Kalypso features

Kalypso is a highly-visual Windows software package for molecular dynamics (MD) simulations of atomic collisions in (primarily) metallic and bimetallic crystals. Kalypso comprises a simulation engine of the same name, and various supporting utility programs. Kalypso should run on any recent Windows system, but has only been tested on Windows 2000, Windows XP and Windows 8. On Linux systems, Kalypso can be loaded and run using Wine, with a ~10% decrease in speed.

Unlike most MD packages, Kalypso is mainly designed for non-equilibrium MD simulations of (metallic) systems that include surface-vacuum interfaces. There is a long list of packages for conventional MD applications to bulk materials at Wikipedia.

MD is an atomistic technique for materials simulation within the framework of classical dynamics. It can be used for purely investigative simulations of phenomena, or for modelling experimental outcomes, but in either case provides a detailed picture of the fundamental processes initiated by particle-solid collisions that is not available by other means. Since the 1960s, MD has been used to study irradiation effects such as sputtering, radiation damage and ion transport. Recent MD studies are often motivated by an interest in nanoscale phenomena.

The physics of a MD simulation is encapsulated in the interatomic potential, which determines material dependent behaviour such as melting, bond strengths, phonon properties, nuclear stopping, etc. Kalypso uses many-body potentials of the embedded atom method (EAM) type which can describe the material and cohesive properties of fcc metals, hcp metals, bcc metals, some impurities in these metals, and bimetallic systems (alloys, films, clusters, multilayers).

EAM potentials are not suitable for modelling the cohesive and material properties of semiconductors like Si or GaAs, or ionic materials such as MgO. However, Kalypso can be used to model energetic ion-surface phenomena in these and other materials that depend mainly on repulsive potentials, for example, ion scattering spectroscopy simulations (LEIS, ICISS, CAICISS, MEIS). In ion scattering simulations, version 3.2 of Kalypso allows for 5 types of atoms in the target.

Typically, energy is imparted to the system by one or more primary projectiles such as an inert gas atom or a metal atom or cluster, or by temperature ramping. The range of particle energies that can be treated by Kalypso is roughly 0.1 eV to 10 keV. The lower energy limit is imposed by quantum effects, while the upper limit is determined by the treatment used for modelling inelastic effects, and by the practical difficulty of containing fast projectiles in nanoscale targets. This energy range covers, for example, deposition of metals by evaporation, sputtering and ion scattering phenomena, and numerous less familiar phenomena such as gamma-ray induced Doppler broadening.

Most Kalypso simulations will involve the calculation of the average effects of N projectile impacts at a statistical sample of different surface impact points. Kalypso can simulate these projectile impacts on a virgin surface (‘zero-fluence’ simulation) or on a surface which accumulates the damage from prior projectile impacts (‘multiple impact’ simulation).

Kalypso will be of interest to researchers who are in the business of doing experiments with ions (e.g. ion bombardment, sputtering, ion scattering) that require interpretation in terms of an atomistic model, and to researchers of nanoscale phenomena in metallic systems. Kalypso can also be used to carry out theoretical enquiries of a more general nature that have no connection to particular experiments, e.g. how do sputtering at glancing and normal projectile incidence differ?

Kalypso permits the modelling of the time evolution of a system that is defined by certain initial conditions and an interaction model. The simulation of events following each incident projectile trajectory is described as a 'run'. For example, a sputtering simulation might consist of 1000 runs, each lasting for 2000 fs. The initial conditions at the start of each run will be quite similar, except for the starting position (impact parameter) of the projectile, which will sample different impact points within the surface unit cell.

The program uses the Verlet integration algorithm with an adaptive timestep to integrate the classical equations of motion for a system of interacting particles. The output from the simulation is a set of particle coordinates and velocities at one or more specified sampling intervals which are stored in the ‘dynamics’ (or ‘trajectory’) file.

Various inelastic effects can be incorporated into the simulations, including temperature clamping or programming (with the Berendsen thermostat), electronic stopping, projectile Auger neutralization, lattice site springs, image potential effects.

Kalypso is not designed to simulate specific experiments, so it is up to the user to manipulate the output trajectory data in a way that can be compared with experimental data (if that is the purpose of the simulation). It is quite easy to generate simulation data, but it is usually more difficult to extract meaningful output in the form of scattering profiles, spectra and so forth. A utility program supplied with the package (Winnow) can be used for most data analysis tasks.

Below: screenshot of Winnow, the data analysis utility of the Kalypso package.

Below: Detail from a Zr self-sputtering simulation, after sputtering ca. 0.1 ML. Red: adatoms; pink: surface layer atoms; orange: implanted projectiles; green: bulk atoms.