mirror of
https://github.com/triqs/dft_tools
synced 2024-12-25 05:43:40 +01:00
Work on documentation
The theme has been improved to be more flexible. Some work on the installation steps to get rid of BOOST_SOURCE_DIR. Took out the bundles. Changed the header items and added a link to documentation.
This commit is contained in:
Michel Ferrero
parent
9c258fa7e1
commit
009f0ea829
5
doc/_templates/sideb.html
vendored
5
doc/_templates/sideb.html
vendored
@ -4,12 +4,9 @@
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<a href="http://www.cnrs.fr"> <img style="width: 60px; margin: 10px 0 0 5px" src='_static/logo_cnrs.png' alt="CNRS"/> </a>
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</p>
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<h3>TRIQS applications</h3>
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<h3><a href="applications.html">TRIQS applications</a></h3>
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<p>
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Some applications are supported by the TRIQS collaboration,
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<a class="reference external" href="{{ pathto("applications") }}">check them out!</a>
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Note that you can obtain
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<a class="reference external" href="{{ pathto("bundles") }}">bundled sources</a>
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that contain both the TRIQS library and the supported applications.
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</p>
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@ -11,9 +11,7 @@ Wien2TRIQS is an interface to Wien2k for LDA+DMFT calculation. It allows
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you to turn band-structure calculations obtained from the Wien2k package to
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inputs to full-fledged LDA+DMFT calculations in a few lines!
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| *Homepage:* `<http://ipht.cea.fr/triqs/new/dft_tools/index.html>`_
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| *Documentation:* `<http://ipht.cea.fr/triqs/new/dft_tools/documentation.html>`_
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| *Installation:* `<http://ipht.cea.fr/triqs/new/dft_tools/install.html>`_
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*Homepage:* `<http://ipht.cea.fr/triqs/new/dft_tools/index.html>`_
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Hybridization-expansion matrix solver
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-------------------------------------
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@ -23,9 +21,7 @@ of a quantum impurity embedded in a conduction bath. It is based on a quantum
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Monte Carlo algorithm that stochastically samples the diagrams of a
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hybridization expansion of the partition function.
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| *Homepage:* `<http://ipht.cea.fr/triqs/new/cthyb_matrix/index.html>`_
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| *Documentation:* `<http://ipht.cea.fr/triqs/new/cthyb_matrix/documentation.html>`_
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| *Installation:* `<http://ipht.cea.fr/triqs/new/cthyb_matrix/install.html>`_
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*Homepage:* `<http://ipht.cea.fr/triqs/new/cthyb_matrix/index.html>`_
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Hubbard I solver
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----------------
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@ -34,6 +30,4 @@ This solver gives the Hubbard I solution of a quantum impurity problem,
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i.e. it solves the atomic limit. This simple approximation allows to have
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very quick answer even for large multiband systems.
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| *Homepage:* `<http://ipht.cea.fr/triqs/new/hubbardI/index.html>`_
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| *Documentation:* `<http://ipht.cea.fr/triqs/new/hubbardI/documentation.html>`_
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| *Installation:* `<http://ipht.cea.fr/triqs/new/hubbardI/install.html>`_
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*Homepage:* `<http://ipht.cea.fr/triqs/new/hubbardI/index.html>`_
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@ -1,4 +0,0 @@
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.. _bundles:
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Bundles
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=======
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@ -35,7 +35,7 @@ extensions += [
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'matplotlib.sphinxext.only_directives',
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'plot_directive',
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# 'matplotlib.sphinxext.ipython_directive',
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'ipython_console_highlighting',
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# 'ipython_console_highlighting',
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# 'inheritance_diagram',
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'numpydoc']
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@ -81,9 +81,8 @@ copyright = u'2011-2013, The TRIQS collaboration'
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# built documents.
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#
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# The short X.Y version.
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version = '1.0'
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# The full version, including alpha/beta/rc tags.
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release = '1.0.0'
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version = '@TRIQS_VERSION@'
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release = '@TRIQS_RELEASE@'
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# The language for content autogenerated by Sphinx. Refer to documentation
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# for a list of supported languages.
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@ -145,6 +144,14 @@ doxylink = { 'doxy' : ('@CMAKE_CURRENT_BINARY_DIR@/doxy.tag', 'doxy_triqs') }
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html_theme_path = ["@TRIQS_SOURCE_DIR@/doc/themes/"]
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html_theme = "triqs"
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html_show_sphinx = False
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html_context = {'header_title': 'triqs',
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'header_subtitle': 'a Toolbox for Research on Interacting Quantum Systems',
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'header_links': [['Install', 'install'],
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['Documentation', 'documentation'],
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['Applications', 'applications'],
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['Issues', 'issues'],
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['About TRIQS', 'about']
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]}
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#html_theme_options = { "pagewidth": "80em", "documentwidth" : "60em" }
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@ -9,7 +9,6 @@ Table of contents
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install
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documentation
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applications
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bundles
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bugs
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authors
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issues
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about
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@ -1,4 +1,4 @@
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.. index:: installation steps
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.. index:: installation
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.. highlight:: bash
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@ -7,43 +7,61 @@
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Installation
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============
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* TRIQS is hosted on **GitHub**, where you can :
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Prerequisite
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------------
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* Download `the current version <https://github.com/TRIQS/TRIQS>`_ (recommended) ::
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git clone git://github.com/TRIQS/TRIQS.git path_to_triqs_sources
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NB : this version is normally never broken (developments are done elsewhere).
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* Download `an older release <https://github.com/TRIQS/TRIQS/tags>`_, which may require less recent versions of compilers, libs...
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* Use the GitHub *Issues* tracker for any problem, questions.
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*Please do NOT contact the developers directly by email*
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Complete installation instructions for standard systems
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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The TRIQS library relies on a certain number of standard libraries described in
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the :ref:`list of requirements <requirements>`. Here are instructions to install
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these necessary libraries on two standard systems:
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.. toctree::
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:maxdepth: 1
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installation/Ubuntu
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installation/linux
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installation/install_on_osx_lion
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installation/ubuntu
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installation/osx_lion
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Installation steps
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------------------
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#. Download the sources of TRIQS from github into a ``src`` directory::
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$ git clone git@github.com:TRIQS/triqs.git src
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#. Create an empty build directory where you will compile the code::
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$ mkdir build && cd build
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#. In the build directory call cmake specifying where the TRIQS library should be installed::
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$ cmake -DCMAKE_INSTALL_PREFIX=path_to_install_directory ../src
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#. Compile the code, run the tests and install the library::
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$ make
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$ make test
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$ make install
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#. After the installation TRIQS has been installed using the standard UNIX
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scheme:
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* executables in ``path_to_install_directory/bin``.
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* c++ and python libraries in ``path_to_install_directory/lib``.
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* c++ headers in ``path_to_install_directory/include/triqs``.
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Details
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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* shared items in ``path_to_install_directory/share/triqs``.
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Further details
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---------------
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.. toctree::
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:maxdepth: 1
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installation/wien2k_inst
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installation/dependencies
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installation/python
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installation/clang
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installation/intel
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installation/install_options
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installation/get_started
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installation/changelog
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@ -1,73 +0,0 @@
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.. index:: Ubuntu
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.. _Ubuntu :
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.. highlight:: bash
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Installation on Ubuntu (12.04 LTS)
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####################################################
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TRIQS can be installed on Ubuntu 12.04 LTS.
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NB : Ubuntu 12.10: there is a bug in Ubuntu 12.10 (hdf5 compiled without hdf5 support).
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On Ubuntu 12.10, you have to recompile hdf5. The problem has been reported and will be fixed in 13.04.
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#. Install the following packages which are necessary to build TRIQS and use it::
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sudo apt-get install cmake git g++ libgfortran3 gfortran openmpi-bin openmpi-common \
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openmpi-checkpoint libopenmpi-dev libblas-dev liblapack-dev libfftw3-dev libgmp-dev \
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hdf5-tools libhdf5-serial-dev python-h5py libboost1.48-all-dev python-dev \
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python-numpy python-scipy python-virtualenv python-matplotlib doxygen\
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python-tornado python-zmq
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#. Download the code::
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git clone git://github.com/TRIQS/TRIQS.git path_to_triqs_sources
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#. Create a build directory (different from the TRIQS source directory nor a subdirectory thereof) ::
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mkdir triqs_build && cd triqs_build
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#. Configure ::
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cmake path_to_triqs_sources -DCMAKE_INSTALL_PREFIX=path_to_install_directory
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NB: the install directory is optional and defaults to `triqs_build/INSTALL_DIR`. It is
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however usually a good idea to have an install directory outside `triqs_build` (after
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a successful installation `triqs_build` can be deleted). The cmake call should end with::
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-- Build files have been written to: *path_to_triqs_build*
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OPTIONAL: To install the documentation, install Sphinx and doxygen: ::
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sudo easy_install -U Sphinx
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sudo apt-get install doxygen
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and add::
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-DBuild_Documentation=ON
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to the above cmake command.
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#. Build TRIQS, test it and install it with (N being the number of cores of your machine) ::
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make -jN && make test && make -jN install
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NB: the tests SingleSite and CDMFT-v2 take longer than the other ones (30s to 1 min).
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#. If you use Wien2TRIQS, please complete the installation as described :ref:`here <wien2k_inst>`.
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#. You can now :ref:`start ... <get_started>`
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#. Optionally, you may be interested in:
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* How to *simply* upgrade the ipython notebook with :ref:`virtualenv <virtualenv>` to the latest version?
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||||
|
||||
* How to use the nice :ref:`clang <clang>` C++ compiler?
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* How to use :ref:`Intel <icc>` C++ compiler?
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.. warning:: For the branch 1.0, you need the latest version of Cython (>=.17, downloadable on Cython.org). If Cython is not found, specify the location of the executable with the option -DCYTHON_EXECUTABLE.
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@ -1,16 +0,0 @@
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Changelog between releases
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=======================================
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v0.9 -> current
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------------------
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* Now use to C++11.
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v0.8 -> v0.9
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-------------
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* To be written
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@ -4,8 +4,8 @@
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.. _install_options:
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Customizing installation : cmake options
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----------------------------------------------------
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Customizing installation: cmake options
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---------------------------------------
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Specifying the compiler or compile/link flags
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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@ -1,51 +0,0 @@
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.. index:: Linux
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.. _Linux:
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.. highlight:: bash
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Installation on a generic Linux distribution
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#######################################################
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TRIQS has been installed successfully on several distributions.
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#. Download the code (this is for the current development version) ::
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git clone git://github.com/TRIQS/TRIQS.git path_to_triqs_sources
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#. Download the `sources of boost <http://ipht.cea.fr/triqs/download/boost_src.tar.bz2>`_ and untar them into ``path_to_boost_sources``.
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**Don't compile boost**.
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#. Create a build directory (different from the TRIQS source directory nor a subdirectory thereof) ::
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mkdir triqs_build && cd triqs_build
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#. Configure ::
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cmake path_to_triqs_sources -DBOOST_SOURCE_DIR=path_to_boost_sources \
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-DCMAKE_INSTALL_PREFIX=path_to_install_directory
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[NB : the install directory is optional, the default value is `triqs_build/INSTALL_DIR`]
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|
||||
Successful run of cmake will finish with ::
|
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|
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-- Build files have been written to: *path_to_triqs_build*
|
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|
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#. Build TRIQS, test it and install it with (N being the number of cores of your machine) ::
|
||||
|
||||
make -jN && make test && make -jN install
|
||||
|
||||
[NB : the tests SingleSite and CDMFT-v2 take longer than the other ones (30s to 1 min) ].
|
||||
|
||||
#. If you use Wien2TRIQS, please complete the installation as described :ref:`here <wien2k_inst>`.
|
||||
|
||||
#. You can now :ref:`start ... <get_started>`
|
||||
|
||||
#. Optionally, you can be interested in :
|
||||
|
||||
* How to *simply* upgrade the ipython notebook with :ref:`virtualenv <virtualenv>` to the latest version ?
|
||||
|
||||
* How to use the nice :ref:`clang <clang>` C++ compiler ?
|
||||
|
||||
* How to use :ref:`Intel <icc>` C++ compiler ?
|
||||
|
||||
@ -3,10 +3,11 @@
|
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.. _install_on_osx_lion:
|
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.. highlight:: bash
|
||||
|
||||
Installation on Mac OS X [Mountain Lion]
|
||||
==============================================
|
||||
Installing required libraries on Mac OS X
|
||||
=========================================
|
||||
|
||||
This installation guide may work for older versions of Mac OS X. However, previous versions of Mac OS X are not supported.
|
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This installation guide has been tried on Mountain Lion. It may work for older
|
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versions of Mac OS X but previous versions of Mac OS X are not supported.
|
||||
|
||||
NB: The installation of TRIQS under previous versions of OS X requires installing clang (via Xcode) or gcc 4.7 (via MacPorts).
|
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On Mountain Lion, clang (llvm) replaces gcc 4.2 as the default C++ compiler.
|
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@ -15,7 +16,7 @@ We strongly recommend the following installation procedure, which provides a cle
|
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of them are compatible with each other. Only the installation via homebrew is supported for the Mac.
|
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|
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Installation of the dependencies
|
||||
________________________________
|
||||
--------------------------------
|
||||
|
||||
1. Install `homebrew <http://mxcl.github.io/homebrew/>`_.
|
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|
||||
@ -76,26 +77,8 @@ NB : you need pyparsing <=1.5.7 since apparently v.2.0 works only for python 3.
|
||||
|
||||
7. Download the latest `sources of boost <http://www.boost.org/users/download/>`_ and untar them into a directory ``BOOST_SRC``.
|
||||
|
||||
|
||||
TRIQS installation
|
||||
__________________
|
||||
|
||||
#. Download the TRIQS sources: ::
|
||||
|
||||
git clone git@github.com:TRIQS/TRIQS.git TRIQS_src
|
||||
|
||||
#. Generate a Makefile using cmake: ::
|
||||
|
||||
cmake TRIQS_src -DBOOST_SOURCE_DIR=BOOST_SRC
|
||||
|
||||
#. Compile TRIQS, its tests and install it into INSTALL_DIR (default) (N is the number of cores of your mac): ::
|
||||
|
||||
make -jN && make test && make install
|
||||
|
||||
#. If you use Wien2TRIQS, please complete the installation as described :ref:`here <wien2k_inst>`.
|
||||
|
||||
Possible issues:
|
||||
________________
|
||||
Possible issues
|
||||
---------------
|
||||
|
||||
If you encounter the following error: ::
|
||||
|
||||
@ -1,42 +1,42 @@
|
||||
.. index:: dependencies
|
||||
.. index:: required libraries
|
||||
|
||||
.. _dependencies:
|
||||
.. _requirements:
|
||||
|
||||
A complete list of dependencies
|
||||
==================================
|
||||
A complete list of requirements
|
||||
================================
|
||||
|
||||
TRIQS is built upon several python and C++ libraries, which, if not present already in your system, can be freely downloaded and installed.
|
||||
All the libraries and tools used by TRIQS are listed in the table :
|
||||
TRIQS is built upon several python and C++ libraries, which, if not present
|
||||
already in your system, can be freely downloaded and installed. All the
|
||||
libraries and tools used by TRIQS are listed in the table:
|
||||
|
||||
================== ================ ================================================================================
|
||||
Libraries/tools Version Comment
|
||||
================== ================ ================================================================================
|
||||
mpi e.g., openmpi Parallelism
|
||||
|
||||
Since standard linux distributions (and macports on OS X)
|
||||
now provides openmpi, even on laptops, we avoid the unnecessary complication
|
||||
of maintaining a non parallel version of TRIQS
|
||||
fftw >= 3.2 Fourier transform
|
||||
boost >= 1.49 C++ librairies
|
||||
hdf5 >= 1.8.0 File storage system. Important: the *serial* version must be installed
|
||||
python* >= 2.6.5
|
||||
scipy* python mathematical library
|
||||
numpy* python scientific library
|
||||
h5py* python interface to hdf5 library
|
||||
sphinx* >= 1.0.1 python documentation tools (to compile documentation)
|
||||
pyparsing* Tool for sphinx (to compile documentation)
|
||||
matplotlib* >= 0.99 python 2D plotting library
|
||||
cython >=0.17 [DEVELOPERS ONLY]
|
||||
python >= 2.6.5
|
||||
scipy python mathematical library
|
||||
numpy python scientific library
|
||||
h5py python interface to hdf5 library
|
||||
sphinx >= 1.0.1 python documentation tools (to compile documentation)
|
||||
pyparsing Tool for sphinx (to compile documentation)
|
||||
matplotlib >= 0.99 python 2D plotting library
|
||||
cython >=0.17 cython package
|
||||
================== ================ ================================================================================
|
||||
|
||||
\* designates the libraries included in the Enthought python distribution.
|
||||
\* designates the libraries included in the Enthought python distribution.
|
||||
|
||||
C++11
|
||||
--------
|
||||
-----
|
||||
|
||||
The current version of TRIQS use the new C++11 standard, and therefore require a recent C++ compiler.
|
||||
|
||||
Tested compilers include :
|
||||
Tested compilers include:
|
||||
|
||||
* g++ 4.6.3, 4.7
|
||||
* clang++ 3.1
|
||||
@ -47,22 +47,10 @@ Note that older compilers will *never* be supported for current and future versi
|
||||
Older releases may accept older compilers.
|
||||
|
||||
F90
|
||||
-------
|
||||
---
|
||||
For the Wien2TRIQS interface only.
|
||||
|
||||
Tested compilers include :
|
||||
Tested compilers include:
|
||||
|
||||
* ifort
|
||||
* gfortran
|
||||
|
||||
Boost
|
||||
--------------------------
|
||||
|
||||
The boost library is often upgraded, and it is rare to have the correct version in your distribution. TRIQS installation process offers two choices :
|
||||
|
||||
* Recommended choice: As explained in the :ref:`page above <installation>`, you can download simply the latest *sources* and TRIQS will do all the job for you by compiling the pieces of boost that are needed in a little boost_for_triqs library.
|
||||
|
||||
* OR you can include and link with an installed boost if the version if high enough as discussed in :ref:`install_options`.
|
||||
|
||||
|
||||
|
||||
31
doc/installation/ubuntu.rst
Normal file
31
doc/installation/ubuntu.rst
Normal file
@ -0,0 +1,31 @@
|
||||
.. index:: ubuntu
|
||||
|
||||
.. _Ubuntu :
|
||||
|
||||
.. highlight:: bash
|
||||
|
||||
Installing required libraries on Ubuntu
|
||||
=======================================
|
||||
|
||||
TRIQS has been installed and tested on Ubuntu 12.04 and 13.04. Note that there
|
||||
is a bug in Ubuntu 12.10 (the hdf5 library has been compiled without hdf5
|
||||
support) so if you are using that version you will have to recompile the hdf5
|
||||
library. The problem has been reported and is fixed in 13.04.
|
||||
|
||||
Install the following packages which are necessary to build TRIQS and use it::
|
||||
|
||||
sudo apt-get install cmake git g++ libgfortran3 gfortran openmpi-bin openmpi-common \
|
||||
openmpi-checkpoint libopenmpi-dev libblas-dev liblapack-dev libfftw3-dev libgmp-dev \
|
||||
hdf5-tools libhdf5-serial-dev python-h5py libboost1.48-all-dev python-dev \
|
||||
python-numpy python-scipy python-virtualenv python-matplotlib doxygen\
|
||||
python-tornado python-zmq
|
||||
|
||||
Optionally, you may be interested in:
|
||||
|
||||
* How to *simply* upgrade the ipython notebook with :ref:`virtualenv <virtualenv>` to the latest version?
|
||||
|
||||
* How to use the nice :ref:`clang <clang>` C++ compiler?
|
||||
|
||||
* How to use :ref:`Intel <icc>` C++ compiler?
|
||||
|
||||
.. warning:: you need the latest version of Cython (>=.17, downloadable on Cython.org). If Cython is not found, specify the location of the executable with the option -DCYTHON_EXECUTABLE.
|
||||
@ -1,27 +0,0 @@
|
||||
.. index:: wien2k_inst
|
||||
|
||||
.. _wien2k_inst:
|
||||
|
||||
Complete the installation of Wien2TRIQS (all platforms)
|
||||
-------------------------------------------------------------
|
||||
|
||||
If you choose to install the Wien2TRIQS interface to the Wien2K package for doing DMFT calculations of
|
||||
realistic systems, you need take the last steps manually since Wien2k installation is not standard on all machines.
|
||||
During TRIQS installation several files will be will be put into ::
|
||||
|
||||
path_to_TRIQS_install_directory/share/triqs/Wien2k_SRC_files/SRC_templates
|
||||
|
||||
Those files are::
|
||||
* :file:`case.cf_f_mm2` and :file:`case.cf_p_cubic` containing matrices for the complex->cubic transformation of the local angular basis
|
||||
|
||||
* :file:`case.indmftpr` is a template for the input file needed by the :program:`dmftproj` program. This program constructs a set of localized orbitals representing correlated states.
|
||||
|
||||
These files then have to be copied manually to :file:`path_to_Wien2k/SRC_templates`, where :file:`path_to_Wien2k` is the path to Wien2K main directory.
|
||||
|
||||
When building the Wien2k extension module, TRIQS will compile :program:`dmftproj` and install it into :file:`path_to_TRIQS_install_directory/bin`.
|
||||
|
||||
In addition, :file:`path_to_Wien2k/SRC_templates` also contains :program:`run_triqs` and :program:`runsp_triqs` scripts for running Wien2k+DMFT fully self-consistent calculations. These files should be copied to :file:`path_to_Wien2k`.
|
||||
|
||||
You will also need to insert manually a correct call of :file:`pytriqs` into these scripts using an appropriate for your system MPI wrapper (mpirun, mpprun...), if needed. Search for *pytriqs* within the scripts to locate the appropriate place for inserting the :file:`pytriqs` call.
|
||||
|
||||
Finally, you will have to change the calls to :program:`python_with_DMFT` to :program:`pytriqs` in the Wien2k :file:`path_to_Wien2k/run*` files.
|
||||
@ -1,6 +1,6 @@
|
||||
|
||||
Reporting bugs
|
||||
==============
|
||||
Reporting issues
|
||||
================
|
||||
|
||||
Please report all problems and bugs directly at the github issue page
|
||||
`<https://github.com/TRIQS/triqs/issues>`_. In order to make it easier
|
||||
17
doc/themes/triqs/layout.html
vendored
17
doc/themes/triqs/layout.html
vendored
@ -34,24 +34,19 @@
|
||||
{% endblock %}
|
||||
|
||||
{% block rootrellink %}
|
||||
{% if hasdoc('documentation') %}
|
||||
<li><a href="{{ pathto('index') }}">Home</a> »</li>
|
||||
{% else %}
|
||||
<li><a href="{{ pathto('index') }}">Documentation</a> »</li>
|
||||
{% endif %}
|
||||
<li><a href="{{ pathto('index') }}">Home</a> »</li>
|
||||
{% endblock %}
|
||||
|
||||
{% block header %}
|
||||
<div class="pageheader">
|
||||
<ul>
|
||||
<li><a href="{{ pathto('install') }}">Install</a></li>
|
||||
<li><a href="{{ pathto('documentation') }}">Documentation</a></li>
|
||||
<li><a href="{{ pathto('bugs') }}">Report Bugs</a></li>
|
||||
<li><a href="{{ pathto('authors') }}">Authors and Quote</a></li>
|
||||
{% for header_link in header_links %}
|
||||
<li><a href="{{ pathto(header_link[1]) }}">{{ header_link[0] }}</a></li>
|
||||
{% endfor %}
|
||||
</ul>
|
||||
<div>
|
||||
<h1 style="padding:0; margin: 10px 0 0 0;"><a class="triqs" href="http://ipht.cea.fr/triqs">TRIQS</a></h1>
|
||||
<span style="font-size: 14px; margin: 0px; padding: 0px;">a Toolbox for Research on Interacting Quantum Systems</span>
|
||||
<h1 style="padding:0; margin: 10px 0 0 0;"><a class="triqs" href="{{ pathto('index') }}">{{ header_title }}</a></h1>
|
||||
<span style="font-size: 14px; margin: 0px; padding: 0px;">{{ header_subtitle }}</span>
|
||||
</div>
|
||||
</div>
|
||||
{% endblock %}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user