Simulation tools and links

On this page, I am gradually collecting links that I find, or hear about, to interesting simulation web sites, especially those with free software that can be used for execution, visualization or analysis of atomistic simulations. (I invite the developers of such software to send me their links and a short descriptive text.)

The star symbol indicates that the software is especially useful for users of Kalypso.

Reading

The molecular dynamics pioneer, W. Hoover, needs no introduction to you, I hope. His web site, found here, contains much of his published work, and thus represents a treasure trove of literature on the fundamentals of molecular dynamics simulation.

Tables and plots of elemental sputter yields predicted by a semi-empirical model [Seah et. al., Surf. Interface Anal. 37 (2005) 444-458, and Seah, Nucl. Instrum. Meth. B 229 (2005) 348-358 (2005)] for Ne, Ar and Xe ions (0.5-10 keV) and most solid elements can be found at the NPL web site. These data include estimates of sputter yields that are impossible to find elsewhere (e.g. for Sc or Mn).

Visualization tools

POV-RAY

Type: Binaries (and source code) for Windows and other platforms. Produces 3D ray-traced graphics. An essential tool for visualization of Kalypso simulations.

PJBMP2AVI

Type: Windows application. Converts a series of bitmap files into an AVI format video file. The best visual effects are produced if POV-RAY is used to create the bitmap files (from Kalypso output data). To create movies in which the camera moves relative to the target, look at the POV-RAY help topic on the clock variable. The "Save image sequence" command in Kalypso's visualization window can also be used to create a simple video record of a simulation.

BALLVIEWER

Type: Java code (should run on several platforms). Ballviewer uses the method of Ackland and Jones [G.J. Ackland, A.P. Jones, Phys. Rev. B. 73, 054104 (2006)] to define and identify local crystal structure. It should work with any input file of (x, y, z) atomic coordinates, and could thus be an interesting tool for analysis of Kalypso output data.

Simulation tools

CAMELION

Type: Unix-oriented source code (Fortran) from Delft University. Molecular dynamics package that can use modified embedded atom method (MEAM) potentials. Not for the casual user, but worthy of study by MD developers. The model of lattice springs that is used in Kalypso was derived from an earlier version of Camelion.

ALINE

Type: Unix-oriented source code (C) from University of Helsinki. ALINE is a graphically-oriented, user-friendly, MD program (for UNIX) for interactive simulations of crystals and defects in crystals with about 100,000 atoms.

NASCAM

Type: Windows executables from Facultés Universitaires de Notre-Dame de la Paix (Belgium). NASCAM is a KMC (Kinetic Monte Carlo) program (including tools for visualization) that can simulate the time evolution of atoms deposited on a substrate on a timescale far in excess of what can be achieved using MD. In the current version, the substrate structure can be amorphous or hexagonal close-packed.

CLUSTER COORDINATE GENERATORS

You may be interested in the Nanoparticle Studio (from Japan), although it is not trivial to use. For icosahedral, octahedral and truncated octahedral clusters with up to 9 layers, you can use this tool by Glasner and Frenkel. You can also download my small package that shows you how to generate coordinates for icosahedral clusters with up to 50 layers (429351 atoms).