.. : YAFF is yet another force-field code. : Copyright (C) 2011 Toon Verstraelen , : Louis Vanduyfhuys , Center for Molecular Modeling : (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise : stated. : : This file is part of YAFF. : : YAFF 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 3 : of the License, or (at your option) any later version. : : YAFF 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, see : : -- Yaff Documentation ################## Yaff stands for "Yet another force field". It is a pythonic force-field (FF) code used at the `Center for Molecular Modeling `_ (CMM) to test-drive new FF models. The original motivation to develop Yaff was to provide a good reference implementation of the force fields developed at the CMM. In its current version, Yaff is general and flexible enough to handle a large variety of force field models. User Guide ========== This guide is a gentle introduction to Yaff with many examples. .. toctree:: :maxdepth: 2 :numbered: ug_features.rst ug_install.rst ug_troubles.rst ug_cite.rst ug_overview.rst ug_system.rst ug_atselect.rst ug_forcefield.rst ug_sampling.rst ug_analysis.rst ug_tune.rst Tutorials ========= .. toctree:: :maxdepth: 2 :numbered: tu_silica.rst Reference Guide =============== This guide is mostly generated automatically based on the doc strings in the source code. .. toctree:: :maxdepth: 2 :numbered: rg_yaff.rst rg_yaff_pes.rst rg_yaff_sampling.rst rg_yaff_analysis.rst rg_yaff_conversion.rst rg_yaff_tune.rst Development information ======================= The git repository is hosted at `Github `_. .. toctree:: :maxdepth: 1 :numbered: dg_todo.rst dg_backprop.rst Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`