Tutorial on binary collision approximation, molecular dynamics and kinetic Monte Carlo of irradiation effects (ICTP school 2016)
Tutorial on molecular dynamics for irradiation effects (ICACS conference 2014)
Tutorial on molecular dynamics and kinetic Monte Carlo for plasma-wall simulations (ICTP school 2012)

A full course on radiation effects in materials
A full course on molecular dynamics

Animations

In all of these animations, one sphere illustrates the position of an atom. When atoms change colors, the color scale is a logarithmic scale in kinetic energy, unless otherwise indicated in the color legend. Most views are a 2-4 atom layer thick cross section through the center of the simulation cell. .

Tutorial animation	Background/explanation
1 keV Xe -> Cu	[WMV] 1 keV Xe ion irradiation of Cu, with a combined 3D and cross-sectional view of the same event. Color scaling by kinetic energy of atoms.
1 keV Xe -> Cu	[WMV] 1 keV Xe ion irradiation of Cu, same as previous but without 3D view. Color scaling by kinetic energy of atoms.
3 keV Au -> Au	[WMV] 3 keV self-recoil in Au, includes visualization of defect formation and migration after the collisional stage of the cascade. Note that since the simulation uses periodic boundaries, there is eventually perfect defect recombination, in reality a few of the defects would likely escape the initial cascade region.
10 keV Au -> Au	[WMV] 10 keV self-recoil in Au, includes display of maximum kinetic energy of any atom in system to illustrate thermalization. Cross-sectional view.
10 keV Fe -> Fe	[WMV] 10 keV self-recoil in Fe plotted in three different color scales: kinetic energy, potential energy and atom displacements. This illustrates the problem with the NRT-dpa standard and the reason for us to develop the improved arc-dpa and rpa equations [Nature comm. 9, 1084 (2018)]
1 keV Si -> Si: 1000 ion trajectories	[WMV] Trajectories of 1000 1 keV Si ions incoming on Si (001), plotting only ion position. Theta varied between 0 and 10 degrees. MDRANGE simulations.
30 keV Xe -> Au	[AVI] 30 keV Xe impact on Au (7 degrees off the 100 direction i.e. partly channeled). Cross-sectional view
5 keV Ar -> Ni	[WMV] 5 keV Ar impact on Ni, tilted top view
5 keV Ar -> Ni	[WMV] 5 keV Ar impact on Ni, cross section (same event as above)
500 eV Au -> Cu	[AVI] 500 eV Au impact on Cu (made for demonstration only, can you spot the minor cheat used only for plotting?). Cross sectional view.
10 keV Au -> Cu3Au	[GIF] Disordering by a 10 keV Au -> Cu3Au cascade. Cross-sectional view, colors are atom type, yellow being Au.
5 keV Si -> Si	[WMV] 5 keV Si recoil in Si, view through whole cell

Gallery of a wide range of animations

Simulation methods

Notes on ion range calculations (mainly from the 1990's but still valid)

Miscellaneous

My personal view on how to give conference presentations; especially how to present equations and graphs