Diffusion of Li in MgO

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

Contents:

• Setting up the bulk MgO Cluster
  • 1. Preparing the cluster
  • 2. Partitioning the cluster
• Localising the electron hole
  • 1. Localising the electron hole
  • 2. Quantum Mechanics (QM)
  • 3. Geometry optimisation
  • 4. Characterisation of the electron hole location
• Calculation of the diffusion barrier
  • 1. Task-farming parallelisation
  • 2. Nudged elastic band simulations
• Vibrational frequency analysis
• Electron paramagnetic resonance
• Appendix: creating a Slurm script

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 ⁺ O ^- ] 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 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.