MDMC Documentation
==================

MDMC is a Python package for optimising classical molecular dynamics (MD)
potential parameters by refining against experimental data, particularly
dynamical data such as the dynamic structure factor. The refinement uses
derivative-free optimisation algorithms (currently CMA-ES).  See
:ref:`introduction-label` and :ref:`installation-label` to start using MDMC.

MDMC was originally developed at the ISIS Neutron and Muon Source,
Chalmers University, the European Spallation Source, and the University of
Copenhagen.

Python
------
Python is a powerful high level programming language which has a simple syntax,
which is why it is commonly used for scripting.  Detailed knowledge of Python
is **not** required to run MDMC, however a basic understanding will make setting
up refinements quicker and scripts more flexible. There is a short introduction
to Python `here <https://www.mantidproject.org/Introduction_To_Python>`_.

Contributing to MDMC
--------------------
MDMC is open source and we welcome contributions to the project.  Please see
:ref:`contributing-label` for more details on how to contribute.

Acknowledgements
----------------
Funding for the development of MDMC has been provided by the Swedish Research
Council under grant 2016-06954, the ISIS Neutron and Muon Source and the University of Copenhagen.

Indices
-------

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


.. toctree::
   :maxdepth: 3
   :numbered:
   :hidden:
   :caption: Overview

   introduction
   contributing

.. toctree::
   :maxdepth: 2
   :hidden:
   :glob:
   :caption: Tutorials

   tutorials/*

.. toctree::
   :maxdepth: 2
   :hidden:
   :caption: How-to

   how-to/use-MDMC
   how-to/installation

.. toctree::
  :maxdepth: 1
  :hidden:
  :caption: Reference

  reference/api/modules

.. toctree::
   :maxdepth: 2
   :hidden:
   :caption: Explanation

   explanation/explanation

.. toctree::
   :maxdepth: 1
   :hidden: 
   :caption: Developer Documentation

   developer/overview