Adaptive QM/MM MD of Fracture in Silicon

This tutorial has not been updated for the Python 3 rewrite of quippy. It is hosted here for archival purposes

This tutorial has been prepared for use at a hands-on session at the ADGLASS Winter School on Advanced Molecular Dynamics Simulations, ICTP, Trieste, February 2013.

Authors:

James Kermode and Gianpietro Moras

Date:

February 2013

• Introduction
  • Scope of the tutorial
  • Practical considerations
• Theoretical background
  • Introduction to Atomic-scale Modelling of Fracture
  • Classical interatomic potentials for silicon
  • QM/MM Force Mixing and the ‘Learn on the Fly’ scheme
• Step 1: Setup of the Silicon model system
  • 1.1 Building the bulk unit cell (30 minutes)
  • 1.2 Calculation of elastic and surface properties of silicon (30 minutes)
  • 1.3 Setup of the crack slab supercell (30 minutes)
• Step 2: Classical MD simulation of fracture in Si
  • 2.1 Initialisation of the atomic system (20 minutes)
  • 2.2 Setup and run the classical MD (20 minutes)
  • 2.3 Visualisation and Analysis (as time permits)
• Step 3: LOTF hybrid MD simulation of fracture in Si
  • 3.1 Initialisation of the QM/MM atomic system (20 minutes)
  • 3.2 Setup and run the adaptive QM/MM MD (20 minutes)
  • 3.3 Visualisation and Analysis (as time permits)
  • 3.4 Checking the predictor/corrector force errors (optional)
  • Further extension tasks
• Solutions
  • Step 1 solution — make_crack.py
  • Step 2 solution — run_crack_classical.py
  • Step 3 solution — run_crack_lotf.py
• References