.. Taskfarming documentation master file, created by
   sphinx-quickstart on Sun Jul 19 19:48:33 2020.
   You can adapt this file completely to your liking, but it should at least
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******************************************************
**Diffusion of Li in MgO**
******************************************************

*A case study by Harry Thomas, Cardiff University. Funding is gratefully acknowledged from CCP5.*

.. LI_MGO TUTORIAL REVISION HISTORY
.. Version 1 by Harry Thomas, summer 2020

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   1_cluster_construction.rst
   2_li_doping.rst
   3_neb.rst
   4_li_vib.rst
   5_li_epr.rst
   appendix_hpc.rst

This tutorial is designed to illustrate the potential of Py-ChemShell for performing massively-parallelised task-farming 
calculations using hybrid QM/MM on high-performance computing (HPC) facilities. Do not worry if 
you do not have access to any HPC facilities, as all of this tutorial can be run on any local machine.

This tutorial will cover how to construct a solid-state Li doped MgO cluster with a [Li :sup:`+` O :sup:`-` ] active site.
Later, the tutorial illustrates how to calculate the diffusion barrier for electron hole migrations using task-farmed nudged 
elastic band (NEB) calculations. Finally, a task-farmed post-calculation analysis is utilised to characterise the 
diffusion barrier transition state and the electron paramagnetic resonance g values are calculated.

The MgO crystal structure used in this tutorial was obtained from the `ICSD <http://icsd.psds.ac.uk/search/basic.xhtml>`_ website.
The structure has a database code of 159376 and the citation is R.M. Hazen, *American Mineralogist*, 1976, **61**, 
266-271. 

.. note:: Whilst this tutorial is standalone, it expands on the ideas introduced in the **'Modelling an MgO surface'** tutorial, 
   and thus it is highly recommended to work through that tutorial first.



   




