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updating doc

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Olivier Parcollet 2013-09-01 17:56:17 +02:00
parent 640941c326
commit de15cf5267
9 changed files with 185 additions and 256 deletions
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2
CMakeLists.txt
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@ -3,7 +3,7 @@ list(APPEND CMAKE_MODULE_PATH ${TRIQS_PATH}/share/triqs/cmake)
# start configuration
cmake_minimum_required(VERSION 2.8)
project(ctseg CXX Fortran)
project(dft_tools CXX Fortran)
set(CMAKE_BUILD_TYPE Release)
enable_testing()

4
doc/CMakeLists.txt
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@ -6,7 +6,7 @@ file(GLOB_RECURSE doc_sources *.rst)
# create documentation target
set(sphinx_top ${CMAKE_CURRENT_BINARY_DIR}/html/index.html)
add_custom_command(OUTPUT ${sphinx_top} DEPENDS ${doc_sources} py_copy
add_custom_command(OUTPUT ${sphinx_top} DEPENDS ${doc_sources} py_copy triqs_DFT
COMMAND ${CMAKE_BINARY_DIR}/build_pytriqs ${TRIQS_SPHINXBUILD_EXECUTABLE} -c . -b html ${CMAKE_CURRENT_SOURCE_DIR} html)
add_custom_target(doc_sphinx ALL DEPENDS ${sphinx_top})
@ -17,7 +17,7 @@ install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/ COMPONENT documentation DEST
PATTERN "*.png"
PATTERN "*.js"
PATTERN "_*"
PATTERN "*.png"
PATTERN "*.jpg"
PATTERN "*.gif"
PATTERN "*.xsl"
PATTERN "*.css"

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doc/about.rst Normal file
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@ -0,0 +1,40 @@
License
=======
Wien2TRIQS is published under the `GNU General Public License, version 3
<http://www.gnu.org/licenses/gpl.html>`_.
Authors & Quotation
=======================
The developement of an interface between the Wien2k electronic structure
package and TRIQS has been motivated by a scientific collaboration between the
research groups of Antoine Georges, Silke Biermann (Ecole Polytechnique),
Olivier Parcollet (CEA Saclay). A first step has been the definition of the
framework and the construction of the projective Wannier functions as input for
the DMFT calculations [#wien2k1]_. This has been followed by the introduction
of full charge self-consistency [#wien2k2]_, necessary for total energy
calculations.
**Developers**: M. Aichhorn, L. Pourovskii, V. Vildosola, C. Martins
**Related papers**:
.. [#wien2k1] `M. Aichhorn, L. Pourovskii, V. Vildosola, M. Ferrero, O. Parcollet, T. Miyake, A. Georges, and S. Biermann, Phys. Rev. B 80, 085101 (2009) <http://link.aps.org/doi/10.1103/PhysRevB.80.085101>`_ (:download:`bibtex file <wien2k1.bib>`)
.. [#wien2k2] `M. Aichhorn, L. Pourovskii, and A. Georges, Phys. Rev. B 84, 054529 (2011) <http://link.aps.org/doi/10.1103/PhysRevB.84.054529>`_ (:download:`bibtex file <wien2k2.bib>`)
This application is a part of our scientific work and we would appreciate if
projects using it will include a citation to the following relevant papers. In
order to help you, we provide a BibTeX entry for each paper.
If you find the application useful, giving proper reference and citation is
indeed a simple way to help convincing funding sources that such projects are
useful for our community and should be supported.
Disclaimer
==========
The program is provided as is, i.e. WITHOUT ANY WARRANTY of any kind, as
stated in the license. In particular, its authors and contributors will take
no responsability for any possible bugs or any improper use of these programs,
including those resulting in incorrect scientific publications.

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doc/conf.py.in
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@ -1,242 +1,37 @@
# -*- coding: utf-8 -*-
#
# TRIQS documentation build configuration file, created by
# sphinx-quickstart on Tue Jul 23 15:29:36 2013.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
# TRIQS documentation build configuration file
import sys, os
extensions = ['sphinx.ext.autodoc',
'sphinx.ext.mathjax',
'sphinx.ext.intersphinx',
'matplotlib.sphinxext.plot_directive']
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#sys.path.insert(0, os.path.abspath('.'))
# -- General configuration -----------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.pngmath', 'sphinx.ext.mathjax', 'matplotlib.sphinxext.plot_directive']
# Add any paths that contain templates here, relative to this directory.
#templates_path = ['_templates']
# The suffix of source filenames.
source_suffix = '.rst'
# The encoding of source files.
#source_encoding = 'utf-8-sig'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'TRIQS interface to Wien2k'
copyright = u'2013, M. Aichhorn, L. Pourovskii, V. Vildosola, C. Martins'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
copyright = u'2011-2013, M. Aichhorn, L. Pourovskii, V. Vildosola, C. Martins'
version = '1.0'
# The full version, including alpha/beta/rc tags.
release = '1.0.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
mathjax_path = "@TRIQS_MATHJAX_PATH@/MathJax.js?config=default"
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = []
# The reST default role (used for this markup: `text`) to use for all documents.
#default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
# -- Options for HTML output ---------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
html_theme = 'agogo'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#html_theme_options = {}
# Add any paths that contain custom themes here, relative to this directory.
html_theme = 'triqs'
html_theme_path = ['@TRIQS_THEMES_PATH@']
html_show_sphinx = False
html_context = {'header_title': 'Wien2TRIQS',
'header_subtitle': 'Connecting <a class="triqs" style="font-size: 12px" href="http://ipht.cea.fr/triqs">TRIQS</a> to the Wien2k package',
'header_links': [['Install', 'install'],
['Documentation', 'documentation'],
['Issues', 'issues'],
['About Wien2TRIQS', 'about']]}
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
templates_path = ['@TRIQS_THEMES_PATH@/../export/_templates']
html_sidebars = {'index': ['sideb_appli.html', 'searchbox.html']}
html_static_path = ['@TRIQS_THEMES_PATH@/../export/_static']
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
htmlhelp_basename = 'TRIQSDftToolsdoc'
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#html_logo = None
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = None
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
#html_static_path = ['_static']
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}
# If false, no module index is generated.
#html_domain_indices = True
# If false, no index is generated.
#html_use_index = True
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#html_show_sphinx = True
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#html_show_copyright = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''
# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None
# Output file base name for HTML help builder.
htmlhelp_basename = 'TRIQSdoc'
# -- Options for LaTeX output --------------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#'preamble': '',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
('index', 'TRIQS.tex', u'TRIQS Documentation',
u'MF OP', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# If true, show page references after internal links.
#latex_show_pagerefs = False
# If true, show URL addresses after external links.
#latex_show_urls = False
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_domain_indices = True
# -- Options for manual page output --------------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('index', 'triqs', u'TRIQS Documentation',
[u'MF OP'], 1)
]
# If true, show URL addresses after external links.
#man_show_urls = False
# -- Options for Texinfo output ------------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
('index', 'TRIQS', u'TRIQS Documentation',
u'MF OP', 'TRIQS', 'One line description of project.',
'Miscellaneous'),
]
# Documents to append as an appendix to all manuals.
#texinfo_appendices = []
# If false, no module index is generated.
#texinfo_domain_indices = True
# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'
intersphinx_mapping = {'python': ('http://docs.python.org/2.7', None),
#'triqscthybmatrix': ('@TRIQS_THEMES_PATH@/../../doc/triqs',None),
'triqslibs': ('@TRIQS_THEMES_PATH@/../../doc/triqs',None)}

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doc/contents.rst Normal file
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@ -0,0 +1,12 @@
Table of contents
=================
.. toctree::
:maxdepth: 2
index
install
documentation
issues
about

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doc/documentation.rst Normal file
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@ -0,0 +1,33 @@
.. module:: pytriqs.applications.dft_tools
.. _documentation:
Documentation
=============
.. toctree::
:maxdepth: 1
interface
LDADMFTmain
advanced
analysis
selfcons
Ce-HI
In addition to the python-related modules, TRIQS also
provides the Wien2k add-on :program:`dmftproj`. It takes the
information about the wave functions calculated by the `Wien2k package
<http://www.wien2k.at>`_, and constructs projected Wannier functions
that are used as localised orbitals for the DMFT calculation.
The program :program:`dmftproj` is written in the flavor of the
`Wien2k package <http://www.wien2k.at>`_ without python
support. A detailed description of the usage and options of
:program:`dmftproj`
can be found in :download:`this extensive tutorial <TutorialDmftproj.pdf>`. In
addition, it contains also a description of the Wien2k scripts that
are necessary to do the full charge self-consistent calculations.

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doc/index.rst
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@ -7,35 +7,10 @@
Wien2TRIQS
========================================================
`Connecting TRIQS to the Wien2k package`
In this section we will learn how we can connect our DMFT calculations with
This application is aimed at DMFT calculations with
realistic band structure calculations.
A priori TRIQS can be connected to various realistic band structure codes.
In this release, we provide the Wien2TRIQS extension module which contains an
interface to the `Wien2k package <http://www.wien2k.at>`_.
.. toctree::
:maxdepth: 1
interface
LDADMFTmain
advanced
analysis
selfcons
Ce-HI
In addition to the python-related modules, TRIQS also
provides the Wien2k add-on :program:`dmftproj`. It takes the
information about the wave functions calculated by the `Wien2k package
<http://www.wien2k.at>`_, and constructs projected Wannier functions
that are used as localised orbitals for the DMFT calculation.
The program :program:`dmftproj` is written in the flavor of the
`Wien2k package <http://www.wien2k.at>`_ without python
support. A detailed description of the usage and options of
:program:`dmftproj`
can be found in :download:`this extensive tutorial <TutorialDmftproj.pdf>`. In
addition, it contains also a description of the Wien2k scripts that
are necessary to do the full charge self-consistent calculations.

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doc/install.rst Normal file
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.. highlight:: bash
Installation
============
Prerequisite
-------------------
#. The :ref:`TRIQS <triqslibs:welcome>` toolkit (see :ref:`TRIQS installation instruction <triqslibs:installation>`).
In the following, we will suppose that it is installed in the ``path_to_triqs`` directory.
#. Likely, you will also need at least one impurity solver, e.g. the The :ref:`CTHYB_matrix solver <triqscthybmatrix:welcome>`.
Installation steps
------------------
#. Download the sources of the solver from github::
$ git clone git@github.com:TRIQS/dft_tools.git src
#. Create an empty build directory where you will compile the code::
$ mkdir build && cd build
#. In the build directory call cmake specifying where the TRIQS library is installed::
$ cmake -DTRIQS_PATH=path_to_triqs ../src
#. Compile the code, run the tests and install the application::
$ make
$ make test
$ make install
Version compatibility
---------------------
Be careful that the version of the TRIQS library and of the solver must be
compatible (more information on the `TRIQS website
<http://ipht.cea.fr/triqs/versions.html>`_). If you want to use a version of
the solver that is not the latest one, go into the directory with the sources
and look at all available versions::
$ cd src && git tag
Checkout the version of the code that you want::
$ git co 1.0.0
Then follow the steps 2 to 4 described above to compile the code.

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Reporting issues
================
Please report all problems and bugs directly at the github issue page
`<https://github.com/TRIQS/dft_tools/issues>`_. In order to make it easier
for us to solve the issue please follow these guidelines:
#. In all cases specify which version of the application you are using. You can
find the version number in the file :file:`README.txt` at the root of the
application sources.
#. If you have a problem during the installation, give us information about
your operating system and the compiler you are using. Include the outputs of
the ``cmake`` and ``make`` commands as well as the ``CMakeCache.txt`` file
which is in the build directory. Please include these outputs in a
`gist <http://gist.github.com/>`_ file referenced in the issue.
#. If you are experiencing a problem during the execution of the application, provide
a script which allows to quickly reproduce the problem.
Thanks!