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doxygen update; yason conversion tool

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1 parent 1f83fe4 commit e8b861d061ffaa0b5a7ce2e08955a9807a09cee7 @mlund committed Feb 7, 2017
Showing with 430 additions and 547 deletions.
  1. +1 −1 .travis.yml
  2. +245 −135 doc/Doxyfile
  3. +15 −8 doc/DoxygenLayout.xml
  4. +0 −143 doc/README.md
  5. +103 −174 doc/{mainpage.doxygen → mainpage.dox}
  6. +0 −45 doc/python.md
  7. +20 −22 include/faunus/analysis.h
  8. +0 −2 include/faunus/move.h
  9. +4 −4 include/faunus/titrate.h
  10. +26 −0 scripts/yason.py
  11. +16 −13 src/examples/minimal.cpp
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@@ -9,5 +9,5 @@ compiler:
script:
- cmake .
- make -j2
- - ctest -V
+ - make test
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Oops, something went wrong.
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@@ -1,8 +1,9 @@
<doxygenlayout version="1.0">
+ <!-- Generated by doxygen 1.8.13 -->
<!-- Navigation index tabs for HTML output -->
<navindex>
- <tab type="mainpage" visible="yes" title=""/>
- <tab type="pages" visible="no" title="" intro=""/>
+ <tab type="mainpage" visible="no" title=""/>
+ <tab type="pages" visible="yes" title="" intro=""/>
<tab type="modules" visible="yes" title="" intro=""/>
<tab type="namespaces" visible="yes" title="">
<tab type="namespacelist" visible="yes" title="" intro=""/>
@@ -23,15 +24,15 @@
<!-- Layout definition for a class page -->
<class>
- <briefdescription visible="no"/>
- <detaileddescription title=""/>
+ <briefdescription visible="yes"/>
<includes visible="$SHOW_INCLUDE_FILES"/>
<inheritancegraph visible="$CLASS_GRAPH"/>
<collaborationgraph visible="$COLLABORATION_GRAPH"/>
- <allmemberslink visible="yes"/>
<memberdecl>
<nestedclasses visible="yes" title=""/>
<publictypes title=""/>
+ <services title=""/>
+ <interfaces title=""/>
<publicslots title=""/>
<signals title=""/>
<publicmethods title=""/>
@@ -61,34 +62,39 @@
<related title="" subtitle=""/>
<membergroups visible="yes"/>
</memberdecl>
+ <detaileddescription title=""/>
<memberdef>
<inlineclasses title=""/>
<typedefs title=""/>
<enums title=""/>
+ <services title=""/>
+ <interfaces title=""/>
<constructors title=""/>
<functions title=""/>
<related title=""/>
<variables title=""/>
<properties title=""/>
<events title=""/>
</memberdef>
+ <allmemberslink visible="yes"/>
<usedfiles visible="$SHOW_USED_FILES"/>
- <authorsection visible="no"/>
+ <authorsection visible="yes"/>
</class>
<!-- Layout definition for a namespace page -->
<namespace>
- <briefdescription visible="no"/>
- <detaileddescription title=""/>
+ <briefdescription visible="yes"/>
<memberdecl>
<nestednamespaces visible="yes" title=""/>
+ <constantgroups visible="yes" title=""/>
<classes visible="yes" title=""/>
<typedefs title=""/>
<enums title=""/>
<functions title=""/>
<variables title=""/>
<membergroups visible="yes"/>
</memberdecl>
+ <detaileddescription title=""/>
<memberdef>
<inlineclasses title=""/>
<typedefs title=""/>
@@ -109,6 +115,7 @@
<memberdecl>
<classes visible="yes" title=""/>
<namespaces visible="yes" title=""/>
+ <constantgroups visible="yes" title=""/>
<defines title=""/>
<typedefs title=""/>
<enums title=""/>
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@@ -1,143 +0,0 @@
-[![Documentation](https://codedocs.xyz/mlund/faunus.svg)](https://codedocs.xyz/mlund/faunus/)
-[![Build Status](https://travis-ci.org/mlund/faunus.svg?branch=master)](https://travis-ci.org/mlund/faunus)
-
-Welcome to Faunus
-=================
-
-Faunus is a C++ framework for Metropolis Monte Carlo simulations of
-molecular systems. Below is a brief overview of features:
-
-- Canonical, Grand Canonical, Isobaric-Isothermal statistical mechanical ensembles
-- General hamiltonian **parallel tempering** (temperature, screening length, bonds etc.)
-- **Anisotropic** atoms (multipoles, sphero-cylinders)
-- Ion titration moves (pKa prediction, Hofmeister effects etc.)
-- Highy modular
-- Free and open source (**GPL**)
-
-Detailed information and support:
-
-- Manual: <https://codedocs.xyz/mlund/faunus>
-- Support: <http://github.com/mlund/faunus/issues>
-- Source code: <http://github.com/mlund/faunus>
-
-Get the latest revision from GitHub:
-
- $ git clone https://github.com/mlund/faunus.git
-
-Requirements
-============
-
-- C/C++11 compiler (clang3.5+, gcc4.9+, intel14+, ...)
-- CMake 2.8.5+
-
-Optional:
-
-- Doxygen (for code manual)
-- MPI (for parallelisation)
-- Python (for python module, experimental)
-
-Developed and tested on Linux and MacOS X.
-
-Compiling
-=========
-
- $ cmake . [options]
- $ make [help]
- $ make test (or use 'ctest -V' for verbose test output)
-
-Build options
--------------
-
-Option | Description
-:--------------------------------- | :----------------------------------------
-`-DENABLE_MPI=OFF` | Build MPI programs (parallel tempering etc.)
-`-DENABLE_OPENMP=OFF` | Enable OpenMP support
-`-DENABLE_STATIC=OFF` | Static linkage of faunus as opposed to default dynamic linkage
-`-DENABLE_UNICODE=ON` | Use Unicode UTF-16 encoding for pretty output
-`-DENABLE_PYTHON=ON` | Build python bindings (experimental)
-`-DENABLE_POWERSASA=OFF` | Enable SASA routines (external download)
-`-DCMAKE_BUILD_TYPE=RelWithDebInfo`| Alternatives: `Debug` or `Release` (faster)
-`-DCMAKE_CXX_FLAGS_RELEASE="..."` | Compiler options for Release mode
-`-DCMAKE_CXX_FLAGS_DEBUG="..."` | Compiler options for Debug mode
-`-DMYPLAYGROUND="absolute path"` | Add additional source directory
-
-Example: Intel's C++ compiler
------------------------------
-
- $ CXX=icpc CC=icc cmake . -DCMAKE_BUILD_TYPE=Release
- $ make
-
-Example: Libraries in odd locations
------------------------------------
-
- $ LDFLAGS=-L/sw/lib CPPFLAGS=-I/sw/include cmake .
-
-Examples: Python support
-------------------------
-Faunus has preliminary python support -- see this Jupyter [notebook](scripts/pyfaunus-test.ipynb)
-for examples.
-If several python distributions are installed, the build system may be guided to specific
-libraries using i.e.:
-
- $ cmake . -DPYTHON_INCLUDE_DIR=$HOME/miniconda/include/python2.7 -DPYTHON_LIBRARY=$HOME/minoconda/lib/libpython2.7.dylib
- $ make pyfaunus
-
-On OSX the linked python library can be probed and, if needed, renamed like this:
-
- $ otool -L pyfaunus.so
- $ install_name_tool -change libpython2.7.dylib $HOME/miniconda/lib/libpython2.7.dylib pyfaunus.so
-
-Resetting the build system
---------------------------
-
- $ make clean
- $ rm -fR CMakeCache.txt CMakeFiles
-
-Contributors
-============
-
-In chronological order:
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- Mikael Lund Bjorn Persson Martin Trulsson
-Ondrej Marsalek Christophe Labbez Andre Teixeira
- Anil Kurut Chris Evers Magnus Ullner
- Robert Vacha Axel Thuresson Bjorn Stenqvist
- Joao Henriques Alexei Abrikossov Giulio Tesei
- Lukas Sukenik Niels Kouwenhoven
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Citing Faunus
-=============
-
-- Stenqvist et al.
- _Molecular Simulation 2013, 39:1233_
-
- [![DOI](https://img.shields.io/badge/DOI-10%2Fnvn-orange.svg)](http://dx.doi.org/10/nvn)
-
-- Lund, M., Persson, B., Trulsson, M.
- _Source Code Biol. Med., 2008, 3:1_
-
- [![DOI](https://img.shields.io/badge/DOI-10%2Fdfqgch-orange.svg)](http://dx.doi.org/10/dfqgch)
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Faunus - A Framework for Molecular Modelling
- Copyright (C) 2002-2017 Mikael Lund
-
- This program is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License along
- with this program; if not, write to the Free Software Foundation, Inc.,
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
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