We have performed molecular dynamics simulations of cascade damage in the gadolinium pyrochlore Gd{sub 2}Zr{sub 2}O{sub 7}, comparing results obtained from traditional methodologies that ignore the effect of electron-ion interactions with a 'two-temperature model' in which the electronic subsystem is modeled using a diffusion equation to determine the electronic temperature. We find that the electron-ion interaction friction coefficient {gamma}{sub p} is a significant parameter in determining the behavior of the system following the formation of the primary knock-on atom (here, a U{sup 3+} ion). The mean final U{sup 3+} displacement and the number of defect atoms formed is shown to decrease uniformly with increasing {gamma}{sub p}; however, other properties, such as the final equilibrium temperature and the oxygen-oxygen radial distribution function show a more complicated dependence on {gamma}{sub p}.
We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.