Computer Physics Communications Program Library

Programs in Physics & Physical Chemistry



Manuscript Title: Three-dimensional interactive Molecular Dynamics program for the study of defect dynamics in crystals.
Authors: M. Patriarca, A. Kuronen, M. Robles, K. Kaski
Program title: ALINE, an Atomic Laboratory for Interactive Numerical Experiments.
Catalogue identifier: ADYJ_v1_0 Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 176(2007)38
Programming language: Standard C and Open-MOTIF libraries.
Computer: DEC ALPHA 300, Intel i386 compatible computers, G4 Apple Computers.
Operating system: True64 UNIX, Linux-i386, Mac OS X 10.3 and 10.4.
RAM: 6 Mbytes but may be larger depending on the system size.
Keywords: Molecular dynamics, Lennard-Jones, Sutton-Chen, EAM, dislocations, cracks, interfaces, visualization.
PACS: 05.10.Gg, 89.75.Kd.
Classification: 7.1, 7.7.
Nature of problem: Some phenomena involving defects take place inside three-dimensional crystals at times which can be hardly predicted. For this reason they are difficult to detect and track even within numerical experiments, especially when one is interested in studying their dynamical properties and time evolution. Furthermore, traditional simulation methods require the storage of a huge amount of data which in turn may imply a long work for their analysis.
Solution method: Simplifications of the simulation work described above strongly depend also on the computer performance. It has now become possible to realize some of such simplifications thanks to the real possibility of using interactive programs. The solution proposed here is based on the development of an interactive graphical simulation program both for avoiding large storage of data and the subsequent elaboration and analysis as well as for visualizing and tracking many phenomena inside three-dimensional samples.
Restrictions: The restrictions on the applicability of the program are related to the computer resources available. The graphical interface and interactivity demand computational resources that depend on the particular numerical simulation to be performed. To preserve a balance between speed and resources, the choice of the number of atoms to be simulated is critical. With an average current computer, simulations of systems with more than 105 atoms may not be easily feasible on an interactive scheme. Another restriction is related to the fact that the program was originally designed to simulate systems in the solid phase, so that problems in the simulation may occur if some particular physical quantities are computed beyond the melting point.
Unusual features: In the program, besides the window in which the system is represented in real space, an additional graphical window presenting the real time distribution histogram for different physical variables (e.g. kinetic or potential energy) was included. Such a tool is very interesting for making demonstrative numerical experiments for teaching purposes as well as for research, e.g. for detecting and tracking crystal defects. The program includes: An initial condition builder, an interactive display of the simulation, a set of tools which allow the user to filter through different physical quantities the information either displayed in real time or printed in the output files and to perform an efficient search of the interesting regions of parameter space.
Running time: It depends on the machine architecture, system size, and user needs.