.. winaks documentation master file, created by
   sphinx-quickstart on Tue Aug 12 15:21:20 2014.
   You can adapt this file completely to your liking, but it should at least
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.. image:: ./winak.png
   :align: center
   :width: 25%

Welcome to winak's documentation!
=====================================

This package contains routines for construction and use of 
curvilinear coordinates in molecular simulation and electronic structure tools. 
Its main purpose at the moment is global structure search for clusters [Panosetti2015]_ 
and molecules at surfaces [Krautgasser2016]_ using these coordinates.
It is meant to be interfaced with the Atomic Simulation Environment (ASE) [ASE]_

Feature List
############

* Internal and Curvilinear coordinate construction for isolated and periodic systems
* Supports sparse matrices and systems of 1000 to 10000 atoms
* Global Geometry optimization / BetterHopping code
* Many helpful data analysis tools

Potential Future Features
#########################

* Interfaces to interpolation software
* local optimization in curvilinear coordinates

Dependencies
############
* Python 2.7.x
* NumPy >= 1.6
* SciPy >= 0.12
* Cython>= 0.20
* scikits.sparse >=0.1 [ Scikits.Sparse ](https://github.com/njsmith/scikits-sparse)
  (depends itself on CHOLMOD/SuiteSparse)
* Atomic Simulation Environment [ASE]_
  (for interface to molecular mechanics and electronic structure codes)

Contents:
=========

.. toctree::
   :maxdepth: 2

   includeme
   Installation.rst
   BetterHopping.rst
   Tutorial.rst 
   Modules <winak>


References
##########

.. [Panosetti2015] C. Panosetti, K. Krautgasser, D. Palagin, K. Reuter, and R. J. Maurer, Global Materials Structure Search with Chemically Motivated Coordinates, *Nano Lett.* **15**, 8044-8048 (2015)
.. [Krautgasser2016] K. Krautgasser, C. Panosetti, D. Palagin, K. Reuter, and R. J. Maurer, Global Structure Search for Molecules on Surfaces: Efficient Sampling with Curvilinear Coordinates, *J. Chem. Phys* **145**, 084117, (2016)
.. [ASE]  `Atomic Simulation Environment (ASE)  <https://wiki.fysik.dtu.dk/ase/>`_

.. [Wales1] Wales and Doye, J. Phys. Chem. A, vol 101 (1997) 5111-5116 
.. [Wales2] David J. Wales and Harold A. Scheraga, Science, Vol. 285, 1368 (1999)


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`