding tutorial script cannot be newer, since if it is, the figure
# generation script is generated from it by patching.
source/code/figure/.%_flag: source/code/figure/%.py
cd $(dir $<) && python3 $(notdir $<)
@if [ ! -f $<.diff -o $< -nt $<.diff ]; then \
wiggle --diff --lines source/code/include/$(notdir $<) $< >$<.diff; \
touch -r $< $<.diff; \
fi
@rm -f $<.porig
@touch $@
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
doc/kwantdoctheme/static/kwantdoctheme.css deleted 100644 → 0
View file @ 488ce42f
/* This theme is based on pydoctheme by Georg Brandl. */
@import url("default.css");
body {
background-color: white;
margin-left: 1em;
margin-right: 1em;
}
/* Disable typewriter font in headings. */
h1 tt, h2 tt, h3 tt, h4 tt, h5 tt, h6 tt {
font-family: "Bitstream Vera Sans", Verdana, sans-serif;
font-size: 100%;
}
div.body p, div.body dd, div.body li {
-webkit-hyphens: auto;
-moz-hyphens: auto;
-ms-hyphens: auto;
-o-hyphens: auto;
hyphens: auto;
}
div.related {
margin-bottom: 1.2em;
padding: 0.5em 0;
border-top: 1px solid #ccc;
margin-top: 0.5em;
}
dt:target, .highlighted {
background-color: #fbf1aa;
}
div.related:first-child {
border-top: 0;
border-bottom: 1px solid #ccc;
}
div.sphinxsidebar {
background-color: #eeeeee;
border-radius: 5px;
line-height: 130%;
font-size: smaller;
overflow: hidden;
}
div.sphinxsidebar h3, div.sphinxsidebar h4 {
margin-top: 1.5em;
}
div.sphinxsidebarwrapper > h3:first-child {
margin-top: 0.2em;
}
div.sphinxsidebarwrapper > ul > li > ul > li {
margin-bottom: 0.4em;
}
div.sphinxsidebar input {
font-family: 'Bitstream Vera Serif', Georgia, serif
border: 1px solid #999999;
font-size: smaller;
border-radius: 3px;
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div.sphinxsidebar input[type=text] {
max-width: 220px;
}
div.body {
padding: 0 0 0 1.2em;
}
div.body p {
line-height: 140%;
}
div.body h1, div.body h2, div.body h3, div.body h4, div.body h5, div.body h6 {
margin: 0;
border: 0;
padding: 0.3em 0;
}
div.body hr {
border: 0;
background-color: #ccc;
height: 1px;
}
div.body pre {
border-radius: 3px;
border: 1px solid #ac9;
}
div.body div.admonition, div.body div.impl-detail {
border-radius: 3px;
}
div.body div.impl-detail > p {
margin: 0;
}
div.body div.seealso {
border: 1px solid #dddd66;
}
tt, pre {
font-family: monospace, sans-serif;
font-size: 96.5%;
-webkit-hyphens: none;
-moz-hyphens: none;
-ms-hyphens: none;
-o-hyphens: none;
hyphens: none;
}
div.body tt {
border-radius: 3px;
}
div.body tt.descname {
font-size: 120%;
}
div.body tt.xref, div.body a tt {
font-weight: normal;
}
p.deprecated {
border-radius: 3px;
}
table.docutils {
border: 1px solid #ddd;
min-width: 20%;
border-radius: 3px;
margin-top: 10px;
margin-bottom: 10px;
}
table.docutils td, table.docutils th {
border: 1px solid #ddd !important;
border-radius: 3px;
}
table p, table li {
text-align: left !important;
}
table.docutils th {
background-color: #eee;
padding: 0.3em 0.5em;
}
table.docutils td {
background-color: white;
padding: 0.3em 0.5em;
}
table.footnote, table.footnote td {
border: 0 !important;
}
div.footer {
line-height: 150%;
margin-top: -2em;
text-align: right;
width: auto;
margin-right: 10px;
}
/* have arguments of functions or classes also a monospace font */
table.longtable.docutils > tbody > tr > td:first-child,
dl.function > dt,
dl.class > dt,
dl.method > dt
{
font-family: "Bitstream Vera Sans Mono", monospace, serif;
font-size: 96.5%;
}
/* rescale font for <tt> so that it is again 96.5% with respect to body */
table.longtable.docutils > tbody > tr > td:first-child tt,
dl.function > dt tt,
dl.class > dt tt,
dl.method > dt tt
{
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td.field-body strong
{
font-family: "Bitstream Vera Sans Mono", monospace, serif;
font-size: 96.5%;
}
doc/kwantdoctheme/theme.conf deleted 100644 → 0
View file @ 488ce42f
# This theme is based on pydoctheme by Georg Brandl
[theme]
inherit = default
stylesheet = kwantdoctheme.css
pygments_style = sphinx
[options]
bodyfont = "Bitstream Vera Serif", Georgia, serif
headfont = "Bitstream Vera Sans", Verdana, sans-serif
footerbgcolor = white
footertextcolor = #555555
relbarbgcolor = white
relbartextcolor = #666666
relbarlinkcolor = #444444
sidebarbgcolor = white
sidebartextcolor = #444444
sidebarlinkcolor = #444444
sidebarwidth = 300
bgcolor = white
textcolor = black
linkcolor = #045e94
visitedlinkcolor = #045e94
headtextcolor = black
headbgcolor = white
headlinkcolor = #aaaaaa
doc/source/_static/kwant.css deleted 100644 → 0
View file @ 488ce42f
@import "kwantdoctheme.css";
/* 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;
}
.field-list th {
/* color: rgb(0,50,150); */
/* background-color: #EEE8AA; */
white-space: nowrap; /* Essential. Otherwise the colons can break
into a new line */
}
table.field-list {
border-collapse: separate; /* Essential. Otherwise Parameters and Returns
are sharing one solid colored field. That looks
weird. */
border-spacing: 10px;
border-style: hidden;
}
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: 10px;
margin-bottom: 10px;
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: -10px;
margin-bottom: 10px;
border-width: 1px;
border-top-width: 0px;
border-color: #546C55;
border-style: solid;
}
doc/source/code/README deleted 100644 → 0
View file @ 488ce42f
This directory contains the code examples from the documentation.
Most scripts are present in three related but different versions that
correspond to three different usages.
* Subdirectory 'figure': scripts used for figure generation. Figures
are not displayed but saved to disk.
* Subdirectory 'include': scripts that display figures on screen.
They contain commented marks for including snippets in the
documentation.
* Subdirectory 'download': complete scripts to be offered for download
by readers. Like 'include' but with the include marks removed.
Most scripts are extracted from corresponding '*.py.diff' files inside
'figure/'. These are patches from the 'include' version to the
'figure' version. The patches include complete context and as such
can be used to recreate both files. It's these patches that are kept
under version control.
running 'make html' or 'make latex' inside '/doc' will automatically
update all these scripts according to the following scheme:
---->------------->------
/ \
/ download/x.py \
figure/x.py.diff ^ \
^ \ | \
| -> include/x.py ---(patch)---> figure/x.py
| | |
| | |
\ v /
----<----------(diff)--------------<--------
Thus, it is possible to update figure/x.py.diff, include/x.py or
figure/x.py and any changes will be propagated automatically when
'make' is run. (Only download/x.py is a dead end.) The user will be
informed about any conflicts. The makefile will only update files
that are older than their sources and is careful to propagate time
stamps in order to avoid infinite loops.
Editing only figure/x.py.diff is a sure way to avoid any conflicts.
doc/source/code/figure/_defs.py deleted 100644 → 0
View file @ 488ce42f
################################################################
# Make matplotlib work without X11
################################################################
import matplotlib
matplotlib.use('Agg')
################################################################
# Prepend Kwant's build directory to sys.path
################################################################
import sys
from distutils.util import get_platform
sys.path.insert(0, "../../../../build/lib.{0}-{1}.{2}".format(
get_platform(), *sys.version_info[:2]))
################################################################
# Define constants for plotting
################################################################
pt_to_in = 1. / 72.
# Default width of figures in pts
figwidth_pt = 600
figwidth_in = figwidth_pt * pt_to_in
# Width for smaller figures
figwidth_small_pt = 400
figwidth_small_in = figwidth_small_pt * pt_to_in
# Sizes for matplotlib figures
mpl_width_in = figwidth_pt * pt_to_in
mpl_label_size = None # font sizes in points
mpl_tick_size = None
# dpi for conversion from inches
dpi = 90
doc/source/code/figure/ab_ring.py.diff deleted 100644 → 0
View file @ 488ce42f
@@ -1,127 +1,196 @@
# Tutorial 2.3.3. Nontrivial shapes
# =================================
#
# 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
+import _defs
from cmath import exp
from math import pi
import kwant
# For plotting
from matplotlib import pyplot
#HIDDEN_BEGIN_eusz
def make_system(a=1, t=1.0, W=10, r1=10, r2=20):
# Start with an empty tight-binding system and a single square lattice.
# `a` is the lattice constant (by default set to 1 for simplicity).
lat = kwant.lattice.square(a)
syst = kwant.Builder()
#### Define the scattering region. ####
# Now, we aim for a more complex shape, namely a ring (or annulus)
def ring(pos):
(x, y) = pos
rsq = x ** 2 + y ** 2
return (r1 ** 2 < rsq < r2 ** 2)
#HIDDEN_END_eusz
# and add the corresponding lattice points using the `shape`-function
#HIDDEN_BEGIN_lcak
syst[lat.shape(ring, (0, r1 + 1))] = 4 * t
syst[lat.neighbors()] = -t
#HIDDEN_END_lcak
# 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 the Builder instance repeatedly, we
# define the modified hoppings as a function that takes the flux as its
# parameter phi.
#HIDDEN_BEGIN_lvkt
def hopping_phase(site1, site2, phi):
return -t * exp(1j * phi)
def crosses_branchcut(hop):
ix0, iy0 = hop[0].tag
# builder.HoppingKind with the argument (1, 0) below
# returns hoppings ordered as ((i+1, j), (i, j))
return iy0 < 0 and ix0 == 1 # ix1 == 0 then implied
# Modify only those hopings in x-direction that cross the branch cut
def hops_across_cut(syst):
for hop in kwant.builder.HoppingKind((1, 0), lat, lat)(syst):
if crosses_branchcut(hop):
yield hop
syst[hops_across_cut] = hopping_phase
#HIDDEN_END_lvkt
#### Define the leads. ####
# left lead
#HIDDEN_BEGIN_qwgr
sym_lead = kwant.TranslationalSymmetry((-a, 0))
lead = kwant.Builder(sym_lead)
def lead_shape(pos):
(x, y) = pos
return (-W / 2 < y < W / 2)
lead[lat.shape(lead_shape, (0, 0))] = 4 * t
lead[lat.neighbors()] = -t
#HIDDEN_END_qwgr
#### Attach the leads and return the system. ####
#HIDDEN_BEGIN_skbz
syst.attach_lead(lead)
syst.attach_lead(lead.reversed())
#HIDDEN_END_skbz
return syst
+def make_system_note1(a=1, t=1.0, W=10, r1=10, r2=20):
+ lat = kwant.lattice.square(a)
+ syst = kwant.Builder()
+ def ring(pos):
+ (x, y) = pos
+ rsq = x**2 + y**2
+ return ( r1**2 < rsq < r2**2)
+ syst[lat.shape(ring, (0, 11))] = 4 * t
+ syst[lat.neighbors()] = -t
+ sym_lead0 = kwant.TranslationalSymmetry((-a, 0))
+ lead0 = kwant.Builder(sym_lead0)
+ 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
+ lead0[lat.neighbors()] = -t
+ lead1 = lead0.reversed()
+ syst.attach_lead(lead0)
+ syst.attach_lead(lead1)
+ return syst
+
+
+def make_system_note2(a=1, t=1.0, W=10, r1=10, r2=20):
+ lat = kwant.lattice.square(a)
+ syst = kwant.Builder()
+ def ring(pos):
+ (x, y) = pos
+ rsq = x**2 + y**2
+ return ( r1**2 < rsq < r2**2)
+ syst[lat.shape(ring, (0, 11))] = 4 * t
+ syst[lat.neighbors()] = -t
+ sym_lead0 = kwant.TranslationalSymmetry((-a, 0))
+ lead0 = kwant.Builder(sym_lead0)
+ 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
+ lead0[lat.neighbors()] = -t
+ lead1 = lead0.reversed()
+ syst.attach_lead(lead0)
+ syst.attach_lead(lead1, lat(0, 0))
+ return syst
+
+
def plot_conductance(syst, energy, fluxes):
# compute conductance
normalized_fluxes = [flux / (2 * pi) for flux in fluxes]
data = []
for flux in fluxes:
smatrix = kwant.smatrix(syst, energy, params=dict(phi=flux))
data.append(smatrix.transmission(1, 0))
- pyplot.figure()
+ fig = pyplot.figure()
pyplot.plot(normalized_fluxes, data)
- pyplot.xlabel("flux [flux quantum]")
- pyplot.ylabel("conductance [e^2/h]")
- pyplot.show()
+ pyplot.xlabel("flux [flux quantum]",
+ fontsize=_defs.mpl_label_size)
+ pyplot.ylabel("conductance [e^2/h]",
+ fontsize=_defs.mpl_label_size)
+ pyplot.setp(fig.get_axes()[0].get_xticklabels(),
+ fontsize=_defs.mpl_tick_size)
+ pyplot.setp(fig.get_axes()[0].get_yticklabels(),
+ fontsize=_defs.mpl_tick_size)
+ fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
+ fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
+ fig.savefig("ab_ring_result.pdf")
+ fig.savefig("ab_ring_result.png", dpi=_defs.dpi)
def main():
syst = make_system()
# Check that the system looks as intended.
- kwant.plot(syst)
+ size = (_defs.figwidth_in, _defs.figwidth_in)
+ for extension in ('pdf', 'png'):
+ kwant.plot(syst, file="ab_ring_syst." + extension,
+ fig_size=size, dpi=_defs.dpi)
+
# Finalize the system.
syst = syst.finalized()
# We should see a conductance that is periodic with the flux quantum
plot_conductance(syst, energy=0.15, fluxes=[0.01 * i * 3 * 2 * pi
for i in range(100)])
+ # Finally, some plots needed for the notes
+ syst = make_system_note1()
+ for extension in ('pdf', 'png'):
+ kwant.plot(syst, file="ab_ring_note1." + extension,
+ fig_size=size, dpi=_defs.dpi)
+ syst = make_system_note2()
+ for extension in ('pdf', 'png'):
+ kwant.plot(syst, file="ab_ring_note2." + extension,
+ fig_size=size, dpi=_defs.dpi)
+
+
# 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/code/figure/band_structure.py.diff deleted 100644 → 0
View file @ 488ce42f
@@ -1,52 +1,62 @@
# Tutorial 2.4.1. Band structure calculations
# ===========================================
#
# 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 _defs
import kwant
# For plotting.
from matplotlib import pyplot
#HIDDEN_BEGIN_zxip
def make_lead(a=1, t=1.0, W=10):
# Start with an empty lead with a single square lattice
lat = kwant.lattice.square(a)
sym_lead = kwant.TranslationalSymmetry((-a, 0))
lead = kwant.Builder(sym_lead)
# build up one unit cell of the lead, and add the hoppings
# to the next unit cell
for j in range(W):
lead[lat(0, j)] = 4 * t
if j > 0:
lead[lat(0, j), lat(0, j - 1)] = -t
lead[lat(1, j), lat(0, j)] = -t
return lead
#HIDDEN_END_zxip
#HIDDEN_BEGIN_pejz
def main():
lead = make_lead().finalized()
- kwant.plotter.bands(lead, show=False)
- pyplot.xlabel("momentum [(lattice constant)^-1]")
- pyplot.ylabel("energy [t]")
- pyplot.show()
+ fig = kwant.plotter.bands(lead, show=False)
+ pyplot.xlabel("momentum [(lattice constant)^-1]",
+ fontsize=_defs.mpl_label_size)
+ pyplot.ylabel("energy [t]", fontsize=_defs.mpl_label_size)
+ pyplot.setp(fig.get_axes()[0].get_xticklabels(),
+ fontsize=_defs.mpl_tick_size)
+ pyplot.setp(fig.get_axes()[0].get_yticklabels(),
+ fontsize=_defs.mpl_tick_size)
+ fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
+ fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
+ for extension in ('pdf', 'png'):
+ fig.savefig("band_structure_result." + extension, dpi=_defs.dpi)
+
#HIDDEN_END_pejz
# 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/code/figure/closed_system.py.diff deleted 100644 → 0
View file @ 488ce42f
@@ -1,144 +1,161 @@
# Tutorial 2.4.2. Closed systems
# ==============================
#
# 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.
+import _defs
from cmath import exp
import numpy as np
import kwant
# For eigenvalue computation
#HIDDEN_BEGIN_tibv
import scipy.sparse.linalg as sla
#HIDDEN_END_tibv
# For plotting
from matplotlib import pyplot
def make_system(a=1, t=1.0, r=10):
# Start with an empty tight-binding system and a single square lattice.
# `a` is the lattice constant (by default set to 1 for simplicity).
#HIDDEN_BEGIN_qlyd
lat = kwant.lattice.square(a, norbs=1)
syst = kwant.Builder()
# Define the quantum dot
def circle(pos):
(x, y) = pos
rsq = x ** 2 + y ** 2
return rsq < r ** 2
def hopx(site1, site2, B):
# The magnetic field is controlled by the parameter B
y = site1.pos[1]
return -t * exp(-1j * B * y)
syst[lat.shape(circle, (0, 0))] = 4 * t
# hoppings in x-direction
syst[kwant.builder.HoppingKind((1, 0), lat, lat)] = hopx
# hoppings in y-directions
syst[kwant.builder.HoppingKind((0, 1), lat, lat)] = -t
# It's a closed system for a change, so no leads
return syst
#HIDDEN_END_qlyd
#HIDDEN_BEGIN_yvri
def plot_spectrum(syst, Bfields):
energies = []
for B in Bfields:
# Obtain the Hamiltonian as a sparse matrix
ham_mat = syst.hamiltonian_submatrix(params=dict(B=B), sparse=True)
# we only calculate the 15 lowest eigenvalues
ev = sla.eigsh(ham_mat.tocsc(), k=15, sigma=0,
return_eigenvectors=False)
energies.append(ev)
- pyplot.figure()
+ fig = pyplot.figure()
pyplot.plot(Bfields, energies)
- pyplot.xlabel("magnetic field [arbitrary units]")
- pyplot.ylabel("energy [t]")
- pyplot.show()
+ pyplot.xlabel("magnetic field [arbitrary units]",
+ fontsize=_defs.mpl_label_size)
+ pyplot.ylabel("energy [t]", fontsize=_defs.mpl_label_size)
+ pyplot.setp(fig.get_axes()[0].get_xticklabels(),
+ fontsize=_defs.mpl_tick_size)
+ pyplot.setp(fig.get_axes()[0].get_yticklabels(),
+ fontsize=_defs.mpl_tick_size)
+ fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
+ fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
+ for extension in ('pdf', 'png'):
+ fig.savefig("closed_system_result." + extension, dpi=_defs.dpi)
#HIDDEN_END_yvri
def sorted_eigs(ev):
evals, evecs = ev
evals, evecs = map(np.array, zip(*sorted(zip(evals, evecs.transpose()))))
return evals, evecs.transpose()
#HIDDEN_BEGIN_wave
def plot_wave_function(syst, B=0.001):
+ size = (_defs.figwidth_in, _defs.figwidth_in)
+
# Calculate the wave functions in the system.
ham_mat = syst.hamiltonian_submatrix(sparse=True, params=dict(B=B))
evals, evecs = sorted_eigs(sla.eigsh(ham_mat.tocsc(), k=20, sigma=0))
# Plot the probability density of the 10th eigenmode.
- kwant.plotter.map(syst, np.abs(evecs[:, 9])**2,
- colorbar=False, oversampling=1)
+ for extension in ('pdf', 'png'):
+ kwant.plotter.map(
+ syst, np.abs(evecs[:, 9])**2, colorbar=False, oversampling=1,
+ file="closed_system_eigenvector." + extension,
+ fig_size=size, dpi=_defs.dpi)
#HIDDEN_END_wave
#HIDDEN_BEGIN_current
def plot_current(syst, B=0.001):
+ size = (_defs.figwidth_in, _defs.figwidth_in)
+
# Calculate the wave functions in the system.
ham_mat = syst.hamiltonian_submatrix(sparse=True, params=dict(B=B))
evals, evecs = sorted_eigs(sla.eigsh(ham_mat.tocsc(), k=20, sigma=0))
# Calculate and plot the local current of the 10th eigenmode.
J = kwant.operator.Current(syst)
current = J(evecs[:, 9], params=dict(B=B))
- kwant.plotter.current(syst, current, colorbar=False)
+ for extension in ('pdf', 'png'):
+ kwant.plotter.current(
+ syst, current, colorbar=False,
+ file="closed_system_current." + extension,
+ fig_size=size, dpi=_defs.dpi)
#HIDDEN_END_current
def main():
syst = make_system()
- # Check that the system looks as intended.
- kwant.plot(syst)
-
# Finalize the system.
syst = syst.finalized()
# The following try-clause can be removed once SciPy 0.9 becomes uncommon.
try:
# We should observe energy levels that flow towards Landau
# level energies with increasing magnetic field.
plot_spectrum(syst, [iB * 0.002 for iB in range(100)])
# Plot an eigenmode of a circular dot. Here we create a larger system for
# better spatial resolution.
syst = make_system(r=30).finalized()
plot_wave_function(syst)
plot_current(syst)
except ValueError as e:
if e.message == "Input matrix is not real-valued.":
print("The calculation of eigenvalues failed because of a bug in SciPy 0.9.")
print("Please upgrade to a newer version of SciPy.")
else:
raise
# 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/code/figure/discretize.py.diff deleted 100644 → 0
View file @ 488ce42f
@@ -1,225 +1,239 @@
# Tutorial 2.9. Processing continuum Hamiltonians with discretize
# ===============================================================
#
# Physics background
# ------------------
# - tight-binding approximation of continuous Hamiltonians
#
# Kwant features highlighted
# --------------------------
# - kwant.continuum.discretize
+import _defs
import kwant
#HIDDEN_BEGIN_import
import kwant.continuum
#HIDDEN_END_import
import scipy.sparse.linalg
import scipy.linalg
import numpy as np
# For plotting
import matplotlib as mpl
from matplotlib import pyplot as plt
+def save_figure(file_name):
+ if not file_name:
+ return
+ for extension in ('pdf', 'png'):
+ plt.savefig('.'.join((file_name,extension)),
+ dpi=_defs.dpi, bbox_inches='tight')
+
+
def stadium_system(L=20, W=20):
#HIDDEN_BEGIN_template
hamiltonian = "k_x**2 + k_y**2 + V(x, y)"
template = kwant.continuum.discretize(hamiltonian)
- print(template)
+ with open('discretizer_verbose.txt', 'w') as f:
+ print(template, file=f)
#HIDDEN_END_template
#HIDDEN_BEGIN_fill
def stadium(site):
(x, y) = site.pos
x = max(abs(x) - 20, 0)
return x**2 + y**2 < 30**2
syst = kwant.Builder()
syst.fill(template, stadium, (0, 0));
syst = syst.finalized()
#HIDDEN_END_fill
return syst
#HIDDEN_BEGIN_plot_eigenstate
def plot_eigenstate(syst, n=2, Vx=.0003, Vy=.0005):
def potential(x, y):
return Vx * x + Vy * y
ham = syst.hamiltonian_submatrix(params=dict(V=potential), sparse=True)
evecs = scipy.sparse.linalg.eigsh(ham, k=10, which='SM')[1]
kwant.plotter.density(syst, abs(evecs[:, n])**2, show=False)
#HIDDEN_END_plot_eigenstate
- plt.show()
+ save_figure('discretizer_gs')
def qsh_system(a=20, L=2000, W=1000):
#HIDDEN_BEGIN_define_qsh
hamiltonian = """
+ C * identity(4) + M * kron(sigma_0, sigma_z)
- B * (k_x**2 + k_y**2) * kron(sigma_0, sigma_z)
- D * (k_x**2 + k_y**2) * kron(sigma_0, sigma_0)
+ A * k_x * kron(sigma_z, sigma_x)
- A * k_y * kron(sigma_0, sigma_y)
"""
template = kwant.continuum.discretize(hamiltonian, grid=a)
#HIDDEN_END_define_qsh
#HIDDEN_BEGIN_define_qsh_build
def shape(site):
(x, y) = site.pos
return (0 <= y < W and 0 <= x < L)
def lead_shape(site):
(x, y) = site.pos
return (0 <= y < W)
syst = kwant.Builder()
syst.fill(template, shape, (0, 0))
lead = kwant.Builder(kwant.TranslationalSymmetry([-a, 0]))
lead.fill(template, lead_shape, (0, 0))
syst.attach_lead(lead)
syst.attach_lead(lead.reversed())
syst = syst.finalized()
#HIDDEN_END_define_qsh_build
return syst
def analyze_qsh():
params = dict(A=3.65, B=-68.6, D=-51.1, M=-0.01, C=0)
syst = qsh_system()
#HIDDEN_BEGIN_plot_qsh_band
kwant.plotter.bands(syst.leads[0], params=params,
momenta=np.linspace(-0.3, 0.3, 201), show=False)
#HIDDEN_END_plot_qsh_band
plt.grid()
plt.xlim(-.3, 0.3)
plt.ylim(-0.05, 0.05)
plt.xlabel('momentum [1/A]')
plt.ylabel('energy [eV]')
- plt.show()
+ save_figure('discretizer_qsh_band')
#HIDDEN_BEGIN_plot_qsh_wf
+
# get scattering wave functions at E=0
wf = kwant.wave_function(syst, energy=0, params=params)
# prepare density operators
sigma_z = np.array([[1, 0], [0, -1]])
prob_density = kwant.operator.Density(syst, np.eye(4))
spin_density = kwant.operator.Density(syst, np.kron(sigma_z, np.eye(2)))
# calculate expectation values and plot them
wf_sqr = sum(prob_density(psi) for psi in wf(0)) # states from left lead
rho_sz = sum(spin_density(psi) for psi in wf(0)) # states from left lead
fig, (ax1, ax2) = plt.subplots(1, 2, sharey=True, figsize=(16, 4))
kwant.plotter.density(syst, wf_sqr, ax=ax1)
kwant.plotter.density(syst, rho_sz, ax=ax2)
#HIDDEN_END_plot_qsh_wf
ax = ax1
im = [obj for obj in ax.get_children()
if isinstance(obj, mpl.image.AxesImage)][0]
fig.colorbar(im, ax=ax)
ax = ax2
im = [obj for obj in ax.get_children()
if isinstance(obj, mpl.image.AxesImage)][0]
fig.colorbar(im, ax=ax)
ax1.set_title('Probability density')
ax2.set_title('Spin density')
- plt.show()
+ save_figure('discretizer_qsh_wf')
def lattice_spacing():
#HIDDEN_BEGIN_ls_def
hamiltonian = "k_x**2 * identity(2) + alpha * k_x * sigma_y"
params = dict(alpha=.5)
#HIDDEN_END_ls_def
def plot(ax, a=1):
#HIDDEN_BEGIN_ls_hk_cont
h_k = kwant.continuum.lambdify(hamiltonian, locals=params)
k_cont = np.linspace(-4, 4, 201)
e_cont = [scipy.linalg.eigvalsh(h_k(k_x=ki)) for ki in k_cont]
#HIDDEN_END_ls_hk_cont
#HIDDEN_BEGIN_ls_hk_tb
template = kwant.continuum.discretize(hamiltonian, grid=a)
syst = kwant.wraparound.wraparound(template).finalized()
def h_k(k_x):
p = dict(k_x=k_x, **params)
return syst.hamiltonian_submatrix(params=p)
k_tb = np.linspace(-np.pi/a, np.pi/a, 201)
e_tb = [scipy.linalg.eigvalsh(h_k(k_x=a*ki)) for ki in k_tb]
#HIDDEN_END_ls_hk_tb
ax.plot(k_cont, e_cont, 'r-')
ax.plot(k_tb, e_tb, 'k-')
ax.plot([], [], 'r-', label='continuum')
ax.plot([], [], 'k-', label='tight-binding')
ax.set_xlim(-4, 4)
ax.set_ylim(-1, 14)
ax.set_title('a={}'.format(a))
ax.set_xlabel('momentum [a.u.]')
ax.set_ylabel('energy [a.u.]')
ax.grid()
ax.legend()
_, (ax1, ax2) = plt.subplots(1, 2, sharey=True, figsize=(12, 4))
plot(ax1, a=1)
plot(ax2, a=.25)
- plt.show()
+ save_figure('discretizer_lattice_spacing')
def substitutions():
#HIDDEN_BEGIN_subs_1
sympify = kwant.continuum.sympify
subs = {'sx': [[0, 1], [1, 0]], 'sz': [[1, 0], [0, -1]]}
e = (
sympify('[[k_x**2, alpha * k_x], [k_x * alpha, -k_x**2]]'),
sympify('k_x**2 * sigma_z + alpha * k_x * sigma_x'),
sympify('k_x**2 * sz + alpha * k_x * sx', locals=subs),
)
- print(e[0] == e[1] == e[2])
+ with open('discretizer_subs_1.txt', 'w') as f:
+ print(e[0] == e[1] == e[2], file=f)
#HIDDEN_END_subs_1
#HIDDEN_BEGIN_subs_2
subs = {'A': 'A(x) + B', 'V': 'V(x) + V_0', 'C': 5}
- print(sympify('k_x * A * k_x + V + C', locals=subs))
+ with open('discretizer_subs_2.txt', 'w') as f:
+ print(sympify('k_x * A * k_x + V + C', locals=subs), file=f)
#HIDDEN_END_subs_2
def main():
#HIDDEN_BEGIN_symbolic_discretization
template = kwant.continuum.discretize('k_x * A(x) * k_x')
- print(template)
+ with open('discretizer_intro_verbose.txt', 'w') as f:
+ print(template, file=f)
#HIDDEN_END_symbolic_discretization
syst = stadium_system()
plot_eigenstate(syst)
analyze_qsh()
lattice_spacing()
substitutions()
# 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()